β-Diversity, Community Assembly, and Ecosystem Functioning

Distinct species turnover patterns shaped the richness of antibiotic resistance genes on eight different microplastic polymers

Elucidating the formation mechanism of plastisphere antibiotic resistance genes (ARGs) on different polymers is necessary to understand the ecological risks of plastisphere ARGs. Here, we explored the turnover and assembly mechanism of plastisphere ARGs on 8 different microplastic polymers (4 biodegradable (bMPs) and 4 non-biodegradable microplastics (nMPs)) by metagenomic sequencing. Our study revealed the presence of 479 ARGs with abundance ranging from 41.37 to 58.17 copies/16S rRNA gene in all plastispheres. These ARGs were predominantly multidrug resistance genes. The richness of plastisphere ARGs on different polymers had a significant correlation with the contribution of species turnover to plastisphere ARGs β diversity. Furthermore, polymer type was the most critical factor affecting the composition of plastisphere ARGs. More opportunistic pathogens carrying diverse ARGs on BMPs (PBAT, PBS, and PHA) with higher horizontal gene transfer potential may further magnify the ecological risks and human health threats. For example, the opportunistic pathogens Riemerella anatipestifer, Vibrio campbellii, and Vibrio cholerae are closely related to human production and life, which were the important potential hosts of many plastisphere ARGs and mobile genetic elements on BMPs. Thus, we emphasize the urgency of developing the formation mechanism of plastisphere ARGs and the necessity of controlling BMPs and ARG pollution, especially BMPs, with ever-increasing usage in daily life.

Parent material influences soil properties to shape bacterial community assembly processes, diversity, and enzyme-related functions

Soil parent material is the second most influential factor in pedogenesis, influencing soil properties and microbial communities. Different assembly processes shape diverse functional microbial communities. The question remains unresolved regarding how these ecological assembly processes affect microbial communities and soil functionality within soils on different parent materials. We collected soil samples developed from typical parent materials, including basalt, granite, metamorphic rock, and marine sediments across soil profiles at depths of 0-20, 20-40, 40-80, and 80-100 cm, within rubber plantations on Hainan Island, China. We determined bacterial community characteristics, community assembly processes, and soil enzyme-related functions using 16S rRNA high-throughput sequencing and enzyme activity analyses. We found homogeneous selection, dispersal limitation, and drift processes were the dominant drivers of bacterial community assembly across soils on different parent materials. In soils on basalt, lower pH and higher moisture triggered a homogeneous selection-dominated assembly process, leading to a less diverse community but otherwise higher carbon and nitrogen cycling enzyme activities. As deterministic process decreased, bacterial community diversity increased with stochastic process. In soils on marine sediments, lower water, carbon, and nutrient content limited the dispersal of bacterial communities, resulting in higher community diversity and an increased capacity to utilize relative recalcitrant substrates by releasing more oxidases. The r-strategy Bacteroidetes and genera Sphingomonas, Bacillus, Vibrionimonas, Ochrobactrum positively correlated with enzyme-related function, whereas k-strategy Acidobacteria, Verrucomicrobia and genera Acidothermus, Burkholderia-Caballeronia-Paraburkholderia, HSB OF53-F07 showed negative correlations. Our study suggests that parent material could influence bacterial community assembly processes, diversity, and soil enzyme-related functions via soil properties.

A climate-induced tree species bottleneck for forest management in Europe

Large pulses of tree mortality have ushered in a major reorganization of Europe's forest ecosystems. To initiate a robust next generation of trees, the species that are planted today need to be climatically suitable throughout the entire twenty-first century. Here we developed species distribution models for 69 European tree species based on occurrence data from 238,080 plot locations to investigate the option space for current forest management in Europe. We show that the average pool of tree species continuously suitable throughout the century is smaller than that under current and end-of-century climate conditions, creating a tree species bottleneck for current management. If the need for continuous climate suitability throughout the lifespan of a tree planted today is considered, climate change shrinks the tree species pool available to management by between 33% and 49% of its current values (40% and 54% of potential end-of-century values), under moderate (Representative Concentration Pathway 2.6) and severe (Representative Concentration Pathway 8.5) climate change, respectively. This bottleneck could have strong negative impacts on timber production, carbon storage and biodiversity conservation, as only 3.18, 3.53 and 2.56 species of high potential for providing these functions remain suitable throughout the century on average per square kilometre in Europe. Our results indicate that the option space for silviculture is narrowing substantially because of climate change and that an important adaptation strategy in forestry-creating mixed forests-might be curtailed by widespread losses of climatically suitable tree species.

Plant beta-turnover rather than nestedness shapes overall taxonomic and phylogenetic beta-diversity triggered by favorable spatial-environmental conditions in large-scale Chinese grasslands

Introduction

Although it is widely acknowledged that biodiversity maintains plant community assembly processes, exploring the patterns and drivers of beta-diversity (β-diversity; species variation among local plant communities) has received much less attention compared to alpha-diversity (α-diversity; species variation within a local plant community). Here, we aim to examine the patterns and spatial-environmental drivers of taxonomic and phylogenetic β-diversity, and their components such as species turnover and nestedness, in large-scale Leymus chinensis grassland communities.

Methods

We collected plant community data from 166 sites across widely distributed L. chinensis communities in northern China, and then calculated the taxonomic and phylogenetic β-diversity indices (overall, turnover and nestedness) using a pairwise dissimilarity approach. To assess the effects and to explain the variation in the patterns of β-diversity, we collected data on geospatial, climate and soil conditions. We applied descriptive statistics, Mental correlations, and multiple linear regression models to assess the patterns and spatial-environmental drivers of β-diversity.

Results

The β-turnover, as compared to β-nestedness, exhibited a predominant influence, constituting 92.6% of the taxonomic β-diversity and 80.4% of the phylogenetic β-diversity. Most of the spatial-environmental variables were significantly positively correlated with the overall taxonomic and phylogenetic β-diversity and β-turnover, but not with β-nestedness. Climatic factors such as MAP and MAT were the strongest predictors of both taxonomic and phylogenetic β-diversity and β-turnover. The variance partitioning analysis showed that the combined effects of spatial and environmental factors accounted for 19% and 16% of the variation in the taxonomic and phylogenetic β-diversity (overall), 17% and 12% of the variation in the β-turnover, and 7% and 1% of the variation in the β-nestedness, respectively, which were higher than independent effects of either spatial or environmental factors.

