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Ecological networks of species interactions are popular and provide powerful analytical tools for understanding variation in community structure and ecosystem functioning. However, network analyses and commonly used metrics such as nestedness and connectance have also attracted criticism. One major concern is that observed patterns are misinterpreted as niche properties such as specialization, whereas they may instead merely reflect variation in sampling, abundance, and/or diversity. As a result, studies potentially draw flawed conclusions about ecological function, stability, or coextinction risks. We highlight potential biases in analyzing and interpreting species-interaction networks and review the solutions available to overcome them, among which we particularly recommend the use of null models that account for species abundances. We show why considering variation across species and networks is important for understanding species interactions and their consequences. Network analyses can advance knowledge on the principles of species interactions but only when judiciously applied. [ABSTRACT FROM AUTHOR]

AbstractThe configuration model is a standard tool for uniformly generating random graphs with a specified degree sequence, and is often used as a null model to evaluate how much of an observed network’s structure can be explained by its degree structure alone. A Markov chain Monte Carlo (MCMC) algorithm, based on a degree-preserving double-edge swap, provides an asymptotic solution to sample from the configuration model. However, accurately and efficiently detecting when this Markov chain is sufficiently close to its stationary distribution remains an unsolved problem. Here, we provide a solution to sample from the configuration model using this standard MCMC algorithm. We develop an algorithm, based on the assortativity of the sampled graphs, for estimating the gap between effectively independent MCMC states, and a computationally efficient gap-estimation heuristic derived from analyzing a corpus of 509 empirical networks. We provide a convergence detection method based on the Dickey-Fuller Generalized Least Squares test, which we show is more accurate and efficient than three alternative Markov chain convergence tests. Supplementary materials for the proposed methods can be found here. [ABSTRACT FROM AUTHOR]

Copyright of Acta Prataculturae Sinica is the property of Acta Prataculturae Sinica Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Bacteria play a crucial role in pollutant degradation, biogeochemical cycling, and energy flow within river ecosystems. However, the underlying mechanisms governing bacterial community assembly and their response to environmental factors at seasonal scales in subtropical rivers remain poorly understood. In this study, we conducted 16S rRNA gene amplicon sequencing on water samples from the Liuxi River to investigate the composition, assembly processes, and co-occurrence relationships of bacterial communities during the wet season and dry season. The results demonstrated that seasonal differences in hydrochemistry significantly influenced the composition of bacterial communities. A more heterogeneous community structure and increased alpha diversity were observed during the dry season. Water temperature emerged as the primary driver for seasonal changes in bacterial communities. Dispersal limitation predominantly governed community assembly, however, during the dry season, its contribution increased due to decreased immigration rates. Co-occurrence network analysis reveals that mutualism played a prevailing role in shaping bacterial community structure. Compared to the wet season, the network of bacterial communities exhibited higher modularity, competition, and keystone species during the dry season, resulting in a more stable community structure. Although keystone species displayed distinct seasonal variations, Proteobacteria and Actinobacteria were consistently abundant keystone species maintaining network structure in both seasons. Our findings provide insights into how bacterial communities respond to seasonal environmental changes, uncovering underlying mechanisms governing community assembly in subtropical rivers, which are crucial for the effective management and conservation of riverine ecosystems. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic bacteria (AAPB) are significant bacterial groups in aquatic ecosystems, known for their rapid growth and photoheterotrophic characteristics. However, the distribution and ecological assembly process of AAPB in low irradiation freshwater basins remain unclear, warranting further investigation. In this study, we present the diversity, abundance, spatial variations, ecological process, and community interaction of AAPB in sediment of Three Gorges Reservoir (TGR) under low irradiation. Our findings demonstrate the dominant genera of AAPB community that exist in the TGR area also are appeared in different waters, with some regional preference. Moreover, the concentration of pufM gene, an indicator for AAPB, maintains a consistently high numerical level ranging from (2.21 ± 0.44) × 104 to (9.98 ± 0.30) × 107 gene copies/g. Although solar irradiation is suggested as the major factor affecting AAPB, it remains unclear whether and how AAPB differ between regions due to varying solar irradiation levels. Our results show spatial differences between total bacteria and AAPB communities, with significant differences observed only in AAPB. Geographical and environmental factor contributed less than 10% to the spatial difference of community, with sediment type and environmental factors being the key factors influencing microbial community structure. The stochastic process plays a dominant role in the aggregation and replacement of AAPB communities, among which the most contribution is dispersal limitation. For AAPB network, Yoonia and Gemmobacter are the hubs for modules. Those results valuable insights into the AAPB communities in TGR with low irradiation. [Display omitted] [ABSTRACT FROM AUTHOR]

The timing of flowering is an important driver of species distribution and community assembly patterns. However, we still have much to learn about the factors that shape flowering diversity (i.e., number of species flowering per period) in plant communities. One potential explanation of flowering diversity is the mid-domain effect, which states that geometric constraints on species ranges within a bounded domain (space or time) will yield a mid-domain peak in diversity regardless of ecological factors. Here, we determine whether the mid-domain effect explains peak flowering time (i.e., when most species of communities are flowering) across China. We used phenological data of 16,267 herbaceous and woody species from the provincial Flora in China and species distribution data from the Chinese Vascular Plant Distribution Database to determine relationships between the observed number of species flowering and the number of species flowering as predicted by the mid-domain effect model, as well as between three climatic variables (mean minimum monthly temperature, mean monthly precipitation, and mean monthly sunshine duration). We found that the mid-domain effect explained a significant proportion of the temporal variation in flowering diversity across all species in China. Further, the mid-domain effect explained a greater proportion of variance in flowering diversity at higher latitudes than at lower latitudes. The patterns of flowering diversity for both herbaceous and woody species were related to both the mid-domain effect and environmental variables. Our findings indicate that including geometric constraints in conjunction with abiotic and biotic predictors will improve predictions of flowering diversity patterns.

Environmental heterogeneity partly drives microbial succession in arthropods, while the microbial assembly mechanisms during environmental changes remain largely unknown. Here, we explored the temporal dynamics and assembly mechanisms within both bacterial and fungal communities in Liriomyza huidobrensis (Blanchard) during the transition from field to laboratory conditions. We observed a decrease in bacterial diversity and complexity of bacterial-fungal co-occurrence networks in leaf miners transitioning from wild to captive environments. Both neutral and null models revealed that stochastic processes, particularly drift (contributing over 70%), play a crucial role in governing bacterial and fungal community assembly. The relative contribution of ecological processes such as dispersal, drift, and selection varied among leaf miners transitioning from wild to captive states. Furthermore, we propose a hypothetical scenario for the assembly and succession of microbial communities in the leaf miner during the short- and long-term transition from the wild to captivity. Our findings suggest that environmental heterogeneity determines the ecological processes governing bacterial and fungal community assembly in leaf miners, offering new insights into microbiome and mycobiome assembly mechanisms in invasive pests amidst environmental change. [ABSTRACT FROM AUTHOR]

Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high‐throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research. [ABSTRACT FROM AUTHOR]

