Extending trait dispersion across trophic levels: Predator assemblages act as top-down filters on prey communities

Studies of community assembly typically focus on the effects of abiotic environmental filters and stabilizing competition on functional trait dispersion within single trophic levels. Predation is a well-known driver of community diversity and composition, yet the role of functionally diverse predator communities in filtering prey community traits has received less attention. We examined functionally diverse communities of predators (fishes) and prey (epifaunal crustaceans) in eelgrass (Zostera marina) beds in two northern California estuaries to evaluate the filtering effects of predator traits on community assembly and how filters acting on predators influence their ability to mediate prey community assembly. Fish traits related to bottom orientation were correlated with more clustered epifauna communities, and epifauna were generally overdispersed while fishes were clustered, suggesting prey may be pushed to disparate areas of trait space to avoid capture by benthic sit-and-wait predators. We also found correlations between the trait dispersions of predator and prey communities that strengthened after accounting for the effects of habitat filters on predator dispersion, suggesting that habitat filtering effects on predator species pools may hinder their ability to affect prey community assembly. Our results present compelling observational evidence that specific predator traits have measurable impacts on the community assembly of prey, inviting experimental tests of predator trait means on community assembly and explicit comparisons of how the relative effects of habitat filters and intraguild competition on predators impact their ability to affect prey community assembly. Integrating our understanding of traits at multiple trophic levels can help us better predict the impacts of community composition on food web dynamics as regional species pools shift with climate change and anthropogenic introductions.

Priority effects alter microbiome composition and increase abundance of probiotic taxa in treefrog tadpoles

Host-associated microbial communities, like other ecological communities, may be impacted by the colonization order of taxa through priority effects. Developing embryos and their associated microbiomes are subject to stochasticity during colonization by bacteria. For amphibian embryos, often developing externally in bacteria-rich environments, this stochasticity may be particularly impactful. For example, the amphibian microbiome can mitigate lethal outcomes from disease for their hosts; however, this may depend on microbiome composition. Here, we examined the assembly of the bacterial community in spring peeper (Pseudacris crucifer) embryos and tadpoles. First, we reared embryos from identified mating pairs in either lab or field environments to examine the relative impact of environment and parentage on embryo and tadpole bacterial communities. Second, we experimentally inoculated embryos to determine if priority effects (i) could be used to increase the relative abundance of Janthinobacterium lividum, an amphibian-associated bacteria capable of preventing fungal infection, and (ii) would lead to observed differences in the relative abundances of two closely related bacteria from the genus Pseudomonas. Using 16S rRNA gene amplicon sequencing, we observed differences in community composition based on rearing location and parentage in embryos and tadpoles. In the inoculation experiment, we found that priority inoculation could increase the relative abundance of J. lividum, but did not find that either Pseudomonas isolate was able to prevent colonization by the other when given priority. These results highlight the importance of environmental source pools and parentage in determining microbiome composition, while also providing novel methods for the administration of a known amphibian probiotic.

IMPORTANCE

Harnessing the functions of host-associated bacteria is a promising mechanism for managing disease outcomes across different host species. In the case of amphibians, certain frog-associated bacteria can mitigate lethal outcomes of infection by the fungal pathogen Batrachochytrium dendrobatidis. Successful probiotic applications require knowledge of community assembly and an understanding of the ecological mechanisms that structure these symbiotic bacterial communities. In our study, we show the importance of environment and parentage in determining bacterial community composition and that community composition can be influenced by priority effects. Further, we provide support for the use of bacterial priority effects as a mechanism to increase the relative abundance of target probiotic taxa in a developing host. While our results show that priority effects are not universally effective across all host-associated bacteria, our ability to increase the relative abundance of specific probiotic taxa may enhance conservation strategies that rely on captive rearing of endangered vertebrates.

Bacterial and fungal community structures in Hulun Lake are regulated by both stochastic processes and environmental factors

Microorganisms are a crucial component of lake ecosystems and significant contributors to biogeochemical cycles. However, the understanding of how primary microorganism groups (e.g., bacteria and fungi) are distributed and constructed within different lake habitats is lacking. We investigated the bacterial and fungal communities of Hulun Lake using high-throughput sequencing techniques targeting 16S rRNA and Internal Transcribed Spacer 2 genes, including a range of ecological and statistical methodologies. Our findings reveal that environmental factors have high spatial and temporal variability. The composition and community structures vary significantly depending on differences in habitats. Variance partitioning analysis showed that environmental and geographical factors accounted for <20% of the community variation. Canonical correlation analysis showed that among the environmental factors, temperature, pH, and dissolved oxygen had strong control over microbial communities. However, the microbial communities (bacterial and fungal) were primarily controlled by the dispersal limitations of stochastic processes. This study offers fresh perspectives regarding the maintenance mechanism of bacterial and fungal biodiversity in lake ecosystems, especially regarding the responses of microbial communities under identical environmental stress.IMPORTANCELake ecosystems are an important part of the freshwater ecosystem. Lake microorganisms play an important role in material circulation and energy flow owing to their unique enzymatic and metabolic capacity. In this study, we observed that bacterial and fungal communities varied widely in the water and sediments of Hulun Lake. The primary factor affecting their formation was identified as dispersal limitation during stochastic processes. Environmental and geographical factors accounted for <20% of the variation in bacterial and fungal communities, with pH, temperature, and dissolved oxygen being important environmental factors. Our findings provide new insights into the responses of bacteria and fungi to the environment, shed light on the ecological processes of community building, and deepen our understanding of lake ecosystems. The results of this study provide a reference for lake management and conservation, particularly with respect to monitoring and understanding microbial communities in response to environmental changes.