Discussion

At larger spatial scales, the turnover component of β-diversity may be associated with the species complementarity effect, but dominant or functionally important species can vary among communities due to the species selection effect. By incorporating β-diversity into grassland management strategies, we can enhance the provision of vital ecosystem services that bolster human welfare, serving as a resilient barrier against the adverse effects of climate change at regional and global scales.

Plant Invasion-Induced Habitat Changes Impact a Bird Community through the Taxonomic Filtering of Habitat Assemblages

Describing the spatial distribution of communities is crucial to understanding how environmental disturbance can affect biodiversity. Agricultural lands are susceptible to disturbances of anthropogenic origin and have been identified as ecosystems of conservation concern. Such lands are vulnerable to invasions by anthropogenically introduced non-native plants disturbing habitats. This research focused on the invasion-induced taxonomic filtering of birds with shared habitat requirements. The birds were surveyed along a gradient of invasion-altered areas (far from the invasion, uninvaded although susceptible to invaders, and invaded) to identify changes in bird assemblages (ground/herb dwellers, bush foragers, ecotone birds, and tree foragers) caused by this disturbance. Data were collected from 112 sites sampled in southeastern Poland. There were significantly fewer bird species from each assemblage on invaded sites than on uninvaded sites, although exposed to invasion, despite the decrease in the abundance of only ground/herb dwellers. Beta diversity analysis showed that sites with invasion contained bird communities significantly different from those at other sites. Invasion-induced changes resulted in a significant reduction in the diversity of ground/herb dwellers in comparison with uninvaded sites and created a distinctive bush bird assemblage. This was most likely due to the transformation of the grassland layer and the thickening of the shrub layer by plant invaders, which resemble shrubs in morphology. The results indicated the filtering effect of invasion on bird species composition at the level of two habitat assemblages despite the decreases in bird abundance and species diversity of the whole community.

Biodiversity loss reduces global terrestrial carbon storage

Natural ecosystems store large amounts of carbon globally, as organisms absorb carbon from the atmosphere to build large, long-lasting, or slow-decaying structures such as tree bark or root systems. An ecosystem's carbon sequestration potential is tightly linked to its biological diversity. Yet when considering future projections, many carbon sequestration models fail to account for the role biodiversity plays in carbon storage. Here, we assess the consequences of plant biodiversity loss for carbon storage under multiple climate and land-use change scenarios. We link a macroecological model projecting changes in vascular plant richness under different scenarios with empirical data on relationships between biodiversity and biomass. We find that biodiversity declines from climate and land use change could lead to a global loss of between 7.44-103.14 PgC (global sustainability scenario) and 10.87-145.95 PgC (fossil-fueled development scenario). This indicates a self-reinforcing feedback loop, where higher levels of climate change lead to greater biodiversity loss, which in turn leads to greater carbon emissions and ultimately more climate change. Conversely, biodiversity conservation and restoration can help achieve climate change mitigation goals.

Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates

Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.

Patterns of Tadpole β Diversity in Temperate Montane Streams

Understanding the spatial variation and formation mechanism of biological diversity is a hot topic in ecological studies. Comparing with α diversity, β diversity is more accurate in reflecting community dynamics. During the past decades, β diversity studies usually focused on plants, mammals, and birds. Studies of amphibian β diversity in montane ecosystems, in particular, tadpoles, are still rare. In this study, Mount Emei, located in southwestern China, was selected as the study area. We explored the tadpole β diversity in 18 streams, based on a two-year survey (2018-2019). Our results indicated a high total β diversity in tadpole assemblages, which was determined by both turnover and nestedness processes, and the dominant component was turnover. Both the total β diversity and turnover component were significantly and positively correlated with geographical, elevational, and environmental distances, but no significant relationship was detected between these and the nestedness component. Moreover, the independent contributions of river width, current velocity, and chlorophyll α were larger than that of geographical and elevational distance. Overall, tadpole β diversity was determined by both spatial and environmental factors, while the contribution of environmental factors was larger. Future studies can focus on functional and phylogenetic structures, to better understand the tadpole assembly process.

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.

Biological interactions control bacterial but not fungal β diversity during vegetation degradation in saline-alkaline soil

The patterns and mechanisms by which soil bacterial and fungal community β-diversity respond to vegetation degradation in saline-alkaline soils are currently not clear, and in particular, the role of biotic interactions is relatively unknown. To investigate the assembly of bacterial and fungal communities in topsoil (0-10 cm) in saline-alkaline soils at different stages of vegetation degradation, the β-Mean Nearest Classification Unit Distance, the β-Nearest Taxon Index, and the Raup-Crick index were calculated. The relative importance of biotic and environmental factors in controlling β diversity under deterministic processes was also quantified by using relative importance analyses. The β diversity of soil bacterial and fungal communities responded differently in different stages of vegetation degradation in saline-alkaline soils, with bacterial β diversity increasing with increasing vegetation degradation but fungal β diversity showing few differences. Deterministic processes regulated soil bacterial community assembly, and biotic factors were important in driving changes in β diversity, whereas both deterministic and stochastic processes were essential in soil fungal community assembly, and environmental factors were important in affecting fungal β diversity. Furthermore, fungal β diversity is far more affected by interactions between fungus and bacteria than bacteria. Our study demonstrates the different effects of vegetation degradation on bacterial and fungal communities in saline soils to provide the overall implications for saline soils microorganisms in deteriorating ecosystems.

Extinction drives recent thermophilization but does not trigger homogenization in forest understorey

The ongoing climate change is triggering plant community thermophilization. This selection process ought to shift community composition towards species adapted to warmer climates but may also lead to biotic homogenization. The link between thermophilization and homogenization and the community dynamics that drive them (colonization and extinction) remain unknown but is critical for understanding community responses under rapid environmental change. We used 14,167 pairs of plots to study shifts in plant community during 10 years of rising temperature in 80 forest ecoregions of France. We computed community mean thermal optimum (thermophilization) and Δβ-diversity (homogenization) for each ecoregion and partitioned these changes into extinction and colonization dynamics of cold- and warm-adapted species. Forest understorey communities thermophilized on average by 0.12 °C per decade and up to 0.20 °C per decade in warm ecoregions. This rate was entirely driven by extinction dynamics. Extinction of cold-adapted species was a driver of homogenization but it was compensated for by the colonization of rare species and the extinction of common species, resulting in the absence of an apparent homogenization trend. Here we show a dieback of present cold-adapted species rather than an adaptation of communities via the arrival of warm-adapted species, with a mutually cancelling effect on β-diversity. These results suggest that a future loss of biodiversity and delayed biotic homogenization should be considered.