Dynamic heterogeneous networks describe the temporal evolution of interactions among nodes and edges of different types. While there is a rich literature on finding communities in dynamic networks, the application of these methods to dynamic heterogeneous networks can be inappropriate, due to the involvement of different types of nodes and edges and the need to treat them differently. In this article, we propose a statistical framework for detecting common communities in dynamic and heterogeneous networks. Under this framework, we develop a fast community detection method called DHNet that can efficiently estimate the community label as well as the number of communities. An attractive feature of DHNet is that it does not require the number of communities to be known a priori, a common assumption in community detection methods. While DHNet does not require any parametric assumptions on the underlying network model, we show that the identified label is consistent under a time-varying heterogeneous stochastic block model with a temporal correlation structure and edge sparsity. We further illustrate the utility of DHNet through simulations and an application to review data from Yelp, where DHNet shows improvements both in terms of accuracy and interpretability over alternative solutions. for this article are available online. [ABSTRACT FROM AUTHOR]

The study of diet is one of the mechanisms by which competition for resources between species that cohabit in the same ecosystem can be inferred. Therefore, the relationships of the indices that measure specialization in the diet of fish species are necessary to characterize the nutritional quality of these populations and the ecosystem's environmental health. Three species of catfish were selected: one invasive (Clarias gariepinus) and two natives (Trachelyopterus striatulus and Rhamdia quelen), with similar distribution along the Guapi‐Macacu River, in the Guapimirim Protection Area (Rio de Janeiro). Fifty‐nine catfish of the three species were collected in total, along 32 collection points in the Guapi‐Macacu River in two periods (dry and rainy) in 2018. Non‐parametric statistics showed the partition of resources between species and the influence of abiotic factors (temperature, pH, transparency, and dissolved oxygen) contributing to the selection of available resources in the environment. Diet‐related indices—repletion index (RI), condition factor (K), niche width, and trophic position (TP) of the specimens collected—contributed to measuring the nutritional status of each of these catfish species, showing that R. quelen has a relationship between RI and K, tending to absorb and metabolize nutrients faster than other species. In addition, the invasive species occupies a wide range of TPs compared to native species, confirming its feeding plasticity. On the contrary, T. striatulus needs large amounts of terrestrial insects to maintain its poor condition factor. Also, the RI showed direct influences of abiotic variables, with the temperature being the most prominent. Our results suggest that the invasive species can benefit from this environment that shows signs of environmental degradation. [ABSTRACT FROM AUTHOR]

Abstract Background Understanding community assembly mechanisms across taxa and space is fundamental for microbial ecology. However, the variability and determinants of assembly processes over taxa and space remain unclear. Here, we investigated taxonomic dependency and spatial heterogeneity in bacterial assembly mechanisms across coastal waters in the East China Sea using neutral and null models with customized visualization strategies. Results Overall, bacterial assembly mechanisms varied across broad taxonomic groups (phyla and proteobacterial classes) and space at the regional scale. A determinism–stochasticity balanced mechanism governed total bacterial assembly, while taxonomic dependency existed in assembly mechanisms and ecological processes. Among community ecological features, niche breadth and negative-to-positive cohesion ratio were strongly associated with the determinism-to-stochasticity ratio of bacterial groups. Bacterial assembly mechanisms commonly exhibited spatial heterogeneity, the extent and determinants of which varied across taxonomic groups. Spatial assembly of total bacteria was directly driven by many environmental factors and potential interactions between taxa, but not directly by geographic factors. Overall, the bacterial groups with higher spatial heterogeneity in assembly mechanisms were more related to environmental and/or geographic factors (except Bacteroidetes), while those with lower heterogeneity were more related to ecological features. Conclusions Our results confirm the pervasiveness of taxonomic dependency and spatial heterogeneity in bacterial assembly, providing a finer understanding about regulation across complex coastal waters.

It is often assumed that community assembly processes, i.e. deterministic or stochastic factors determining the structure of communities, vary with spatial scale. However, evidence showing such scale‐dependency is challenging to gather, especially in microbial communities. Here we studied the relative importance of potential community assembly processes of bacterial and fungal communities across the coastline of China. We used null models based on phylogenetic and compositional turnover to quantify the relative importance of the processes at three spatial scales (local, regional and subcontinental). We used a generalized multinomial logistic regression to estimate the probability of observing the different assembly processes along environmental and spatial gradients. We found that, overall, deterministic processes are stronger in driving the assembly of bacterial communities compared to fungal communities, especially at the local scale. Moreover, the assembly processes in bacterial communities exhibit clear scale‐dependency, with homogeneous selection being the dominant process at the local scale, and dispersal limitation dominating at regional and subcontinental scales. Conversely, drift is consistently the dominant driver of fungal community assembly across all spatial scales. Our findings demonstrate scale‐dependency in community assembly processes between two marine microbial groups, and highlight the importance of adopting a multi‐scale approach to gain insights into the complex and dynamic spatial patterns of microbial communities. [ABSTRACT FROM AUTHOR]

Damming of large rivers has promoted well‐documented ecosystem changes that constitute critical threats to freshwater fish biodiversity. However, it is unclear how trait–environment relationships drive community assembly in older (>50 years) tropical river‐reservoir systems. We assessed physical features filtering functional traits (RLQ and fourth‐corner approaches) in seven tropical reservoirs along a major river, in southeastern Brazil, and correlated taxonomic and functional counterparts of local and beta diversity to assess niche‐based assembly processes under prevailing environmental conditions (null model approach). Lower littoral habitat availability (smaller area, volume, and riverine influence) favored species inhabiting open areas that feed on the bottom (mostly migratory species). Downstream position (lower elevation and inflow of water from the mainstem) allowed migrators to enter the reservoirs and promoted environmental heterogeneity, favoring detritivores, invertivores, and carnivorous generalists. Total blocking of the main channel excluded most migratory species from reservoirs at upstream reaches, whereas higher riverine influence and hydrological stability (larger area, volume, and water residence time) favored small‐sized sedentary species (omnivores and piscivores with parental care, mostly non‐native species) in the littoral zone. Correlations differing from null expectations for alpha diversity and nestedness revealed that niche‐based processes support species richness and loss under higher riverine influence and hydrological stability. Our study supports the importance of physical features to set functional spaces available for fish species, but random processes that boost taxonomic differences between reservoirs, largely related to non‐native species introductions, are the primary drivers of fish assemblage structure in tropical reservoirs long‐term disconnected from riverine dynamics. [ABSTRACT FROM AUTHOR]