Tracking arbuscular mycorrhizal fungi to their source: active inoculation and passive dispersal differentially affect community assembly in urban soils

Communities of arbuscular mycorrhizal (AM) fungi assemble passively over time via biotic and abiotic mechanisms. In degraded soils, AM fungal communities can assemble actively when humans manage mycorrhizas for ecosystem restoration. We investigated mechanisms of urban AM fungal community assembly in a 2-yr green roof experiment. We compared AM fungal communities in inoculated and uninoculated trays to samples from two potential sources: the inoculum and air. Active inoculation stimulated more distinct and diverse AM fungal communities, an effect that intensified over time. In the treatment trays, 45% of AM fungal taxa were detected in the inoculum, 2% were detected in aerial samples, 23% were detected in both inoculum and air, and 30% were not detected in either source. Passive dispersal of AM fungi likely resulted in the successful establishment of a small number of species, but active inoculation with native AM fungal species resulted in an immediate shift to a diverse and unique fungal community. When urban soils are constructed or modified by human activity, this is an opportunity for intervention with AM fungi that will persist and add diversity to that system.

Time-dependent interaction modification generated from plant-soil feedback

Pairwise interactions between species can be modified by other community members, leading to emergent dynamics contingent on community composition. Despite the prevalence of such higher-order interactions, little is known about how they are linked to the timing and order of species' arrival. We generate population dynamics from a mechanistic plant-soil feedback model, then apply a general theoretical framework to show that the modification of a pairwise interaction by a third plant depends on its germination phenology. These time-dependent interaction modifications emerge from concurrent changes in plant and microbe populations and are strengthened by higher overlap between plants' associated microbiomes. The interaction between this overlap and the specificity of microbiomes further determines plant coexistence. Our framework is widely applicable to mechanisms in other systems from which similar time-dependent interaction modifications can emerge, highlighting the need to integrate temporal shifts of species interactions to predict the emergent dynamics of natural communities.

The Geography of Metacommunities: Landscape Characteristics Drive Geographic Variation in the Assembly Process through Selecting Species Pool Attributes

AbstractThe nonrandom association between landscape characteristics and the dominant life history strategies observed in species pools is a typical pattern in nature. Here, we argue that these associations determine predictable changes in the relative importance of assembly mechanisms along broadscale geographic gradients (i.e., the geographic context of metacommunity dynamics). To demonstrate that, we employed simulation models in which groups of species with the same initial distribution of niche breadths and dispersal abilities interacted across a wide range of landscapes with contrasting characteristics. By assessing the traits of dominant species in the species pool in each landscape type, we determined how different landscape characteristics select for different life history strategies at the metacommunity level. We analyzed the simulated data using the same analytical approaches used in the study of empirical metacommunities to derive predictions about the causal relationships between landscape characteristics and dominant life histories in species pools, as well as their reciprocal influence on empirical inferences regarding the assembly process. We provide empirical support for these predictions by contrasting the assembly of moth metacommunities in a tropical versus a temperate mountainous landscape. Together, our model framework and empirical analyses demonstrate how the geographic context of metacommunities influences our understanding of community assembly across broadscale ecological gradients.

Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Association between Soil Physicochemical Properties and Bacterial Community Structure in Diverse Forest Ecosystems

Although the importance of the soil bacterial community for ecosystem functions has long been recognized, there is still a limited understanding of the associations between its community composition, structure, co-occurrence patterns, and soil physicochemical properties. The objectives of the present study were to explore the association between soil physicochemical properties and the composition, diversity, co-occurrence network topological features, and assembly mechanisms of the soil bacterial community. Four typical forest types from Liziping Nature Reserve, representing evergreen coniferous forest, deciduous coniferous forest, mixed conifer-broadleaf forest, and its secondary forest, were selected for this study. The soil bacterial community was analyzed using Illumina MiSeq sequencing of 16S rRNA genes. Nonmetric multidimensional scaling was used to illustrate the clustering of different samples based on Bray-Curtis distances. The associations between soil physicochemical properties and bacterial community structure were analyzed using the Mantel test. The interactions among bacterial taxa were visualized with a co-occurrence network, and the community assembly processes were quantified using the Beta Nearest Taxon Index (Beta-NTI). The dominant bacterial phyla across all forest soils were Proteobacteria (45.17%), Acidobacteria (21.73%), Actinobacteria (8.75%), and Chloroflexi (5.06%). Chao1 estimator of richness, observed ASVs, faith-phylogenetic diversity (faith-PD) index, and community composition were distinguishing features of the examined four forest types. The first two principal components of redundancy analysis explained 41.33% of the variation in the soil bacterial community, with total soil organic carbon, soil moisture, pH, total nitrogen, carbon/nitrogen (C/N), carbon/phosphorous (C/P), and nitrogen/phosphorous (N/P) being the main soil physicochemical properties shaping soil bacterial communities. The co-occurrence network structure in the mixed forest was more complex compared to that in pure forests. The Beta-NTI indicated that the bacterial community assembly of the four examined forest types was collaboratively influenced by deterministic and stochastic ecological processes.

Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland

Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.

Scale-dependent influences of environmental, historical, and spatial processes on taxonomic and functional beta diversity of Japanese bat assemblages

This study investigated the relative influences of environmental, spatial, and historical factors, including the island-specific history of land connectivity, on bat assemblages in the Japanese Archipelago. We collected bat distribution data from 1408 studies and assigned them to Japan's First Standard Grid (approximately 6400 km2). Japanese bat assemblages were analyzed at two scales: the entire Japanese Archipelago comprised 16 islands and exclusively the four main islands. At first, we calculated taxonomic and functional total beta diversity (β total) by Jaccard pairwise dissimilarity and then divided this into turnover (β repl) and richness-difference (β rich) components. We conducted hierarchical clustering of taxonomic beta diversity to examine the influence of the two representative sea straits, Tsugaru and Tokara, which are considered biogeographical borders. Variation partitioning was conducted to evaluate the relative effects of the three factors on the beta diversity. Clustering revealed that the Tokara Strait bordered the two major clades; however, the Tsugaru Strait did not act as a biogeographical border for bats. In the variation partitioning, shared fraction between spatial and historical factors significantly explained taxonomic and functional β total and taxonomic β repl at the entire archipelago scale, but not at the four main islands scale extending only Tsugaru Strait but not Tokara Strait. Pure environmental factors significantly explained functional β total at both scales and taxonomic β total only at the four main islands scale. These results suggest that spatial and historical factors are more pronounced in biogeographical borders, primarily structuring assemblage composition at the entire archipelago scale, especially in taxonomic dimension. However, current environmental factors primarily shape the assemblage composition of Japanese bats at the main island scale. The difference in results between the two scales highlights that the primary processes governing assemblages of both dimensions depend on the quality of the dispersal barriers between terrestrial and aquatic barriers for bats.

Stochastic processes shape the functional and phylogenetic structure of bird assemblages at the mine area in southwest China

Understanding the mechanisms of community assembly is a key question in ecology. Metal pollution may result in significant changes in bird community structure and diversity, with implications for ecosystem processes and function. However, the relative importance of these processes in shaping the bird community at the polluted area is still not clear. Here, we explored bird species richness, functional, and phylogenetic diversity, and the assembly processes of community at the mine region of southwest China. Our results showed that the 3 dimensions of diversity at the mine area were lower than that at the reference sites. In the community assembly, the result was 0 < NRI/ NFRI < 1.96, which indicated deterministic processes (environmental filtering) might drive community clustering. The results of the neutral community model, and normalized stochasticity ratio, showed the dominant role of stochastic processes in shaping the bird community assembly. We further quantified the community-level habitat niche breadth (Bcom), and we found that there was no difference in Bcom-value between the mine area and reference sites. This indicates that the bird communities at the mine area and 3 reference sites were not subjected to extreme environmental selection (same or different resource allocation) to form a highly specialized niche. These findings provide insights into the distribution patterns and dominant ecological processes of bird communities under metal exposure, and extend the knowledge in community assembly mechanisms of bird communities living in the mine area.

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

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

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.

Distinct Gut Microbial Enterotypes and Functional Dynamics in Wild Striped Field Mice (Apodemus agrarius) across Diverse Populations

Rodents, including the striped field mouse (Apodemus agrarius), play vital roles in ecosystem functioning, with their gut microbiota contributing significantly to various ecological processes. Here, we investigated the structure and function of 94 wild A. agrarius individuals from 7 geographic populations (45°57' N, 126°48' E; 45°87' N, 126°37' E; 45°50' N, 125°31' E; 45°59' N, 124°37' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E; 46°01' N, 124°88' E), revealing two distinct enterotypes (Type1 and Type2) for the first time. Each enterotype showed unique microbial diversity, functions, and assembly processes. Firmicutes and Bacteroidetes dominated, with a significant presence of Lactobacillus and Muribaculaceae. Functional analysis highlighted metabolic differences, with Type1 emphasizing nutrient processing and Type2 showing higher energy production capacity. The analysis of the neutral model and the null model revealed a mix of stochastic (drift and homogenizing dispersal) and deterministic processes (homogenous selection) that shape the assembly of the microbiota, with subtle differences in the assembly processes between the two enterotypes. Correlation analysis showed that elevation and BMI were associated with the phylogenetic turnover of microbial communities, suggesting that variations in these factors may influence the composition and diversity of the gut microbiota in A. agrarius. Our study sheds light on gut microbial dynamics in wild A. agrarius populations, highlighting the importance of considering ecological and physiological factors in understanding host-microbiota interactions.

Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters

The Yangtze River estuary (YRE) are strongly influenced by the Kuroshio and terrigenous input from rivers, leading to the formation of distinct water masses, however, there remains a limited understanding of the full extent of this influence. Here the variation of water masses and bacterial communities of 58 seawater samples from the YRE and its adjacent waters were investigated. Our findings suggested that there were 5 water masses in the studied area: Black stream (BS), coastal water in the East China Sea (CW), nearshore mixed water (NM), mixed water in the middle and deep layers of the East China Sea (MM), and deep water blocks in the middle of the East China Sea (DM). The CW mass harbors the highest alpha diversity across all layers, whereas the NM mass exhibits higher diversity in the surface layer but lower in the middle layers. Proteobacteria was the most abundant taxa in all water masses, apart from that, in the surface layer masses, Cyanobacterium, Bacteroidota, and Actinobacteriota were the highest proportion in CW, while Bacteroidota and Actinobacteriota were the highest proportion in NM and BS; in the middle layer, Bacteroidota and Actinobacteriota were dominant phylum in CW and BS masses, but Cyanobacterium was main phylum in NM mass; in the bottom layer, Bacteroidota and Actinobacteriota were the dominant phylum in CW, while Marininimicrobia was the dominated phylum in DM and MM masses. Network analysis suggests water masses have obvious influence on community topological characteristics, moreover, community assembly across masses also differ greatly. Taken together, these results emphasized the significant impact of water masses on the bacterial composition, topological characteristics and assembly process, which may provide a theoretical foundation for predicting alterations in microbial communities within estuarine ecosystems under the influence of water masses.

Priority effects transcend scales and disciplines in biology

Although primarily studied through the lens of community ecology, phenomena consistent with priority effects appear to be widespread across many different scenarios spanning a broad range of spatial, temporal, and biological scales. However, communication between these research fields is inconsistent and has resulted in a fragmented co-citation landscape, likely due to the diversity of terms used to refer to priority effects across these fields. We review these related terms, and the biological contexts in which they are used, to facilitate greater cross-disciplinary cohesion in research on priority effects. In breaking down these semantic barriers, we aim to provide a framework to better understand the conditions and mechanisms of priority effects, and their consequences across spatial and temporal scales.

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE

The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Parallel evolution in an island archipelago revealed by genomic sequencing of Hipposideros leaf-nosed bats

Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The non-sister relationship between large-bodied H. dinops lineages found on different islands indicates large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.

Invasive-dominated grasslands in Hawai'i are resilient to disturbance

Non-native-dominated landscapes may arise from invasion by competitive plant species, disturbance and invasion of early-colonizing species, or some combination of these. Without knowing site history, however, it is difficult to predict how native or non-native communities will reassemble after disturbance events. Given increasing disturbance levels across anthropogenically impacted landscapes, predictive understanding of these patterns is important. We asked how disturbance affected community assembly in six invaded habitat types common in dryland, grazed landscapes on Island of Hawai'i. We mechanically disturbed 100 m2 plots in six vegetation types dominated by one of four invasive perennial grasses (Cenchrus ciliaris, Cenchrus clandestinus, Cenchrus setaceus, or Melinis repens), a native shrub (Dodonaea viscosa), or a native perennial bunchgrass (Eragrostis atropioides). We censused vegetation before disturbance and monitored woody plant colonization and herbaceous cover for 21 months following the disturbance, categorizing species as competitors, colonizers, or a combination, based on recovery patterns. In addition, we planted individuals of the native shrub and bunchgrass and monitored survival to overcome dispersal limitation of native species when exploring these patterns. We found that the dominant vegetation types showed variation in post-disturbance syndrome, and that the variation in colonizer versus competitor syndrome occurred both between species, but also within species among different vegetation types. Although there were flushes of native shrub seedlings, these did not survive to 21 months within invaded habitats, probably due to regrowth by competitive invasive grasses. Similarly, survival of planted native individuals was related to the rate of regrowth by dominant species. Regardless of colonization/competitor syndrome, however, all dominant vegetation types were relatively resilient to change. Our results highlight that the altered post-agricultural, invaded grassland landscapes in Hawai'i are stable states. More generally, they point to the importance of resident communities and their effects on species interactions and seed availability in shaping plant community response to disturbance.

Environmental heterogeneity influences liana community differentiation across a Neotropical rainforest landscape

We examined the variation in liana community composition and structure across geopedological land units to test the hypothesis that environmental heterogeneity is a driving force in liana community assembly. The study site was the Los Tuxtlas Tropical Biology Station, SE Mexico, a reserve that encompasses 640 ha of tropical rainforest. We sampled all lianas with basal diameter ≥1 cm in three 0.5-ha plots established in each of five land units (totaling 15 plots and 7.5 ha). We censused 6055 individuals and 110 species. Overall, the most speciose families were also the most abundant ones. Density and basal area of some dominant liana species differed among land units, and a permutational multivariate analysis of variance (PERMANOVA) and a non-metric multidimensional scaling ordination (NMDS) revealed differences in the presence, density, and basal area of liana species across the landscape. Liana composition and structure were highly heterogeneous among land units, suggesting that variations in soil water availability and relief are key drivers of liana community spatial differentiation. By showing that soil and topography play an important role at the landscape scale, we underscore the ecological relevance of environmental heterogeneity for liana community assembly. In the future, as our ability to assess the local environmental complexity increases, we will gain a better understanding of the liana community assembly process and their heterogeneous distribution in tropical forests.