Contrasting responses of α- and β-multifunctionality to aboveground plant community in the Qinghai-Tibet Plateau

The aboveground plant communities are crucial in driving ecosystem functioning, particularly being the primary producers in terrestrial ecosystems. Numerous studies have investigated the impacts of aboveground plant communities on multiple ecosystem functions at α-scale. However, such critical effects have been unexplored at β-scale and the comparative assessment of the effects and underlying mechanisms of aboveground plant communities on α- and β-multifunctionality has been lacking. In this study, we examined the effects of aboveground plant communities on soil multifunctionality both at α- and β-scale in the alpine meadow of the Tibetan Plateau. Additionally, we quantified the direct effects of aboveground plant communities, as well as the indirect effects mediated by changes in biotic and abiotic factors, on soil multifunctionality at both scales. Our findings revealed that: 1) Aboveground plant communities had significantly positive effects on α-multifunctionality whereas, β-multifunctionality was not affected significantly. 2) Aboveground plant communities directly influence α- and β-multifunctionality in contrasting ways, with positive and negative effects, respectively. Apart from the direct effects of plant community, we found that soil water content and bacterial β-diversity serving as the primary predictors for the responses of α- and β-multifunctionality to the presence of aboveground plant communities, respectively. And β-soil biodiversity appeared to be a stronger predictor of multifunctionality relative to α-soil biodiversity. Our findings provide novel insights into the drivers of ecosystem multifunctionality at different scales, highlight the importance of maintaining biodiversity at multiple scales and offer valuable knowledge for the maintenance of ecosystem functioning and the restoration of alpine meadow ecosystems.

Kelp forests collapse reduces understorey seaweed β-diversity

BACKGROUND AND AIMS

Kelps are the primary foundation species in temperate subtidal rocky shores worldwide. However, global change is causing their decline with consequences for the organisms that rely on them. An accurate assessment of these consequences may depend on which attributes of the associated community are considered. This study shows that conventional α-diversity approaches may overlook some of these consequences compared to spatially explicit approaches such as with β-diversity.

METHODS

A 1-year seasonal study was conducted to compare the macroalgal understorey between healthy reefs with a Laminaria ochroleuca canopy and degraded reefs where the canopy collapsed years ago due to excessive fish herbivory. At each reef, the understorey seaweed assemblage was recorded in five replicate quadrats to estimate α-diversity (total richness, species density, Shannon index) and β-diversity (intra- and inter-reef scale).

KEY RESULTS

The understorey assemblage exhibited a distinct seasonal dynamic in both healthy and degraded reefs. α-Diversity attributes increased in spring and summer; turf-forming algae were particularly dominant in degraded reefs during summer. β-Diversity also showed seasonal variability, but mostly due to the changes in degraded reefs. None of the α-diversity estimates differed significantly between healthy and degraded reefs. In contrast, spatial β-diversity was significantly lower in degraded reefs.

CONCLUSIONS

Although the loss of the kelp canopy affected the composition of the macroalgal understorey, none of the conventional indicators of α-diversity detected significant differences between healthy and degraded reefs. In contrast, small-scale spatial β-diversity decreased significantly as a result of deforestation, suggesting that the loss of kelp canopy may not significantly affect the number of species but still have an effect on their spatial arrangement. Our results suggest that small-scale β-diversity may be a good proxy for a more comprehensive assessment of the consequences of kelp forest decline.

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

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

Drivers of desert plant beta diversity on the Qinghai-Tibet plateau

The desert ecosystem of the Qinghai-Tibet Plateau (QTP) is an important component of China's desert ecosystem. Studying the mechanisms shaping the taxonomic, phylogenetic, and functional beta diversity of plant communities in the QTP desert will help us to promote scientific conservation and management of the region's biodiversity. This study investigated the effects of environmental (including altitude, climate factors, and soil factors) and geographic distances on three facets of beta diversity as well as their turnover and nestedness components based on field survey data. The results showed that turnover components dominate the three facets of beta diversity. However, the turnover contributions to phylogenetic and functional beta diversity were lower than for taxonomic beta diversity. Environmental distance had a greater influence than geographic distance, with the former uniquely explaining 15.2%-22.8% of beta diversity and the latter explaining only 1.7%-2.4%. Additionally, the explanatory power of different factors for beta diversity differed between herbs and shrubs, with environmental distance being more important for the latter. Distance-based redundancy analysis suggested that soil total potassium content had a substantial impact on the beta diversity of three dimensions, with mean temperature of the coldest month and soil total phosphorus content having a substantial impact on taxonomic and functional beta diversity as well. Our results support that environmental sorting plays a predominant role in shaping plant community composition across QTP desert ecosystems. To maintain the plant diversity of this region, it is crucial to prioritize the conservation of its diverse environmental conditions and actively mitigate its degradation by anthropogenic pressures.

A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation

Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.

Plant life history strategies vary in subtropical forests with different disturbance histories: an assessment of biodiversity, biomass, and functional traits

Disturbance alters environmental conditions in forests. Plants growing in forests with different disturbance histories in diverse environments may adopt varying life history strategies, but few studies focus on this effect. This study comprehensively investigated plant biodiversity, biomass, and functional traits in subtropical forests with two different disturbance histories in east China to explore differences in life history strategies. Biodiversity was slightly higher in disturbed compared to conserved forests. Significantly higher biomass was measured in conserved relative to disturbed evergreen broadleaved forests (P < 0.05). In conserved forests, leaf tissue density (LTD) was significantly higher and leaf thickness (LT), leaf dry matter content (LDMC), twig tissue density (TTD), twig dry matter content (TDMC), bark tissue density (BTD) and dry matter content (BDMC), and stem tissue density (STD) and dry matter content (SDMC) were significantly lower than in disturbed forests (P < 0.05). In terms of associated plant biodiversity, biomass, and functional traits, conserved forests adopted a resource acquisition strategy, reducing biodiversity and developing multiple functional traits such as high leaf area and specific leaf area and low LT, LDMC, TTD, TDMC, BTD, BDMC, STD, and SDMC to support a high biomass accumulation rate. Disturbed forests adopted a resource conservation strategy, enhancing biodiversity and developing converse trait combinations to lower the rate of biomass accumulation. A comprehensive investigation of plant biodiversity, biomass, and functional traits and subsequent assessment of plant life history strategies in conserved and disturbed forests will aid investigations of regional biodiversity and carbon reserves, contribute data to the TRY and Chinese plant trait databases, and improve ecological management and restoration efforts in east China.