Background: Understanding community assembly mechanisms across taxa and space is fundamental for microbial ecology. However, the variability and determinants of assembly processes over taxa and space remain unclear. Here, we investigated taxonomic dependency and spatial heterogeneity in bacterial assembly mechanisms across coastal waters in the East China Sea using neutral and null models with customized visualization strategies. Results: Overall, bacterial assembly mechanisms varied across broad taxonomic groups (phyla and proteobacterial classes) and space at the regional scale. A determinism–stochasticity balanced mechanism governed total bacterial assembly, while taxonomic dependency existed in assembly mechanisms and ecological processes. Among community ecological features, niche breadth and negative-to-positive cohesion ratio were strongly associated with the determinism-to-stochasticity ratio of bacterial groups. Bacterial assembly mechanisms commonly exhibited spatial heterogeneity, the extent and determinants of which varied across taxonomic groups. Spatial assembly of total bacteria was directly driven by many environmental factors and potential interactions between taxa, but not directly by geographic factors. Overall, the bacterial groups with higher spatial heterogeneity in assembly mechanisms were more related to environmental and/or geographic factors (except Bacteroidetes), while those with lower heterogeneity were more related to ecological features. Conclusions: Our results confirm the pervasiveness of taxonomic dependency and spatial heterogeneity in bacterial assembly, providing a finer understanding about regulation across complex coastal waters. [ABSTRACT FROM AUTHOR]

Copyright of Caldasia is the property of Universidad Nacional de Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Granular sludge is a biofilm process used for wastewater treatment which is currently being implemented worldwide. It is important to understand how disturbances affect the microbial community and performance of reactors. Here, two acetate-fed replicate reactors were inoculated with acclimatized sludge and the reactor performance, and the granular sludge microbial community succession were studied for 149 days. During this time, the microbial community was challenged by periodically removing half of the reactor biomass, subsequently increasing the food-to-microorganism (F/M) ratio. Diversity analysis together with null models show that overall, the microbial communities were resistant to the disturbances, observing some minor effects on polyphosphate-accumulating and denitrifying microbial communities and their associated reactor functions. Community turnover was driven by drift and random granule loss, and stochasticity was the governing ecological process for community assembly. These results evidence the aerobic granular sludge process as a robust system for wastewater treatment.

Identifying the potential factors associated with the impact of long-term drip irrigation (DI) on soil ecosystems is essential for responding to the environmental changes induced by extensive application of DI technology in arid regions. Herein, we examined the effects of the length of time that DI lasts in years (NDI) on soil bacterial diversity as well as the soil bacterial community assembly process and the factors influencing it. The results showed that long-term DI substantially reduced soil salinity and increased soil bacterial diversity while affecting the soil bacterial community structure distinctly. Null model results showed that the soil bacterial community assembly transitioned from stochastic processes to deterministic processes, as NDI increased. Homogeneous selection, a deterministic process, emerged as the dominant process when NDI exceeded 15  years. Both random forest and structural equation models showed that soil salinity was the primary factor affecting the bacterial community assembly process. In summary, this study suggested that soil bacteria respond differently to long-term DI and depends on the NDI, influencing the soil bacterial community assembly process under long-term DI. [ABSTRACT FROM AUTHOR]

Explaining the mechanisms underlying spatial and temporal variation in community composition is a major challenge. Nevertheless, the processes controlling temporal variation at a site (i.e. temporal β‐diversity, including its turnover and nestedness components) are less understood than those affecting variation among sites (i.e. spatial β‐diversity). Short‐term temporal turnover (e.g. throughout an annual cycle) is expected to correlate positively with seasonal environmental variability and landscape connectivity, but also species pool size (γ‐diversity). We use the megadiverse Amazonian freshwater ichthyofauna as a model to ask whether seasonality and landscape connectivity drive variation in temporal species turnover among geomorphological habitat types, while accounting for between‐habitat variation in γ‐diversity. We collected 11 397 fish representing 260 species during a year‐long sampling program from an area containing the lowland Amazon's four major geomorphological habitat types: rivers, floodplains, terra firme streams, and shield streams. River‐floodplain systems exhibit strong but predictable seasonality (via a high‐amplitude annual flood pulse), high connectivity, and high species richness with many rare species. Terra firme and shield streams exhibit low seasonality, low connectivity, and low species richness with proportionally fewer rare species. Based on these parameters we predicted that river‐floodplain systems should have higher temporal turnover than stream systems. Using a null model approach combined with β‐deviation calculations, we confirmed that rivers and floodplains do exhibit higher turnover (but not nestedness) than terra firme and shield streams, even when controlling for the potentially confounding effect of higher species richness in river‐floodplain systems. All habitats exhibit low temporal nestedness, indicating that short‐term changes in community composition result primarily from temporal species turnover. Our results provide a timely reminder that efforts to conserve the Amazon's threatened aquatic biodiversity should account for the distinct temporal dynamics of habitat types and variation in hydrological seasonality. [ABSTRACT FROM AUTHOR]

Biological nitrogen fixation (BNF) is a crucial process that provides bioavailable nitrogen and supports primary production in freshwater lake ecosystems. However, the characteristics of diazotrophic community and nitrogenase activity in freshwater lake sediments remain poorly understood. Here, we investigated the diazotrophic communities and nitrogenase activities in the sediments of three large river-connected freshwater lakes in eastern China using 15N-isotope tracing and nif H sequencing. The sediments in these lakes contained diverse nitrogenase genes that were phylogenetically grouped into Clusters I and III. The diazotrophic communities in the sediments were dominated by stochastic processes in Hongze Lake and Taihu Lake, which had heterogeneous habitats and shallower water depths, while in Poyang Lake, which had deeper water and a shorter hydraulic retention time, the assembly of the diazotrophic community in the sediments was dominated by homogeneous selection processes. Temperature and water depth were also found the key environmental factors affecting the sediment diazotrophic communities. Sediment nitrogenase activities varied in the three lakes and within distinct regions of an individual lake, ranging from 0 to 14.58 nmol/(kg·hr). Nitrogenase activity was significantly correlated with ferric iron, total phosphorus, and organic matter contents. Our results suggested that freshwater lake sediment contain high diversity of nitrogen-fixing microorganisms with potential metabolic diversity, and the community assembly patterns and nitrogenase activities varied with the lake habitat. [Display omitted] [ABSTRACT FROM AUTHOR]

Analysis of the phylogenetic structure of a community based on the phylogenetic relationships among species in the community can reflect the ecological process of community composition and determine the mechanism of plant community construction. In this study, we analyzed the characteristics of the phylogenetic structure and diversity of plant communities in the Gurbantunggut Desert and their interactions with soil factors and explored the mechanisms of species maintenance in the communities. The results showed that the ecological traits of plants were conserved, habitat filtering was the primary process affecting plant communities, and the diversity of phylogeny was ranked as fixed dunes > semifixed dunes > mobile dunes. At different slope positions within the dune, there is greater phylogenetic diversity at the bottom and lower slope, and habitat filtering dominates community construction, with the dominant role of habitat filtering in the community diminishing as the slope position rises. The phylogenetic diversity of plant communities of different life types is ranked as short-lived plants > small trees and shrubs > annual and perennial herbs. On the bottom and lower slopes, short-lived plants and annual and perennial herbaceous communities are mainly influenced by habitat filtering. Habitat filterability decreased with increasing slope position. On the upper slopes and at the top, competitive exclusion effects between small trees and shrubs dominated. Our analysis shows that soil water content and organic carbon affect phylogenetic diversity mainly by influencing community species richness and that the interaction between soil water content, grain size and plant diversity leads to clustering of species with similar soil preferences, which in turn affects the phylogenetic structure of the community. In addition, the change from habitat filtering to intraspecific competition in plant community construction from the bottom to the top of the slope is mainly influenced by short-lived plant communities, and this type of plant needs to be given priority consideration in the conservation and restoration of desert plant communities.

Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms. [ABSTRACT FROM AUTHOR]

Long‐term monitoring programs are fundamental to detect changes in ecosystem health and understand ecological processes. In the current context of increasing anthropogenic threats on marine ecosystems, understanding the dynamics and response of communities becomes essential. We used data collected over 14 years in the REBENT benthic coastal invertebrates monitoring program, at a regional scale in the North‐East Atlantic, covering a total of 26 sites and 979 taxa. Four distinct habitats were studied: two biogenic habitats associated with foundation species in the intertidal and subtidal zones and two bare sedimentary habitats in the same respective tidal zones. We used community trajectory analysis (CTA), a statistical approach that allows for quantitative measures and comparisons of temporal trajectories of ecosystems. We compared observed community trajectories to trajectories simulated under a non‐directional null model in order to better understand the dynamics of the communities, their potential drivers, and the role of the studied habitats in these dynamics. Despite strong differences in the community compositions between sites and habitats, the communities followed non‐directional dynamics during the 14 years monitored, which suggested stability at the regional scale. However, the shape, size, and direction of the trajectories of benthic communities were more similar within than among habitats, also suggesting the influence of the nature of the habitat on community dynamics. Results showed a higher variability in community composition the first years of the monitoring in the intertidal bare habitat and confirmed the role of biogenic habitats in maintaining temporal stability. They also highlighted the need to apprehend the role of transient and rare species and the scale of observation in temporal beta diversity analyses. Finally, our study confirmed the usefulness of CTA to link observed trajectory patterns to fundamental ecological processes. [ABSTRACT FROM AUTHOR]

Bacteria play an important role as decomposers in karst ecosystems, which can be associated with karst soil and plants, promoting the cycling of nutrients between plants and soil. To reveal the diversity and structure of soil bacterial communities in some karst land-use types after the Grain for Green pattern, soil samples were collected from different land-use types (crops, grasses, and plantations) for analysis. Changes in the structure and assembly of karst soil bacteria were examined using 16S rRNA Illumina sequencing and soil chemical properties. We found that 18 years after the Grain for Green program, the soil chemical properties of available nitrogen (AN), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM) of grassland were significantly different from those of farmland. The soil chemical properties in plantations were also significantly lower than those in farmlands. Different land-use types did not significantly affect the soil bacterial community structure. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in all the plots. The relative abundance of Proteobacteria was higher in grasslands and plantations than in farmlands, whereas that of Actinobacteria was lower in grasslands. Furthermore, no significant correlations were observed between the soil chemical factors and soil bacterial groups at the genus level. The null model analysis indicated that dispersal limitations in stochastic processes predominated for the different land-use systems. Combined with previous analyses of the factors driving bacterial core species diversity in karst soils, we speculated that stochastic processes play a more important role in the construction of core bacterial species in restored karst soils at the plot scale. [ABSTRACT FROM AUTHOR]

Grassland degradation caused by increases in livestock grazing threatens a variety of ecosystem services. Understanding changes in plant community assembly during the process of grassland degradation in the presence of grazing is important to help restore degraded grasslands worldwide but has received little attention thus far. The grassland degradation process is typified by heterogeneous degradation, that is, gradual formation of degraded patches (hereafter "patchy degradation"). Here, we experimentally examined the effects of herbivore grazing and patchy degradation on plant community assembly using nine pairs of non‐degraded (intact) and patch‐degraded (fragmented) grasslands subject to grazing by different‐sized herbivores (i.e., NG, no grazing; SG, sheep grazing; CG, cattle grazing) over 4 years. Using a null‐model approach, we estimated the relative magnitude of deterministic processes of community assembly by comparing the observed and expected β‐diversity. We found that in the absence of herbivore grazing, deterministic processes played a greater role in community assembly, regardless of whether patchy degradation had occurred. However, the deterministic processes resulted in plant communities being more spatially similar in non‐degraded grasslands while being more dissimilar in patchy degraded grasslands. Compared with non‐degraded grasslands, species with strong competitive abilities (i.e., Leymus chinensis) were less dominant in patchy degraded grasslands, indicating relaxed competition and a reduced role of species interactions over plant communities. Instead, patchy degradation added the role of environmental variables over plant communities. SG consistently promoted more stochastic plant community assembly in both non‐degraded and patch‐degraded grasslands, while CG promoted more stochastic plant community assembly only in the non‐degraded state, having no effect in the patch‐degraded state. Our study offers important insights into changes in plant community assembly during ongoing patch‐degradation of grasslands, indicating the role of increased environmental filtering of soil and reduced species interactions in driving plant community dynamics with increasing grassland patchy degradation. We also uncovered an herbivore species‐specific effect on plant community assembly during the process of grassland degradation, which will better inform and improve future grassland restoration planning efforts. [ABSTRACT FROM AUTHOR]

To explore the taxon‐dependent contribution of dispersal limitation versus environmental filters to bryophyte assemblages. We investigated bryophytes and six environmental variables on 168 islands in the Thousand Island Lake,China. We compared the observed beta diversity with the expected values based on six null models (EE, EF, FE, FF, PE, and PF), detected the partial correlation of beta diversity with geographical distances. We quantified the contributions of spatial versus environmental variables and island isolation per se to species composition (SC) using variance partitioning. We modeled the species‐area relationships (SARs) for bryophytes and the other eight biotas. To explore the taxon‐dependent effects of spatial versus environmental filters on bryophytes, 16 taxa including five categories (total bryophytes, total mosses, liverworts, acrocarpous, and pleurocarpous mosses) and 11 species‐richest families were included in the analyses. The observed beta diversity values were significantly different from the predicted values for all 16 taxa. For all five categories, the observed partial correlations between beta diversity and geographical distance after controlling environmental effects were not only positive, but also significantly different from the predicted values based on the null models. Spatial eigenvectors are more important in shaping SC than environmental variables for all 16 taxa except Brachytheciaceae and Anomodontaceae. Spatial eigenvectors contributed more to SC variation in liverworts than in mosses and in pleurocarpous mosses than in acrocarpous mosses. The effects of island isolation on SC were significant for all five categories, highly varied at the family level. The z values of the SARs for the five bryophyte categories were all larger than those of the other eight biotas. In subtropical fragmented forests, dispersal limitation exerted significant, taxon‐dependent effects on bryophyte assemblages. It was dispersal limitation rather than environmental filtering that predominantly regulated the SC patterns of bryophytes. [ABSTRACT FROM AUTHOR]

Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity.We aimed to understand the relative contribution of multi‐scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale.We applied a Markov Random Fields model and assessed measures of β‐diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models.We showed that β‐diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β‐diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within‐host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within‐host parasite interactions, providing a mechanism for the observed infracommunity modularity.An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for. [ABSTRACT FROM AUTHOR]