Eukaryotes may play an important ecological role in the gut microbiome of Graves' disease

The prevalence of autoimmune diseases worldwide has risen rapidly over the past few decades. Increasing evidence has linked gut dysbiosis to the onset of various autoimmune diseases. Thanks to the significant advancements in high-throughput sequencing technology, the number of gut microbiome studies has increased. However, they have primarily focused on bacteria, so our understanding of the role and significance of eukaryotic microbes in the human gut microbial ecosystem remains quite limited. Here, we selected Graves' disease (GD) as an autoimmune disease model and investigated the gut multi-kingdom (bacteria, fungi, and protists) microbial communities from the health control, diseased, and medication-treated recovered patients. The results showed that physiological changes in GD increased homogenizing dispersal processes for bacterial community assembly and increased homogeneous selection processes for eukaryotic community assembly. The recovered patients vs. healthy controls had similar bacterial and protistan, but not fungal, community assembly processes. Additionally, eukaryotes (fungi and protists) may play a more significant role in gut ecosystem functions than bacteria. Overall, this study gives brief insights into the potential contributions of eukaryotes to gut and immune homeostasis in humans and their potential influence in relation to therapeutic interventions.

Variations in species diversity patterns and community assembly rules among vegetation types in the karst landscape

The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.

Functional and Compositional Changes in Sirex noctilio Gut Microbiome in Different Habitats: Unraveling the Complexity of Invasive Adaptation

The mutualistic symbiosis relationship between the gut microbiome and their insect hosts has attracted much scientific attention. The native woodwasp, Sirex nitobei, and the invasive European woodwasp, Sirex noctilio, are two pests that infest pines in northeastern China. Following its encounter with the native species, however, there is a lack of research on whether the gut microbiome of S. noctilio changed, what causes contributed to these alterations, and whether these changes were more conducive to invasive colonization. We used high-throughput and metatranscriptomic sequencing to investigate S. noctilio larval gut and frass from four sites where only S. noctilio and both two Sirex species and investigated the effects of environmental factors, biological interactions, and ecological processes on S. noctilio gut microbial community assembly. Amplicon sequencing of two Sirex species revealed differential patterns of bacterial and fungal composition and functional prediction. S. noctilio larval gut bacterial and fungal diversity was essentially higher in coexistence sites than in separate existence sites, and most of the larval gut bacterial and fungal community functional predictions were significantly different as well. Moreover, temperature and precipitation positively correlate with most of the highly abundant bacterial and fungal genera. Source-tracking analysis showed that S. noctilio larvae at coexistence sites remain dependent on adult gut transmission (vertical transmission) or recruitment to frass (horizontal transmission). Meanwhile, stochastic processes of drift and dispersal limitation also have important impacts on the assembly of S. noctilio larval gut microbiome, especially at coexistence sites. In summary, our results reveal the potential role of changes in S. noctilio larval gut microbiome in the successful colonization and better adaptation of the environment.

Local tree cover predicts mosquito species richness and disease vector presence in a tropical countryside landscape

Context

Land use change drives both biodiversity loss and zoonotic disease transmission in tropical countryside landscapes. Developing solutions for protecting countryside biodiversity, public health, and livelihoods requires understanding the scales at which habitat characteristics such as land cover shape biodiversity, especially for arthropods that transmit pathogens. Evidence increasingly shows that species richness for many taxa correlates with local tree cover.

Objectives

We investigated whether mosquito species richness, community composition, and presence of disease vector species responded to land use and tree cover - and if so, whether at spatial scales similar to other taxa.

Methods

We paired a field survey of mosquito communities in agricultural, residential, and forested lands in rural southern Costa Rica with remotely sensed tree cover data. We compared mosquito community responses to tree cover surrounding survey sites measured across scales, and analyzed community responses to land use and environmental gradients.

Results

Tree cover was positively correlated with mosquito species richness, and negatively correlated with the presence of the common invasive dengue vector Aedes albopictus, particularly at small spatial scales of 80 - 200m. Land use predicted community composition and Ae. albopictus presence. Environmental gradients of tree cover, temperature, and elevation explained 7% of species turnover among survey sites.

Conclusions

The results suggest that preservation and expansion of tree cover at local scales can protect biodiversity for a wide range of taxa, including arthropods, and also confer protection against disease vector occurrence. The identified spatial range of tree cover benefits can inform land management for conservation and public health protection.

The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea

Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.

A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.

Establishment from seed is more important for exotic than for native plant species

Climate change has initiated movement of both native and non-native (exotic) species across the landscape. Exotic species are hypothesized to establish from seed more readily than comparable native species. We tested the hypothesis that seed limitation is more important for exotic species than native grassland species. We compared seed limitation and invasion resistance over three growing seasons between 18 native and 18 exotic species, grown in both monocultures and mixtures in a field experiment. Half of the plots received a seed mix of the contrasting treatment (i.e., exotic species were seeded into native plots, and native species were seeded into exotic plots), and half served as controls. We found that (1) establishment in this perennial grassland is seed limited, (2) establishment from seed is greater in exotic than native species, and (3) community resistance to seedling establishment was positively related to diversity of extant species, but only in native communities. Native-exotic species diversity and composition differences did not converge over time. Our results imply that native to exotic transformations occur when diversity declines in native vegetation and exotic seeds arrive from adjacent sites, suggesting that managing for high diversity will reduce transformations to exotic dominance.