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.

When Do Traits Tell More Than Species about a Metacommunity? A Synthesis across Ecosystems and Scales

AbstractLinking species traits with the variation in species assemblages across habitats has often proved useful for developing a more mechanistic understanding of species distributions in metacommunities. However, summarizing the rich tapestry of a species in all of its nuance with a few key ecological traits can also lead to an abstraction that provides less predictability than when using taxonomy alone. As a further complication, taxonomic and functional diversities can be inequitably compared, either by integrating taxonomic-level information into the calculation of how functional aspects of communities vary or by detecting spurious trait-environment relationships. To remedy this, we here synthesize analyses of 80 datasets on different taxa, ecosystems, and spatial scales that include information on abundance or presence/absence of species across sites with variable environmental conditions and the species' traits. By developing analyses that treat functional and taxonomic diversity equitably, we ask when functional diversity helps to explain metacommunity structure. We found that patterns of functional diversity explained metacommunity structure and response to environmental variation in only 25% of the datasets using a multitrait approach but up to 59% using a single-trait approach. Nevertheless, an average of only 19% (interquartile range = 0%-29%) of the traits showed a significant signal across environmental gradients. Species-level traits, as typically collected and analyzed through functional diversity patterns, often do not bring predictive advantages over what the taxonomic information already holds. While our assessment of a limited advantage of using traits to explain variation in species assemblages was largely true across ecosystems, traits played a more useful role in explaining variation when many traits were used and when trait constructs were more related to species' status, life history, and mobility. We propose future research directions to make trait-based approaches and data more helpful for inference in metacommunity ecology.

Tracking long-term shifts in non-native freshwater macroinvertebrates across three European countries

Non-native species introductions have been acknowledged as one of the main drivers of freshwater biodiversity decline worldwide, compromising provided ecosystem services and functioning. Despite growing introduction numbers of non-native species, their impacts in conjunction with anthropogenic stressors remain poorly documented. To fill this gap, we studied temporal changes in α (local scale) and γ (regional scale), as well as β (ratio between γ and α) diversity of non-native freshwater macroinvertebrate species in three European countries (the Netherlands, England and Hungary) using long-term time series data of up to 17 years (2003-2019). We further calculated four ecological and four biological trait metrics to identify changes in trait occurrences over time. We found that α and γ diversities of non-native species were increasing across all countries whereas β diversity remained stable. We did not identify any significant changes in any trait metric over time, while the predictors tested (land use, climatic predictors, site-specific factor) were similar across countries (e.g., site characteristics or climatic predictors on non-native species trends). Additionally, we projected trends of α, β, and γ diversity and trait metrics until 2040, which indicated that non-native species will decline across all countries to lower levels except in England for γ diversity and the Netherlands for α diversity where an increase was observed. Thus, our findings indicate shifts in non-native freshwater macroinvertebrate diversity at both local and regional scales in response to the various growing anthropogenic pressures. Our findings underscore the continuous dynamics of non-native species distribution, with the diversity of individual communities and overall landscapes witnessing changes. However, the differentiation in species composition between communities remains unaltered. This could have profound implications for conservation strategies and ecological management in the face of continuously changing biodiversity patterns.

Hill-Chao numbers allow decomposing gamma multifunctionality into alpha and beta components

Biodiversity-ecosystem functioning (BEF) research has provided strong evidence and mechanistic underpinnings to support positive effects of biodiversity on ecosystem functioning, from single to multiple functions. This research has provided knowledge gained mainly at the local alpha scale (i.e. within ecosystems), but the increasing homogenization of landscapes in the Anthropocene has raised the potential that declining biodiversity at the beta (across ecosystems) and gamma scales is likely to also impact ecosystem functioning. Drawing on biodiversity theory, we propose a new statistical framework based on Hill-Chao numbers. The framework allows decomposition of multifunctionality at gamma scales into alpha and beta components, a critical but hitherto missing tool in BEF research; it also allows weighting of individual ecosystem functions. Through the proposed decomposition, new BEF results for beta and gamma scales are discovered. Our novel approach is applicable across ecosystems and connects local- and landscape-scale BEF assessments from experiments to natural settings.

Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps

Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO32-, and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO32-. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.

Anti-Helicobacter pylori activity and gastroprotective effects of human stomach-derived Lactobacillus paragasseri strain LPG-9

The eradication of Helicobacter pylori is an urgent global issue. However, the traditional regimens have several limitations. Thus, we propose the idea of treating bacterial gastric disease with the objective of eliminating gastric pathogenic bacteria and enhancing gastroprotective effects using gastric probiotics. In this study, a total of 12 Lactobacillus strains were isolated from the gastric mucosa of healthy donors. After evaluation using a weight scoring system, Lactobacillus paragasseri strain LPG-9 was identified as the most promising probiotic for gastric disease, with the highest acid-resistance and the best adhesion characteristics. Gastric colonisation, H. pylori inhibition, anti-inflammatory, and gastric homeostasis effects of LPG-9 were confirmed in C57BL/6 mice. Finally, a safety evaluation and whole-genome sequencing were performed. Based on the results of this study, LPG-9 originates from the gastric microbiota and is a promising probiotic for gastric disease, particularly H. pylori-induced gastritis, providing a solution to this global issue.

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

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

Influence of Ecological Multiparameters on Facets of β-Diversity of Freshwater Plankton Ciliates

Understanding the relative importance of the factors that drive global patterns of biodiversity is among the major topics of ecological and biogeographic research. In freshwater bodies, spatial, temporal, abiotic, and biotic factors are important structurers of these ecosystems and can trigger distinct responses according to the facet of biodiversity considered. The objective was to evaluate how different facets of β-diversity (taxonomic, functional, and phylogenetic) based on data from the planktonic ciliate community of a Neotropical floodplain, are influenced by temporal, spatial, abiotic, and biotic factors. The research was conducted in the upper Paraná River floodplain between the years 2010 and 2020 in different water bodies. All predictors showed significant importance on the facets of β-diversity, except the abiotic predictors on species composition data, for the taxonomic facet. The functional and phylogenetic facets were mostly influenced by abiotic, biotic, and spatial factors. For temporal predictors, results showed influence on taxonomic (structure and composition data) and functional (structure data) facets. Also, a fraction of shared explanation between the temporal and abiotic components was observed for the distinct facets. Significant declines in β-diversity in continental ecosystems have been evidenced, especially those with drastic implications for ecosystemic services. Therefore, the preservation of a high level of diversity in water bodies, also involving phylogenetic and functional facets, should be a priority in conservation plans and goals, to ensure the maintenance of important ecological processes involving ciliates.