The introduction of nurse species on degraded sites of Permanently Protected Areas represents a useful strategy for vegetation recovery in riparian forest. Species of the genus Baccharis (Asteraceae) have been documented as potential nurse plants being able of restructuring the native plant community. This study was aimed to evaluate the potential nursing role of Baccharis dracunculifolia in the recovery of a native plant community of a degraded Atlantic rainforest in a short-time period. The study was developed in two abandoned pasture areas in a riparian forest in the River Piranga basin, one in which B. dracunculifolia was planted (Restored treatment) to promote restoration, and a second area with no intervention (Degraded = Control treatment). Sampling took place 18 months after the planting of B. dracunculifolia. We set up 20 plots of 2 × 2 m in each treatment type (n = 40 plots), where all plant species were recorded (with the exception of the introduced Baccharis individuals and grasses), classifying them as native, ruderal, or alien. Plant richness was twice higher in the Restored treatment than the Degraded treatment. Furthermore, the observed values of alpha, gamma and beta diversity were also higher in Restored treatment. Restored treatment had 17 exclusive native species, while the Degraded treatment had only three non-exclusive native species. In addition, fewer ruderal and alien species were recorded in the restored plots with B. dracunculifolia compared to degraded plots. We concluded that, even in a short time period, planting B. dracunculifolia had a positive effect on promoting the assembly of the native plant community and possibly decreasing the chances of invasion by alien species.

Due to rapid urbanization, the Beibu Gulf, a semi-closed gulf in the northwestern South China Sea, faces escalating ecological and environmental threats. Understanding the assembly mechanisms and driving factors of bacterioplankton in the Beibu Gulf is crucial for preserving its ecological functions and services. In the present study, we investigated the spatiotemporal dynamics of bacterioplankton communities and their assembly mechanisms in the Beibu Gulf based on the high-throughput sequencing of the bacterial 16 S rRNA gene. Results showed significantly higher bacterioplankton diversity during the wet season compared to the dry season. Additionally, distinct seasonal variations in bacterioplankton composition were observed, characterized by an increase in Cyanobacteria and Thermoplasmatota and a decrease in Proteobacteria and Bacteroidota during the wet season. Null model analysis revealed that stochastic processes governed bacterioplankton community assembly in the Beibu Gulf, with drift and homogenizing dispersal dominating during the dry and wet seasons, respectively. Enhanced deterministic assembly of bacterioplankton was also observed during the wet season. Redundancy and random forest model analyses identified the physical properties (e.g., temperature) and nutrient content (e.g., nitrate) of water as primary environmental drivers influencing bacterioplankton dynamics. Moreover, variation partitioning and distance-decay of similarity revealed that environmental filtering played a significant role in shaping bacterioplankton variations in this rapidly developed coastal ecosystem. These findings advance our understanding of bacterioplankton assembly in coastal ecosystems and establish a theoretical basis for effective ecological health management amidst ongoing global changes. [Display omitted] • Spatiotemporal variations of bacterioplankton in the Beibu Gulf were investigated. • Stochastic processes governed the bacterioplankton community assembly. • Enhanced deterministic assembly of bacterioplankton was observed in the wet season. • Water physical properties dominantly regulated the dynamics of bacterioplankton. • Environmental filtering played a significant role in shaping bacterioplankton. [ABSTRACT FROM AUTHOR]

Abstract Salt marshes are unique habitats between sea or saline lakes and land that need to be conserved from the effects of global change. Understanding the variation in functional structure of plant community along environmental gradients is critical to predict the response of plant communities to ongoing environmental changes. We evaluated the changes in the functional structure of halophytic communities along soil gradients including salinity, in Iranian salt marshes; Lake Urmia, Lake Meyghan, Musa estuary, and Nayband Bay (Iran). We established 48 plots from 16 sites in four salt marshes and sampled 10 leaves per species to measure leaf functional traits. Five soil samples were sampled from each plot and 30 variables were analyzed. We examined the changes in the functional structure of plant communities (i.e., functional diversity [FD] and community weighted mean [CWM]) along local soil gradients using linear mixed effect models. Our results showed that FD and CWM of leaf thickness tended to increase with salinity, while those indices related to leaf shape decreased following soil potassium content. Our results suggest that the variations in functional structure of plant communities along local soil gradients reveal the effect of different ecological processes (e.g., niche differentiation related to the habitat heterogeneity) that drive the assembly of halophytic plant communities in SW Asian salt marshes.

Abstract To explore the taxon‐dependent contribution of dispersal limitation versus environmental filters to bryophyte assemblages. We investigated bryophytes and six environmental variables on 168 islands in the Thousand Island Lake,China. We compared the observed beta diversity with the expected values based on six null models (EE, EF, FE, FF, PE, and PF), detected the partial correlation of beta diversity with geographical distances. We quantified the contributions of spatial versus environmental variables and island isolation per se to species composition (SC) using variance partitioning. We modeled the species‐area relationships (SARs) for bryophytes and the other eight biotas. To explore the taxon‐dependent effects of spatial versus environmental filters on bryophytes, 16 taxa including five categories (total bryophytes, total mosses, liverworts, acrocarpous, and pleurocarpous mosses) and 11 species‐richest families were included in the analyses. The observed beta diversity values were significantly different from the predicted values for all 16 taxa. For all five categories, the observed partial correlations between beta diversity and geographical distance after controlling environmental effects were not only positive, but also significantly different from the predicted values based on the null models. Spatial eigenvectors are more important in shaping SC than environmental variables for all 16 taxa except Brachytheciaceae and Anomodontaceae. Spatial eigenvectors contributed more to SC variation in liverworts than in mosses and in pleurocarpous mosses than in acrocarpous mosses. The effects of island isolation on SC were significant for all five categories, highly varied at the family level. The z values of the SARs for the five bryophyte categories were all larger than those of the other eight biotas. In subtropical fragmented forests, dispersal limitation exerted significant, taxon‐dependent effects on bryophyte assemblages. It was dispersal limitation rather than environmental filtering that predominantly regulated the SC patterns of bryophytes.

Recent developments in sexual selection theory suggest that on their own, mate preferences can promote the maintenance of sexual trait diversity. However, how mate preferences constrain the permissiveness of sexual trait diversity in different environmental regimes remains an open question. Here, we examine how a range of mate choice parameters affect the permissiveness of sexual trait polymorphism under several selection regimes. We use the null model of sexual selection and show that environments with strong assortative mating significantly increase the permissiveness of sexual trait polymorphism. We show that for a given change in mate choice parameters, the permissiveness of polymorphism changes more in environments with strong natural selection on sexual traits than in environments with weak selection. Sets of nearly stable polymorphic populations with weak assortative mating are more likely to show accidental divergence in sexual traits than sets of populations with strong assortative mating. The permissiveness of sexual trait polymorphism critically depends upon particular combinations of natural selection and mate choice parameters.