Environmental context shapes the relationship between grass consumption and body size in African herbivore communities

Though herbivore grass dependence has been shown to increase with body size across herbivore species, it is unclear whether this relationship holds at the community level. Here we evaluate whether grass consumption scales positively with body size within African large mammalian herbivore communities and how this relationship varies with environmental context. We used stable carbon isotope and community occurrence data to investigate how grass dependence scales with body size within 23 savanna herbivore communities throughout eastern and central Africa. We found that dietary grass fraction increased with body size for the majority of herbivore communities considered, especially when complete community data were available. However, the slope of this relationship varied, and rainfall seasonality and elephant presence were key drivers of the variation-grass dependence increased less strongly with body size where rainfall was more seasonal and where elephants were present. We found also that the dependence of the herbivore community as a whole on grass peaked at intermediate woody cover. Intraspecific diet variation contributed to these community-level patterns: common hippopotamus (Hippopotamus amphibius) and giraffe (Giraffa camelopardalis) ate less grass where rainfall was more seasonal, whereas Cape buffalo (Syncerus caffer) and savanna elephant (Loxodonta africana) grass consumption were parabolically related to woody cover. Our results indicate that general rules appear to govern herbivore community assembly, though some aspects of herbivore foraging behavior depend upon local environmental context.

Coexistence of many species under a random competition-colonization trade-off

The competition-colonization (CC) trade-off is a well-studied coexistence mechanism for metacommunities. In this setting, it is believed that the coexistence of all species requires their traits to satisfy restrictive conditions limiting their similarity. To investigate whether diverse metacommunities can assemble in a CC trade-off model, we study their assembly from a probabilistic perspective. From a pool of species with parameters (corresponding to traits) sampled at random, we compute the probability that any number of species coexist and characterize the set of species that emerges through assembly. Remarkably, almost exactly half of the species in a large pool typically coexist, with no saturation as the size of the pool grows, and with little dependence on the underlying distribution of traits. Through a mix of analytical results and simulations, we show that this unlimited niche packing emerges as assembly actively moves communities toward overdispersed configurations in niche space. Our findings also apply to a realistic assembly scenario where species invade one at a time from a fixed regional pool. When diversity arises de novo in the metacommunity, richness still grows without bound, but more slowly. Together, our results suggest that the CC trade-off can support the robust emergence of diverse communities, even when coexistence of the full species pool is exceedingly unlikely.

Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments

The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.

An Assessment of Human Opportunistic Pathogenic Bacteria on Daily Necessities in Nanjing City during Plum Rain Season

The plum rain season is a special climatic phenomenon in east Asia, which is characterized by persistent rainfall, a high temperature, and humidity, providing suitable environmental conditions for certain pathogenic bacteria, thus increasing the incidence of respiratory, gastrointestinal, and urinary diseases. However, studies on human opportunistic pathogenic bacteria communities during the plum rain season are still limited. In this study, the characteristics of human opportunistic pathogenic bacterial communities on daily necessities during the non-plum and plum rain seasons were investigated using high-throughput sequencing technology. The results revealed that the relative abundance of human opportunistic pathogenic bacteria was higher in the plum rain season (cotton cloth: 2.469%, electric bicycles: 0.724%, rice: 3.737%, and washbasins: 5.005%) than in the non-plum rain season (cotton cloth: 1.425%, electric bicycles: 0.601%, rice: 2.426%, and washbasins: 4.801%). Both temperature and relative humidity affected human opportunistic pathogenic bacterial communities. Stochastic processes dominated the assembly process of human opportunistic pathogenic bacterial communities, and undominated processes prevailed. The stability of the co-occurrence network was higher in the non-plum rain season than that in the plum rain season. In addition, the proportion of deterministic processes showed the same trend as the complexity of the co-occurrence network.

Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China

Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.

Structure and assembly process of fungal communities in the Yangtze River Estuary

Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.

Uncovering Broad Macroecological Patterns by Comparing the Shape of Species' Distributions along Environmental Gradients

AbstractSpecies' distributions can take many different forms. For example, fat-tailed or skewed distributions are very common in nature, as these can naturally emerge as a result of individual variability and asymmetric environmental tolerances, respectively. Studying the basic shape of distributions can teach us a lot about the ways climatic processes and historical contingencies shape ecological communities. Yet we still lack a general understanding of how their shapes and properties compare to each other along gradients. Here, we use Bayesian nonlinear models to quantify range shape properties in empirical plant distributions. With this approach, we are able to distil the shape of plant distributions and compare them along gradients and across species. Studying the relationship between distribution properties, we revealed the existence of broad macroecological patterns along environmental gradients-such as those expected from Rapoport's rule and the abiotic stress limitation hypothesis. We also find that some aspects of the shape of observed ranges-such as kurtosis and skewness of the distributions-could be intrinsic properties of species or the result of their historical contexts. Overall, our modeling approach and results untangle the general shape of plant distributions and provide a mapping of how this changes along environmental gradients.