Distinct spatiotemporal succession of bacterial generalists and specialists in the lacustrine plastisphere

The assembly processes of generalists and specialists and their driving mechanisms during spatiotemporal succession is a central issue in microbial ecology but a poorly researched subject in the plastisphere. We investigated the composition variation, spatiotemporal succession, and assembly processes of bacterial generalists and specialists in the plastisphere, including non-biodegradable (NBMPs) and biodegradable microplastics (BMPs). Although the composition of generalists and specialists on NBMPs differed from that of BMPs, colonization time mainly mediated the composition variation. The relative abundance of generalists and the relative contribution of species replacement were initially increased and then decreased with colonization time, while the specialists initially decreased and then increased. Besides, the richness differences also affected the composition variation of generalists and specialists in the plastisphere, and the generalists were more susceptible to richness differences than corresponding specialists. Furthermore, the assembly of generalists in the plastisphere was dominated by deterministic processes, while stochastic processes dominated the assembly of specialists. The network stability test showed that the community stability of generalists on NBMPs and BMPs was lower than corresponding specialists. Our results suggested that different ecological assembly processes shaped the spatiotemporal succession of bacterial generalists and specialists in the plastisphere, but were less influenced by polymer types.

Environmental filtering and biotic interactions act on different facets of the diversity of benthic assemblages associated with eelgrass

Eelgrass supports diverse benthic communities that ensure a variety of ecosystem functions. To better understand the ecological processes that shape community composition in eelgrass at local and regional scales, taxonomic and functional α- and β-diversity were quantified for communities inhabiting five meadows in France. The extent to which environmental factors affected local and regional benthic communities was quantified by considering their direct and indirect effects (through morphological traits of eelgrass) using piecewise structural equation modeling (pSEM). Communities supported by eelgrass had higher species abundances, as well as taxonomic and functional diversity compared to nearby bare sediments. No significant differences were found between communities from the center relative to the edges of meadows, indicating that both habitats provide similar benefits to biodiversity. The presence of a few abundant species and traits suggests moderate levels of habitat filtering and close associations of certain species with eelgrass. Nevertheless, high turnover of a large number of rare species and traits was observed among meadows, resulting in meadows being characterized by their own distinct communities. High turnover indicates that much of the community is not specific to eelgrass, but rather reflects local species pools. pSEM showed that spatial variation in community composition (β-diversity) was primarily affected by environmental conditions, with temperature, current velocity, and tidal amplitude being the most significant explanatory variables. Local richness and abundance (α-diversity) were affected by both environment and morphological traits. Importantly, morphological traits of Zostera marina were also influenced by environmental conditions, revealing cascading effects of the environment on assemblages. In sum, the environment exerted large effects on community structure at both regional and local scales, while plant traits were only pertinent in explaining local diversity. This complex interplay of processes acting at multiple scales with indirect effects should be accounted for in conservation efforts that target the protection of biodiversity.

Alterations of gut microbiota biodiversity and relative abundance in women with PCOS: A systematic review and meta-analysis

BACKGROUND

Numerous studies have implicated that the gut microbiota is associated with polycystic ovary syndrome (PCOS). However, a comprehensive data-based summary shown that the effects of the PCOS on the gut microbiota is minimal. We aim to assess the alterations of gut microbiota in women with PCOS.

METHODS

An electronic search of PubMed, Web of Science, Embase, Cochrane Library and Ovid was conducted for eligible studies published from inception to 28 March 2023, without any language or regional restrictions. We used Newcastle-Ottawa Quality Assessment Scale (NOS) to complete the assessment of the risk of bias and Stata 15.1 software to performed meta-analysis.

RESULTS

There were 19 human observational studies in total with 617 women with PCOS and 439 healthy individuals were identified. Compared to the control group, the Chao index (WMD -28.88, 95% CI -45.78 to -11.98, I2 = 100%), Shannon index (WMD -0.11, 95% CI -0.18 to 0.00, I2 = 92.2%); and observed operational taxonomic units (OTUs) counts (WMD - 23.48, 95% CI -34.44 to -12. 53, I2 = 99.6%) were significantly lower in women with PCOS. The relative abundance of Bacteroidaceae was significantly higher (WMD 0.12, 95% CI 0.02 to 0.22, I2 = 9.2%), however there were no statistical differences in Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Alcaligenaceae, Bifidobacteriaceae, Clostridiaceae, Enterobacteriaceae, Lachnospiraceae, Prevotellaceae, Ruminococcaceae, Veillonellaceae, Bacteroides, Bifidobacterium, Blautia, Dialister, Escherichia-Shigella, Faecalibacterium, Lachnoclostridium, Lachnospira, Megamonas, Phascolarctobacterium, Prevotella, Roseburia, and Subdoligranulum.

CONCLUSION

We demonstrated the alpha diversity of gut microbiota and the relative abundance of Bacteroidaceae in women with PCOS are altered. The results indicates that dysbiosis may be a potential pathogenetic factor in PCOS and provided reliable information to investigate the role of gut microbiota in the development and progression of PCOS.