Treeline patches are among Earth’s most sensitive and are important model ecosystems for assessing climate change trends. To explore ecological factors that limit the species’ survival in treelines, the treeline patch of Li Mountain National Nature Reserve was selected as the research site. Pinus armandii (P. armandii), Betula albo-sinensis (B. albo-sinensis), and Betula utilis (B. utilis) were selected as research species based on their dominance. Two 50 m × 50 m plots were established separately from the upper and lower limits of the highest treeline patch for point pattern analysis. Five 10 m × 10 m quadrats per plot were sampled to investigate the flora and environmental factors. The results showed that: (1) Slope and community composition at tree layer in quadrates had significant differences between upper and lower limits. Pinus armandii had a greater population size at the upper limit. Seedling recruitment restricted population development for B. albo-sinensis at the lower limit and B. utilis at the upper limit and less regeneration of B. albo-sinensis at the upper limit. (2) More aggregation scales occurred at the upper limit, and P. armandii had more aggregation scales than the other two species at 0–25 m. The heterogeneity caused by density distribution affected P. armandii pattern at the upper limit, and heterogeneity of seed dispersal could explain species patterns in both limits. Distinctness of size difference may have an influence on inter-specific species correlations. [ABSTRACT FROM AUTHOR]

Contemporary plant communities are simultaneously the reflection of current habitat conditions and historic processes. The observed patterns in the diversity, abundance, and composition of these communities are the result of the combination of stochastic and deterministic factors. Deterministic factors such as environmental filters often leverage a greater influence in wetlands, though this may not be the case with geographically isolated communities. We evaluated the influence of environmental factors on plant community composition and richness in the Eastern Highland Rim physiographic region of the Southeastern United States. Plant communities were sampled at 27 open wetland sites. We determined that water permanence, change in water depth, grazing, and site area were important predictors of plant species richness, community composition, and the degree of stochasticity driving plant community composition. There was a negative relationship between site area and richness, and species composition was weakly correlated with geographic distance between sites. There was greater stochasticity in species composition among sites when environmental characteristics differed. The apparent influence of stochastic factors at sites appears to be dependent upon the strength of environmental filters present. This suggests that the assembly of isolated wetland plant communities may be driven first by dispersal limitations and then subsequently by environmental constraints once propagules arrive. A strong environmental filter may limit the successful colonization of new species to a site which can prevent the introduction of non-native species but inhibit restoration efforts. This has important implications for the management and conservation of imperiled wetland ecosystems. [ABSTRACT FROM AUTHOR]

Navarro and Manly (Popul Ecol 51:505–512, 2009) (NM) have proposed a randomization protocol for null model analysis of species occurrences at discrete locations based on probability distributions and generalized linear models. In the NM method, presences-absences are governed by independent Bernoulli random variables. In addition, a non-observable non-negative random variable ("quasi-abundance") from either Poisson, Binomial or Negative Binomial distributions are log-linearly related to the qualitative effects of species and location. By connecting the probability of occurrence of each species on each location and the quasi-abundance distributions, one generalized linear model for the observed presences-absences is selected by profile deviance, and the resulting fitted probabilities of the null model with minimum deviance is used to generate random matrices via parametric bootstrap. This work contributes with a unified theoretical formulation of the NM method, based on Faddy distributions, to allow general distributions of over-dispersed and under-dispersed discrete random variables. For a subset of the Faddy models, the log concave property of the inverse link function guarantees convergence to a global minimum deviance thus providing unique estimates for the linear parameters of the models. The method is illustrated using presence-absence data of island lizard communities. Interpretations of this combined GLM-parametric bootstrap protocol are discussed, highlighting the way fitted probabilities under the chosen null model are related to the row and column totals of the observed table. Additional properties of the probabilistic NM protocol, with possible avenues of future research, are also discussed. [ABSTRACT FROM AUTHOR]

β‐Diversity, commonly defined as the compositional variation among localities that links local diversity (α‐diversity) and regional diversity (γ‐diversity), can arise from two different ecological phenomena, namely the spatial species turnover (i.e., species replacement) and the nestedness of assemblages (i.e., species loss). However, any assessment that does not account for stochasticity in community assembly could be biased and misinform conservation management. In this study, we aimed to provide a better understanding of the overall ecological phenomena underlying stream β‐diversity along elevation gradients and to contribute to the rich debate on null model approaches to identify nonrandom patterns in the distribution of taxa. Based on presence‐absence data of 78 stream invertebrate families from 309 sites located in the Swiss Alpine region, we analyzed the effect size of nonrandom spatial distribution of stream invertebrates on the β‐diversity and its two components (i.e., turnover and nestedness). We used a modeling framework that allows exploring the complete range of existing algorithms used in null model analysis and assessing how distribution patterns vary according to an array of possible ecological assumptions. Overall, the turnover of stream invertebrates and the nestedness of assemblages were significantly lower and higher, respectively, than the ones expected by chance. This pattern increased with elevation, and the consistent trend observed along the altitudinal gradient, even in the most conservative analysis, strengthened our findings. Our study suggests that deterministic distribution of stream invertebrates in the Swiss Alpine region is significantly driven by differential dispersal capacity and environmental stress gradients. As long as the ecological assumptions for constructing the null models and their implications are acknowledged, we believe that they still represent useful tools to measure the effect size of nonrandom spatial distribution of taxa on β‐diversity. [ABSTRACT FROM AUTHOR]

Investigations of phenotypic disparity across geography often ignore macroevolutionary processes. As a corollary, the random null expectations to which disparity is compared and interpreted may be unrealistic. We tackle this issue by representing, in geographical space, distinct processes of phenotypic evolution underlying ecological disparity. Under divergent natural selection, assemblages in a given region should have empirical disparity higher than expected under an evolutionarily oriented null model, whereas the opposite may indicate constraints on phenotypic evolution. We gathered phylogenies, biogeographic distributions, and data on the skull morphology of sigmodontine rodents to discover which regions of the Neotropics were more influenced by divergent, neutral, or constrained phenotypic evolution. We found that regions with higher disparity than expected by the evolutionary‐oriented null model, in terms of both size and shape, were concentrated in the Atlantic Forest, suggesting a larger role for divergent natural selection there. Phenotypic disparity in the rest of South America, mainly the Amazon basin, northeastern Brazil, and Southern Andes, was constrained—lower than predicted by the evolutionary model. We also demonstrated equivalence between the disparity produced by randomization‐based null models and constrained‐evolution null models. Therefore, including evolutionary simulations into the null modeling framework used in ecophylogenetics can strengthen inferences on the processes underlying phenotypic evolution. [ABSTRACT FROM AUTHOR]