Convergence effect during spatiotemporal succession of lacustrine plastisphere: loss of priority effects and turnover of microbial species

Succession is a fundamental aspect of ecological theory, but studies on temporal succession trajectories and ecological driving mechanisms of plastisphere microbial communities across diverse colonization environments remain scarce and poorly understood. To fill this knowledge gap, we assessed the primary colonizers, succession trajectories, assembly, and turnover mechanisms of plastisphere prokaryotes and eukaryotes from four freshwater lakes. Our results show that differences in microbial composition similarity, temporal turnover rate, and assembly processes in the plastisphere do not exclusively occur at the kingdom level (prokaryotes and eukaryotes), but also depend on environmental conditions and colonization time. Thereby, the time of plastisphere colonization has a stronger impact on community composition and assembly of prokaryotes than eukaryotes, whereas for environmental conditions, the opposite pattern holds true. Across all lakes, deterministic processes shaped the assembly of the prokaryotes, but stochastic processes influenced that of the eukaryotes. Yet, they share similar assembly processes throughout the temporal succession: species turnover over time causes the loss of any priority effect, which leads to a convergent succession of plastisphere microbial communities. The increase and loss of microbial diversity in different kingdoms during succession in the plastisphere potentially impact the stability of entire microbial communities and related biogeochemical cycles. Therefore, research needs to integrate temporal dynamics along with spatial turnovers of the plastisphere microbiome. Taking the heterogeneity of global lakes and the diversity of global climate patterns into account, we highlight the urgency to investigate the spatiotemporal succession mechanism of plastisphere prokaryotes and eukaryotes in more lakes around the world.

Decoupled responses of above- and below-ground beta-diversity to nitrogen enrichment in a typical steppe

Increased atmospheric nitrogen (N) deposition affects biodiversity in terrestrial ecosystems. However, we do not know whether the effects of N on above-ground plant β-diversity are coupled with changes occurring in the soil seed bank. We conducted a long-term N-addition experiment in a typical steppe and found that above-ground β-diversity increased and then decreased with increasing N addition, whereas below-ground β-diversity decreased linearly. This suggests decoupled dynamics of plant communities and their soil seed bank under N enrichment. Species substitution determined above- and below-ground β-diversity change via an increasing role of deterministic processes with N addition. These effects were mostly driven by differential responses of the above-ground vegetation and the soil seed bank β-diversities to N-induced changes in environmental heterogeneity, increased soil inorganic N concentrations and soil acidification. Our findings highlight the importance of considering above- and below-ground processes simultaneously for effectively conserving grassland ecosystems under N enrichment.

Reciprocal inhibition and competitive hierarchy cause negative biodiversity-ecosystem function relationships

The relationship between biodiversity and ecosystem function (BEF) captivates ecologists, but the factors responsible for the direction of this relationship remain unclear. While higher ecosystem functioning at higher biodiversity levels ('positive BEF') is not universal in nature, negative BEF relationships seem puzzlingly rare. Here, we develop a dynamical consumer-resource model inspired by microbial decomposer communities in pitcher plant leaves to investigate BEF. We manipulate microbial diversity via controlled colonization and measure their function as total ammonia production. We test how niche partitioning among bacteria and other ecological processes influence BEF in the leaves. We find that a negative BEF can emerge from reciprocal interspecific inhibition in ammonia production causing a negative complementarity effect, or from competitive hierarchies causing a negative selection effect. Absent these factors, a positive BEF was the typical outcome. Our findings provide a potential explanation for the rarity of negative BEF in empirical data.

Functional consequences of animal community changes in managed grasslands: An application of the CAFE approach

In the midst of an ongoing biodiversity crisis, much research has focused on species losses and their impacts on ecosystem functioning. The functional consequences (ecosystem response) of shifts in communities are shaped not only by changes in species richness, but also by compositional shifts that result from species losses and gains. Species differ in their contribution to ecosystem functioning, so species identity underlies the consequences of species losses and gains on ecosystem functions. Such research is critical to better predict the impact of disturbances on communities and ecosystems. We used the "Community Assembly and the Functioning of Ecosystems" (CAFE) approach, a modification of the Price equation to understand the functional consequences and relative effects of richness and composition changes in small nonvolant mammal and dung beetle communities as a result of two common disturbances in North American prairie restorations, prescribed fire and the reintroduction of large grazing mammals. Previous research in this system has shown dung beetles are critically important decomposers, while small mammals modulate much energy in prairie food webs. We found that dung beetle communities were more responsive to bison reintroduction and prescribed fires than small nonvolant mammals. Dung beetle richness increased after bison reintroduction, with higher dung beetle community biomass resulting from changes in remaining species (context-dependent component) rather than species turnover (richness components); prescribed fire caused a minor increase in dung beetle biomass for the same reason. For small mammals, bison reintroduction reduced energy transfer through the loss of species, while prescribed fire had little impact on either small mammal richness or energy transfer. The CAFE approach demonstrates how bison reintroduction controls small nonvolant mammal communities by increasing prairie food web complexity, and increases dung beetle populations with possible benefits for soil health through dung mineralization and soil bioturbation. Prescribed fires, however, have little effect on small mammals and dung beetles, suggesting a resilience to fire. These findings illustrate the key role of re-establishing historical disturbance regimes when restoring endangered prairie ecosystems and their ecological function.

Deterministic and stochastic processes generating alternative states of microbiomes

The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating the mechanisms that generate such "alternative states" of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the "stability landscapes" of ecological community compositions.

Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient

Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants

Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that Blautia and Ruminococcaceae UCG 014, two unidentified genera from the Ruminococcaceae family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while Prevotellaceae, Blautia, and Escherichia-Shigella were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.