Unveiling the ecological significance of phosphorus fractions in shaping bacterial and archaeal beta diversity in mesotrophic lakes

Both community variation and phosphorus (P) fractions have been extensively studied in aquatic ecosystems, but how P fractions affect the mechanism underlying microbial beta diversity remains elusive, especially in sediment cores. Here, we obtained two sediment cores to examine bacterial and archaeal beta diversity from mesotrophic lakes Hongfeng Lake and Aha Lake, having historically experienced severe eutrophication. Utilizing the Baselga's framework, we partitioned bacterial and archaeal total beta diversity into two components: species turnover and nestedness, and then examined their sediment-depth patterns and the effects of P fractions on them. We found that total beta diversity, species turnover or nestedness consistently increased with deeper sediment layers regarding bacteria and archaea. Notably, there were parallel patterns between bacteria and archaea for total beta diversity and species turnover, which is largely underlain by equivalent processes such as environmental selection. For both microbial taxa, total beta diversity and species turnover were primarily constrained by metal oxide-bound inorganic P (NaOH-Pi) and sediment total phosphorus (STP) in Hongfeng Lake, while largely affected by reductant-soluble total P or calcium-bound inorganic P in Aha Lake. Moreover, NaOH-Pi and STP could influence bacterial total beta diversity by driving species nestedness in Hongfeng Lake. The joint effects of organic P (Po), inorganic P (Pi) and total P fractions indicated that P fractions are important to bacterial and archaeal beta diversity. Compared to Po fractions, Pi fractions had greater pure effects on bacterial beta diversity. Intriguingly, for total beta diversity and species turnover, archaea rather than bacteria are well-explained by Po fractions in both lakes, implying that the archaeal community may be involved in Po mineralization. Overall, our study reveals the importance of P fractions to the mechanism underlying bacterial and archaeal beta diversity in sediments, and provides theoretical underpinnings for controlling P sources in biodiversity conservation.

Community recovery of benthic macroinvertebrates in a stream influenced by mining activity: Importance of microhabitat monitoring

The decrease in freshwater biodiversity owing to anthropogenic disturbances such as mining activity is a global challenge; hence, there is an urgent need for systematic approaches to continuously monitor such disturbances and/or the recovery of biodiversity in freshwater habitats. The Hwangjicheon Stream is the source of South Korea's longest river and has been subjected to runoff from coal mining. We investigated changes in the diversity of the benthic macroinvertebrate community in various microhabitats, including riffle, run, and pool, to monitor the recovery of biodiversity in the stream following the improvement of a mining water treatment plant in 2019. The dataset comprised 111 samples obtained from four types of microhabitats (riffle, run, pool, and riparian) over a four-year period from 2018 to 2021. The mining-affected sites had lower macroinvertebrate community complexities according to a network analysis, and grouped into the same cluster based on self-organizing map (SOM) analysis. Moreover, 51 taxa selected as indicator species represented each cluster obtained through the SOM analysis. Among them, only Limnodrilus gotoi and Radix auricularia were included as indicator species at the mining-affected sites. However, after 2020, the benthic macroinvertebrate community complexity increased, and some of the microhabitats at the mining-affected sites were included in the same cluster as the reference sites in the SOM analysis, indicating that the recovery of benthic macroinvertebrate communities had initiated in certain microhabitats (e.g., riparian). Further analysis confirmed that the macroinvertebrate community clearly differed according to the survey year, even in different microhabitats at the same sites. This suggests that more acute microhabitat monitoring may be necessary to quickly confirm biodiversity restoration when assessing the degree of the recovery in river biodiversity from anthropogenic disturbances.

Reclamation of tidal flats to paddy soils reshuffles the soil microbiomes along a 53-year reclamation chronosequence: Evidence from assembly processes, co-occurrence patterns and multifunctionality

Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation.

Alpha and beta diversity jointly drive the aboveground biomass in temperate and tropical forests

Changes in biodiversity often affect ecosystem functioning. However, most previous biodiversity and ecosystem functioning (BEF) studies have generally been limited to very small spatial grains. Thus, knowledge regarding the biodiversity-ecosystem functioning relationships across spatial scales is lacking. Moreover, the multiscale nature of biodiversity, and specifically β diversity (i.e., spatial heterogeneity in species composition) was still largely missing in BEF studies. Here, using the vegetation and functional trait data collected from four 6-ha forest dynamics plots (FDPs) in temperate and tropical forests in China, we examine the scale-dependent relationships between tree diversity and the aboveground biomass (AGB), as well as the roles of species spatial heterogeneity in determining the AGB. In tropical forests, the effect of species richness on AGB decreased with spatial grains, while functional dominance played a stronger role at larger spatial grains. In temperate forests, positive relationship between diversity and AGB occurred at all spatial grains, especially on smaller scales. In both temperate and tropical forests, β diversity was positively correlated with AGB, but weaker than α diversity in determining AGB. Overall, complementarity and selection hypothesis play dominant role in determining AGB in temperate and tropical forests, respectively. The roles of these underlying mechanisms are more pronounced with increasing spatial scales. β diversity, a hitherto underexplored facet of biodiversity, is likely to increase ecosystem functions by species spatial turnover and should not be neglected in BEF explorations. Our findings have practical implications for forest management and demonstrate that biotic heterogeneity plays an important positive role in ecosystem functioning.

How Biodiversity, Climate and Landscape Drive Functional Redundancy of British Butterflies

Biodiversity promotes the functioning of ecosystems, and functional redundancy safeguards this functioning against environmental changes. However, what drives functional redundancy remains unclear. We analyzed taxonomic diversity, functional diversity (richness and β-diversity) and functional redundancy patterns of British butterflies. We explored the effect of temperature and landscape-related variables on richness and redundancy using generalized additive models, and on β-diversity using generalized dissimilarity models. The species richness-functional richness relationship was saturating, indicating functional redundancy in species-rich communities. Assemblages did not deviate from random expectations regarding functional richness. Temperature exerted a significant effect on all diversity aspects and on redundancy, with the latter relationship being unimodal. Landscape-related variables played a role in driving observed patterns. Although taxonomic and functional β-diversity were highly congruent, the model of taxonomic β-diversity explained more deviance than the model of functional β-diversity did. Species-rich butterfly assemblages exhibited functional redundancy. Climate- and landscape-related variables emerged as significant drivers of diversity and redundancy. Τaxonomic β-diversity was more strongly associated with the environmental gradient, while functional β-diversity was driven more strongly by stochasticity. Temperature promoted species richness and β-diversity, but warmer areas exhibited lower levels of functional redundancy. This might be related to the land uses prevailing in warmer areas (e.g., agricultural intensification).