Abstract Aim The mechanisms underlying the maintenance of biodiversity remain to be elucidated. Taxonomic diversity alone remains an unresolved issue, especially in terms of the mechanisms of species co‐existence. We hypothesized that phylogenetic information could help to elucidate the mechanism of community assembly and the services and functions of ecosystems. The aim of this study was to explore the mechanisms driving floral diversity in subtropical forests and evaluate the relative effects of these mechanisms on diversity variation, by combining taxonomic and phylogenetic information. Location We examined 35 1‐ha tree stem‐mapped plots across eight national nature reserves in Guangxi Zhuang Autonomous Region, China. Taxon Trees. Methods We quantified the taxonomic and phylogenetic β‐diversity between each pair of plots using the (abundance‐based) Rao's quadratic entropy and the (incidence‐based) Sørensen dissimilarity indices. Using a null model approach, we compared the observed β‐diversity with the expected diversity at random and calculated the standard effect size of the observed β‐diversity deviation. Furthermore, we used distance‐based redundancy analysis (dbRDA) to partition the variations in taxonomic and phylogenetic observed β‐diversity and β‐deviation into four parts to assess the environmental and spatial effects. Results The taxonomic β‐deviation was related to and higher than the phylogenetic β‐deviation (r = .74). This indicated that the species turnover between pairwise plots was mainly the turnover of closely related species. Higher taxonomic and phylogenetic β‐deviation were mainly concentrated in the pairwise karst and nonkarst forest plots, indicating that the species in karst forests and nonkarst forests were predominantly from distantly related clades. A large proportions of the variation in taxonomic and phylogenetic β‐deviation were explained by the joint effect of environmental and spatial variables, while the contribution of environmental variables was greater than that of spatial variables, probably owing to the influence of the sampling scale dependence, integrality of sampling size and species pool, and the unique climatic and geomorphic characteristics. Main conclusions Our study highlights the importance of phylogeny in biodiversity research. The incorporation of taxonomic and phylogenetic information provides a perspective to explore potential underlying mechanisms that have shaped species assemblages and phylogenetic patterns in biodiversity hotspots.

Abstract Most existing functional diversity indices focus on a single facet of functional diversity. Although these indices are useful for quantifying specific aspects of functional diversity, they often present some conceptual or practical limitations in estimating functional diversity. Here, we present a new functional extension and evenness (FEE) index that encompasses two important aspects of functional diversity. This new index is based on the straightforward notion that a community has high diversity when its species are distant from each other in trait space. The index quantifies functional diversity by evaluating the overall extension of species traits and the interspecific differences of a species assemblage in trait space. The concept of minimum spanning tree (MST) of points was adopted to obtain the essential distribution properties for a species assembly in trait space. We combined the total length of MST branches (extension) and the variation of branch lengths (evenness) into a raw FEE0 metric and then translated FEE0 to a species richness‐independent FEE index using a null model approach. We assessed the properties of FEE and used multiple approaches to evaluate its performance. The results show that the FEE index performs well in quantifying functional diversity and presents the following desired properties: (a) It allows a fair comparison of functional diversity across different species richness levels; (b) it preserves the essence of single‐facet indices while overcoming some of their limitations; (c) it standardizes comparisons among communities by taking into consideration the trait space of the shared species pool; and (d) it has the potential to distinguish among different community assembly processes. With these attributes, we suggest that the FEE index is a promising metric to inform biodiversity conservation policy and management, especially in applications at large spatial and/or temporal scales.

Abstract Tropical forests are notable for their high species diversity, even on small spatial scales, and right‐skewed species and size abundance distributions. The role of individual species as drivers of the spatial organization of diversity in these forests has been explained by several hypotheses and processes, for example, stochastic dilution, negative density dependence, or gap dynamics. These processes leave a signature in spatial distribution of small trees, particularly in the vicinity of large trees, likely having stronger effects on their neighbors. We are exploring species diversity patterns within the framework of various diversity‐generating hypotheses using individual species–area relationships. We used the data from three tropical forest plots (Wanang—Papua New Guinea, Barro Colorado Island—Panama, and Sinharaja—Sri Lanka) and included also the saplings (DBH ≥ 1 cm). Resulting cross‐size patterns of species richness and evenness reflect the dynamics of saplings affected by the distribution of large trees. When all individuals with DBH ≥1 cm are included, ~50% of all tree species from the 25‐ or 50‐ha plot can be found within 35 m radius of an individual tree. For all trees, 72%–78% of species were identified as species richness accumulators, having more species present in their surroundings than expected by null models. This pattern was driven by small trees as the analysis of DBH >10 cm trees showed much lower proportion of accumulators, 14%–65% of species identified as richness repellers and had low richness of surrounding small trees. Only 11%–26% of species had lower species evenness than was expected by null models. High proportions of species richness accumulators were probably due to gap dynamics and support Janzen–Connell hypothesis driven by competition or top‐down control by pathogens and herbivores. Observed species diversity patterns show the importance of including small tree size classes in analyses of the spatial organization of diversity.

Abstract β‐Diversity, commonly defined as the compositional variation among localities that links local diversity (α‐diversity) and regional diversity (γ‐diversity), can arise from two different ecological phenomena, namely the spatial species turnover (i.e., species replacement) and the nestedness of assemblages (i.e., species loss). However, any assessment that does not account for stochasticity in community assembly could be biased and misinform conservation management. In this study, we aimed to provide a better understanding of the overall ecological phenomena underlying stream β‐diversity along elevation gradients and to contribute to the rich debate on null model approaches to identify nonrandom patterns in the distribution of taxa. Based on presence‐absence data of 78 stream invertebrate families from 309 sites located in the Swiss Alpine region, we analyzed the effect size of nonrandom spatial distribution of stream invertebrates on the β‐diversity and its two components (i.e., turnover and nestedness). We used a modeling framework that allows exploring the complete range of existing algorithms used in null model analysis and assessing how distribution patterns vary according to an array of possible ecological assumptions. Overall, the turnover of stream invertebrates and the nestedness of assemblages were significantly lower and higher, respectively, than the ones expected by chance. This pattern increased with elevation, and the consistent trend observed along the altitudinal gradient, even in the most conservative analysis, strengthened our findings. Our study suggests that deterministic distribution of stream invertebrates in the Swiss Alpine region is significantly driven by differential dispersal capacity and environmental stress gradients. As long as the ecological assumptions for constructing the null models and their implications are acknowledged, we believe that they still represent useful tools to measure the effect size of nonrandom spatial distribution of taxa on β‐diversity.

Arctic marine environments are experiencing rapid changes due to the polar amplification of global warming. These changes impact the habitat of the cold-adapted microbial communities, which underpin biogeochemical cycles and marine food webs. We comparatively investigated the differences in prokaryotic and microeukaryotic taxa between summer surface water microbiomes sampled along a latitudinal transect from the ice-free southern Barents Sea and into the sea-ice-covered Nansen Basin to disentangle the dominating community (ecological) selection processes driving phylogenetic diversity. The community structure and richness of each site-specific microbiome were assessed in relation to the physical and biogeochemical conditions of the environment. A strong homogeneous deterministic selection process was inferred across the entire sampling transect via a phylogenetic null modeling approach. The microbial species richness and diversity were not negatively influenced by northward decreasing temperature and salinity. The results also suggest that regional phytoplankton blooms are a major prevalent factor in governing the bacterial community structure. This study supports the consideration that strong homogeneous selection is imposed across these cold-water marine environments uniformly, regardless of geographic assignments within either the Nansen Basin or the Barents Sea.