The neglected roles of adjacent natural ecosystems in maintaining bacterial diversity in agroecosystems

A central aim of community ecology is to understand how local species diversity is shaped. Agricultural activities are reshaping and filtering soil biodiversity and communities; however, ecological processes that structure agricultural communities have often overlooked the role of the regional species pool, mainly owing to the lack of large datasets across several regions. Here, we conducted a soil survey of 941 plots of agricultural and adjacent natural ecosystems (e.g., forest, wetland, grassland, and desert) in 38 regions across diverse climatic and soil gradients to evaluate whether the regional species pool of soil microbes from adjacent natural ecosystems is important in shaping agricultural soil microbial diversity and completeness. Using a framework of multiscales community assembly, we revealed that the regional species pool was an important predictor of agricultural bacterial diversity and explained a unique variation that cannot be predicted by historical legacy, large-scale environmental factors, and local community assembly processes. Moreover, the species pool effects were associated with microbial dormancy potential, where taxa with higher dormancy potential exhibited stronger species pool effects. Bacterial diversity in regions with higher agricultural intensity was more influenced by species pool effects than that in regions with low intensity, indicating that the maintenance of agricultural biodiversity in high-intensity regions strongly depends on species present in the surrounding landscape. Models for community completeness indicated the positive effect of regional species pool, further implying the community unsaturation and increased potential in bacterial diversity of agricultural ecosystems. Overall, our study reveals the indubitable role of regional species pool from adjacent natural ecosystems in predicting bacterial diversity, which has useful implication for biodiversity management and conservation in agricultural systems.

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest

Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.

Dynamics of the sedimentary bacterial communities in a plain river network: similar coalescence patterns with bacterioplankton communities driven by distinct assembly processes

IMPORTANCE

Microorganisms play important roles in driving the biogeochemical cycles within river ecosystems. It has been suggested that hydrologic conditions could influence microbial communities in rivers, but their specific effects on the behaviours of microbial coalescence have not been thoroughly investigated. In this study, the dynamics of sedimentary bacterial communities within a plain river network were analyzed by amplicon sequencing followed by several ecological models to uncover the underlying assembly processes. Additionally, a comparative analysis between bacterioplankton communities and sedimentary bacterial communities was performed to unveil their coalescence patterns. The results suggested that similar coalescence patterns between sedimentary bacterial and bacterioplankton communities were driven by distinct assembly processes under dynamic hydrological conditions. These findings enhanced our understanding of microbial diversity features within river ecosystems.

Temporal and geographic distribution of gut microbial enterotypes associated with host thermogenesis characteristics in plateau pikas

IMPORTANCE

The gut microbiotas of small mammals play an important role in host energy homeostasis. However, it is still unknown whether small mammals with different enterotypes show differences in thermogenesis characteristics. Our study confirmed that plateau pikas with different bacterial enterotypes harbored distinct thermogenesis capabilities and employed various strategies against cold environments. Additionally, we also found that pikas with different fungal enterotypes may display differences in coprophagy.

Linking functional composition moments of the sub-Mediterranean ecotone with environmental drivers

Introduction

Functional trait-based approaches are extensively applied to the study of mechanisms governing community assembly along environmental gradients. These approaches have been classically based on studying differences in mean values among species, but there is increasing recognition that alternative metrics of trait distributions should be considered to decipher the mechanisms determining community assembly and species coexistence. Under this framework, the main aim of this study is to unravel the effects of environmental conditions as drivers of plant community assembly in sub-Mediterranean ecotones.

Methods

We set 60 plots in six plant communities of a sub-Mediterranean forest in Central Spain, and measured key above- and belowground functional traits in 411 individuals belonging to 19 species, along with abiotic variables. We calculated community-weighted mean (CWM), skewness (CWS) and kurtosis (CWK) of three plant dimensions, and used maximum likelihood techniques to analyze how variation in these functional community traits was driven by abiotic factors. Additionally, we estimated the relative contribution of intraspecific trait variability and species turnover to variation in CWM.

Results and discussion

The first three axes of variation of the principal component analyses were related to three main plant ecological dimensions: Leaf Economics Spectrum, Root Economics Spectrum and plant hydraulic architecture, respectively. Type of community was the most important factor determining differences in the functional structure among communities, as compared to the role of abiotic variables. We found strong differences among communities in their CWMs in line with their biogeographic origin (Eurosiberian vs Mediterranean), while differences in CWS and CWK indicate different trends in the functional structure among communities and the coexistence of different functional strategies, respectively. Moreover, changes in functional composition were primarily due to intraspecific variability.

Conclusion

We observed a high number of strategies in the forest with the different communities spreading along the acquisitive-conservative axis of resource-use, partly matching their Eurosiberian-Mediterranean nature, respectively. Intraspecific trait variability, rather than species turnover, stood as the most relevant factor when analyzing functional changes and assembly patterns among communities. Altogether, our data support the notion that ecotones are ecosystems where relatively minor environmental shifts may result in changes in plant and functional composition.

Bridging theory and experiments of priority effects

Priority effects play a key role in structuring natural communities, but considerable confusion remains about how they affect different ecological systems. Synthesizing previous studies, we show that this confusion arises because the mechanisms driving priority and the temporal scale at which they operate differ among studies, leading to divergent outcomes in species interactions and biodiversity patterns. We suggest grouping priority effects into two functional categories based on their mechanisms: frequency-dependent priority effects that arise from positive frequency dependence, and trait-dependent priority effects that arise from time-dependent changes in interacting traits. Through easy quantification of these categories from experiments, we can construct community models representing diverse biological mechanisms and interactions with priority effects, therefore better predicting their consequences across ecosystems.