Biotic homogenisation and differentiation as directional change in beta diversity: synthesising driver-response relationships to develop conceptual models across ecosystems

Biotic homogenisation is defined as decreasing dissimilarity among ecological assemblages sampled within a given spatial area over time. Biotic differentiation, in turn, is defined as increasing dissimilarity over time. Overall, changes in the spatial dissimilarities among assemblages (termed 'beta diversity') is an increasingly recognised feature of broader biodiversity change in the Anthropocene. Empirical evidence of biotic homogenisation and biotic differentiation remains scattered across different ecosystems. Most meta-analyses quantify the prevalence and direction of change in beta diversity, rather than attempting to identify underlying ecological drivers of such changes. By conceptualising the mechanisms that contribute to decreasing or increasing dissimilarity in the composition of ecological assemblages across space, environmental managers and conservation practitioners can make informed decisions about what interventions may be required to sustain biodiversity and can predict potential biodiversity outcomes of future disturbances. We systematically reviewed and synthesised published empirical evidence for ecological drivers of biotic homogenisation and differentiation across terrestrial, marine, and freshwater realms to derive conceptual models that explain changes in spatial beta diversity. We pursued five key themes in our review: (i) temporal environmental change; (ii) disturbance regime; (iii) connectivity alteration and species redistribution; (iv) habitat change; and (v) biotic and trophic interactions. Our first conceptual model highlights how biotic homogenisation and differentiation can occur as a function of changes in local (alpha) diversity or regional (gamma) diversity, independently of species invasions and losses due to changes in species occurrence among assemblages. Second, the direction and magnitude of change in beta diversity depends on the interaction between spatial variation (patchiness) and temporal variation (synchronicity) of disturbance events. Third, in the context of connectivity and species redistribution, divergent beta diversity outcomes occur as different species have different dispersal characteristics, and the magnitude of beta diversity change associated with species invasions also depends strongly on alpha and gamma diversity prior to species invasion. Fourth, beta diversity is positively linked with spatial environmental variability, such that biotic homogenisation and differentiation occur when environmental heterogeneity decreases or increases, respectively. Fifth, species interactions can influence beta diversity via habitat modification, disease, consumption (trophic dynamics), competition, and by altering ecosystem productivity. Our synthesis highlights the multitude of mechanisms that cause assemblages to be more or less spatially similar in composition (taxonomically, functionally, phylogenetically) through time. We consider that future studies should aim to enhance our collective understanding of ecological systems by clarifying the underlying mechanisms driving homogenisation or differentiation, rather than focusing only on reporting the prevalence and direction of change in beta diversity, per se.

Multifunctional redundancy: Impossible or undetected?

The diversity-functioning relationship is a pillar of ecology. Two significant concepts have emerged from this relationship: redundancy, the asymptotic relationship between diversity and functioning, and multifunctionality, a monotonic relationship between diversity and multiple functions occurring simultaneously. However, multifunctional redundancy, an asymptotic relationship between diversity and multiple functions occurring simultaneously, is rarely detected in research. Here we assess whether this lack of detection is due to its true rarity, or due to systematic research error. We discuss how inconsistencies in the use of terms such as 'function' lead to mismatched research. We consider the different techniques used to calculate multifunctionality and point out a rarely considered issue: how determining a function's maximum rate affects multifunctionality metrics. Lastly, we critique how a lack of consideration of multitrophic, spatiotemporal, interactions and community assembly processes in designed experiments significantly reduces the likelihood of detecting multifunctional redundancy. Multifunctionality research up to this stage has made significant contributions to our understanding of the diversity-functioning relationship, and we believe that multifunctional redundancy is detectable with the use of appropriate methodologies.

Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions

Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.

Making protected areas effective for biodiversity, climate and food

The spatial extent of marine and terrestrial protected areas (PAs) was among the most intensely debated issues prior to the decision about the post-2020 Global Biodiversity Framework (GBF) of the Convention on Biological Diversity. Positive impacts of PAs on habitats, species diversity and abundance are well documented. Yet, biodiversity loss continues unabated despite efforts to protect 17% of land and 10% of the oceans by 2020. This casts doubt on whether extending PAs to 30%, the agreed target in the Kunming-Montreal GBF, will indeed achieve meaningful biodiversity benefits. Critically, the focus on area coverage obscures the importance of PA effectiveness and overlooks concerns about the impact of PAs on other sustainability objectives. We propose a simple means of assessing and visualising the complex relationships between PA area coverage and effectiveness and their effects on biodiversity conservation, nature-based climate mitigation and food production. Our analysis illustrates how achieving a 30% PA global target could be beneficial for biodiversity and climate. It also highlights important caveats: (i) achieving lofty area coverage objectives alone will be of little benefit without concomitant improvements in effectiveness, (ii) trade-offs with food production particularly for high levels of coverage and effectiveness are likely and (iii) important differences in terrestrial and marine systems need to be recognized when setting and implementing PA targets. The CBD's call for a significant increase in PA will need to be accompanied by clear PA effectiveness goals to reduce and revert dangerous anthropogenic impacts on socio-ecological systems and biodiversity.

Exploring the characteristics of gut microbiome in patients of Southern Fujian with hypocitraturia urolithiasis and constructing clinical diagnostic models

PURPOSE

Hypocitraturia is an important cause of urolithiasis. Exploring the characteristics of the gut microbiome (GMB) of hypocitriuria urolithiasis (HCU) patients can provide new ideas for the treatment and prevention of urolithiasis.

METHODS

The 24 h urinary citric acid excretion of 19 urolithiasis patients was measured, and patients were divided into the HCU group and the normal citrate urolithiasis (NCU) group. The 16 s ribosomal RNA (rRNA) was used to detect GMB composition differences and construct operational taxonomic units (OTUs) coexistence networks. The key bacterial community was determined by Lefse analysis, Metastats analysis and RandomForest analysis. Redundancy analysis (RDA) and Pearson correlation analysis visualized the correlation between key OTUs and clinical features and then established the disease diagnosis model of microbial-clinical indicators. Finally, PICRUSt2 was used to explore the metabolic pathway of related GMB in HCU patients.

RESULTS

The alpha diversity of GMB in HCU group was increased and Beta diversity analysis suggested significant differences between HCU and NCU groups, which was related to renal function damage and urinary tract infection. Ruminococcaceae_ge and Turicibacter are the characteristic bacterial groups of HCU. Correlation analysis showed that the characteristic bacterial groups were significantly associated with various clinical features. Based on this, the diagnostic models of microbiome-clinical indicators in HCU patients were constructed with the areas under the curve (AUC) of 0.923 and 0.897, respectively. Genetic and metabolic processes of HCU are affected by changes in GMB abundance.

CONCLUSION

GMB disorder may be involved in the occurrence and clinical characteristics of HCU by influencing genetic and metabolic pathways. The new microbiome-clinical indicator diagnostic model is effective.