Bacteria play an important role as decomposers in karst ecosystems, which can be associated with karst soil and plants, promoting the cycling of nutrients between plants and soil. To reveal the diversity and structure of soil bacterial communities in some karst land-use types after the Grain for Green pattern, soil samples were collected from different land-use types (crops, grasses, and plantations) for analysis. Changes in the structure and assembly of karst soil bacteria were examined using 16S rRNA Illumina sequencing and soil chemical properties. We found that 18 years after the Grain for Green program, the soil chemical properties of available nitrogen (AN), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM) of grassland were significantly different from those of farmland. The soil chemical properties in plantations were also significantly lower than those in farmlands. Different land-use types did not significantly affect the soil bacterial community structure. Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria were the dominant phyla in all the plots. The relative abundance of Proteobacteria was higher in grasslands and plantations than in farmlands, whereas that of Actinobacteria was lower in grasslands. Furthermore, no significant correlations were observed between the soil chemical factors and soil bacterial groups at the genus level. The null model analysis indicated that dispersal limitations in stochastic processes predominated for the different land-use systems. Combined with previous analyses of the factors driving bacterial core species diversity in karst soils, we speculated that stochastic processes play a more important role in the construction of core bacterial species in restored karst soils at the plot scale.

Denitrifying bacteria are a crucial component of aquatic ecosystem in nitrogen cycle. However, the denitrifying bacterial community dynamics and structure in epiphytic biofilms remain unexplored. The abundance of denitrification gene (nir) and structure of nirS-denitrifying bacterial community in the epiphytic biofilms collected in July and November of 2018 from a typical plateau lake (Caohai Wetland, Guizhou, China) were studied by Real-time Quantitative Polymerase Chain Reaction (qPCR) and high-throughput sequencing. Results show that the gene abundance of nirK was higher than that of nirS (P<0.05), and it was significantly different during the growth period (July) than the decline period (November). The denitrifying bacterial species was similar in the two months and shared 76.18% of OTUs. Proteobacteria (56.55%±22.15%) was the dominant phylum in all the samples. Epiphytic biofilms between growth period and decline period displayed significantly different microbial community structures due to differences in species abundance. Water temperature was the crucial factor that affected the denitrifying microbial community structure in our study. Environmental factors explain only partially the dynamic characteristics of denitrifying microbial communities, implying that the stochastic processes affected the construction of denitrifying microbial communities. As the null model analysis results show, dispersal limitation (stochastic) and undominated processes significantly influenced the assembly of denitrifying microbial communities. This study broadened our understanding of the denitrifying bacterial community structure and its function on epiphytic biofilms in freshwater ecosystems with new information provided. [ABSTRACT FROM AUTHOR]

Revealing community assembly and their impacts on ecosystem service is a core issue in microbial ecology. However, what ecological factors play dominant roles in phyllosphere fungal community assembly and how they link to crop quality are largely unknown. Here, we applied internal transcriptional spacer high-throughput sequencing to investigate foliar fungal community assembly across three cultivars of a Solanaceae crop (tobacco) and two planting regions with different climatic conditions. Network analyses were used to reveal the pattern in foliar fungal co-occurrence, and phylogenetic null model analysis was used to elucidate the ecological assembly of foliar fungal communities. We found that the sensory quality of crop leaves and the composition of foliar fungal community varied significantly across planting regions and cultivars. In Guangcun (GC), a region with relatively high humidity and low precipitation, there was a higher diversity and more unique fungal species than the region of Wuzhishan (WZS). Further, we found that the association network of foliar fungal communities in GC was more complex than that in WZS, and the network properties were closely related to the sensory quality of crop. Finally, the results of the phylogenetic analyses show that the stochastic processes played important roles in the foliar fungal community assembly, and their relative importance was significantly correlated with the sensory quality of crop leaves, which implies that ecological assembly processes could affect crop quality. Taken together, our results highlight that climatic conditions, and plant cultivars play key roles in the assembly of foliar fungal communities and crop quality, which enhances our understanding of the connections between the phyllosphere microbiome and ecosystem services, especially in agricultural production. [ABSTRACT FROM AUTHOR]

Beta diversity is the key and central issue of theoretical and applied ecological questions, including those regarding spatial variation along gradients and conservation biodiversity. In contrast to the alpha diversity of stream fish assemblages, little concern has been reached regarding the factor affecting of spatial variation in beta diversity along longitudinal gradients, which may be modified by scale, indices of beta diversity and pairwise methods. To understand the spatial patterns and processes in the species composition of stream fish assemblages along the river continuum, we need to disentangle the influence of different beta diversity indices and pairwise methods on the longitudinal patterns of beta diversity. In this study, we chose four beta diversity indices (Jaccard, Sørensen, Simpson and additive partitioning) and two pairwise methods (mean beta diversity between the focal assemblage and all other assemblages; beta diversity between focal and immediate neighbouring assemblages downstream) to quantify the spatial pattern of fish beta diversity along the river continuum. We found that (1) although the four diversity indices differed in emphasis, they showed the same pattern of spatial variation in the longitudinal gradients of the river; (2) the same diversity index using different pairwise methods calculation may result in completely different spatial patterns; (3) beta diversity indices and pairwise may not have a significant effect on the ecological application of beta diversity, at least in community assembly. In conclusion, the results of our study suggest that at least in the longitudinal gradient of the river there may not be much difference in quantifying the spatial variation of beta diversity; however, pairwise methods between sampling sites need to be chosen according to specific research objectives. [ABSTRACT FROM AUTHOR]

Understanding the effects of random versus niche‐based processes on biodiversity patterns is a central theme in ecology, and an important tool for predicting effects of habitat loss and fragmentation on biodiversity. We investigated the predictive power of random processes to explain species richness and species dissimilarity of amphibian assemblages in a fragmented tropical landscape of the Atlantic Forest of South America.We analyzed a large database of amphibian abundance and occupancy, sampled in 21 forest fragments ranging in size from 1.9 to 619 ha. We compared observed species richness and species dissimilarity with the outcomes of two null (random placement) models: 1‐ the traditional Coleman's area‐based model and 2‐ an abundance‐based model (based on the number of individuals observed in each fragment). We applied these models for all species combined, and separately for forest‐dependent and habitat‐generalist species.The abundance‐based model fitted the observed species richness data better than the area‐based model for all species, forest‐dependent species, and generalist species. The area‐based and the abundance‐based models were also able to significantly explain species dissimilarity for all species and for generalists, but not for forest dependent species.The traditional area‐based model assigned too many individuals to large fragments, thus failing to accurately explain species richness within patches across the landscape.Although niche‐based processes may be important to structuring the regional pool of species in fragmented landscapes, our results suggest that part of the variation in species richness and species dissimilarity can be successfully explained by random placement models, especially for generalist species. Evaluating which factors cause variation in the number of individuals among patches should be a focus in future studies aiming to understand biodiversity patterns in fragmented landscapes. [ABSTRACT FROM AUTHOR]