Assembly processes of bacterial and fungal communities in metal(loid)s smelter soil

There are few studies on concurrent bacterial and fungal community assembly processes that govern the metal(loid)s biogeochemical cycles at smelters. Here, a systematic investigation combined geochemical characterization, co-occurrence patterns, and assembly mechanisms of bacterial and fungal communities inhabiting soils around an abandoned arsenic smelter. Acidobacteriota, Actinobacteriota, Chloroflexi, and Pseudomonadota were dominant in bacterial communities, whereas Ascomycota and Basidiomycota dominated fungal communities. The random forest model indicated the bioavailable fractions of Fe (9.58%) were the main positive factor driving the beta diversity of bacterial communities, and the total N (8.09%) was the main negative factor for fungal communities. Microbe-contaminant interactions demonstrate the positive impact of the bioavailable fractions of certain metal(loid)s on bacteria (Comamonadaceae and Rhodocyclaceae) and fungi (Meruliaceae and Pleosporaceae). The fungal co-occurrence networks exhibited more connectivity and complexity than the bacterial networks. The keystone taxa were identified in bacterial (including Diplorickettsiaceae, norank_o_Candidatus_Woesebacteria, norank_o_norank_c_AT-s3-28, norank_o_norank_c_bacteriap25, and Phycisphaeraceae) and fungal (including Biatriosporaceae, Ganodermataceae, Peniophoraceae, Phaeosphaeriaceae, Polyporaceae, Teichosporaceae, Trichomeriaceae, Wrightoporiaceae, and Xylariaceae) communities. Meanwhile, community assembly analysis revealed that deterministic processes dominated the microbial community assemblies, which were highly impacted by pH, total N, and total and bioavailable metal(loid) content. This study provides helpful information to develop bioremediation strategies for the mitigation of metal(loid)s-polluted soils.

Habitat complexity, connectivity, and introduced fish drive pond community structure along an urban to rural gradient

Urbanization can influence local richness (alpha diversity) and community composition (beta diversity) in numerous ways. For instance, reduced connectivity and land cover change may lead to the loss of native specialist taxa, decreasing alpha diversity. Alternatively, if urbanization facilitates nonnative species introductions and generalist taxa, alpha diversity may remain unchanged or increase, while beta diversity could decline due to the homogenization of community structure. Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand the consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated how landscape and local pond factors were correlated with the alpha diversity of aquatic plants, macroinvertebrates, and aquatic vertebrates. We also analyzed whether surrounding land use was associated with changes in community composition and the presence of specific taxa. We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites and a 15% decrease from rural to greenspace pond sites. Among landscape factors, adjacent developed land, mowed lawn cover, and greater distances to other waterbodies were negatively correlated with observed pond richness. Among pond level factors, habitat complexity was associated with increased richness, while nonnative fishes were associated with decreased richness. Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more nonnative species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. Our results suggest that integrating ponds into connected greenspaces, maintaining riparian vegetation, preventing nonnative fish introductions, and promoting habitat complexity may mitigate the negative effects of urbanization on aquatic richness. While ponds are small in size and rarely incorporated into urban conservation planning, the high beta diversity of distinct pond communities emphasizes their importance for supporting urban biodiversity.

Multiple anthropogenic stressors influence the taxonomic and functional homogenization of macroinvertebrate communities on the mainstream of an urban-agricultural river in China

Biodiversity loss is caused by intensive human activities and threatens human well-being. However, less is known about how the combined effects of multiple stressors on the diversity of internal (alpha diversity) and multidimensional (beta diversity) communities. Here, we conducted a long-term experiment to quantify the contribution of environmental stressors (including water quality, land use, climate factors, and hydrological regimes) to macroinvertebrate communities alpha and beta diversity in the mainstream of the Songhua River, the third largest river in China, from 2012 to 2019. Our results demonstrated that the alpha and beta diversity indices showed a decline during the study period, with the dissimilarity in community composition between sites decreasing significantly, especially in the impacted river sections (upper and midstream). Despite overall improvement in water quality after management intervention, multiple human-caused stressors still have led to biotic homogenization of macroinvertebrate communities in terms of both taxonomic and functional diversities in the past decade. Our study revealed the increased human land use explained an important portion of the variation of diversities, further indirectly promoting biotic homogenization by changing the physical and chemical factors of water quality, ultimately altering assemblage ecological processes. Furthermore, the facets of diversity have distinct response mechanisms to stressors, providing complementary information from the perspective of taxonomy and function to better reflect the ecological changes of communities. Environmental filtering determined taxonomic beta diversity, and functional beta diversity was driven by the joint efforts of stressors and spatial processes. Finally, we proposed that traditional water quality monitoring alone cannot fully reveal the status of river ecological environment protection, and more importantly, we should explore the continuous changes in biodiversity over the long term. Meanwhile, our results also highlight timely control of nutrient input and unreasonable expansion of land use can better curb the ecological degradation of rivers and promote the healthy and sustainable development of floodplain ecosystems.

Alien flora causes biotic homogenization in the biodiversity hotspot regions of India

Biotic homogenization by invasive alien species is one of dominant drivers of global environmental change. However, little is known about the patterns of biotic homogenization in global biodiversity hotspots. Here we fill this knowledge gap by studying the patterns of biotic homogenization and associated geographic and climatic correlates in Indian Himalayan Region (IHR). For this, we use a novel biodiversity database comprising 10,685 native and 771 alien plant species across 12 provinces of the IHR. The database was assembled by screening 295 and 141 studies published from 1934 to 2022 for natives and aliens, respectively. Our results revealed that each native species on average was distributed among 2.8 provinces, whereas the alien species in 3.6 provinces, thereby indicating wider distribution range of alien species in the IHR. The Jaccard's similarity index between the provinces was higher for alien species (mean = 0.29) as compared to natives (mean = 0.16). Addition of alien species pool has homogenized most of the provincial pairwise floras (89.4 %) across the IHR, with greater dissimilarity in their native floras. Our results suggest that the alien species have strong homogenization effect on the provincial floras, regardless of their differences in geographic and climatic distances. The biogeographic patterns of alien and native species richness in the IHR were better explained by a different set of climatic variables, with former by precipitation of driest month and the latter by annual mean temperature. Our study contributes to better understanding of the patterns of biotic homogenization and its impacts on native biodiversity in the IHR. Looking ahead, in an era of Anthropocene, we discuss the wide implications of our findings in guiding biodiversity conservation and ecosystem restoration in global hotspot regions.

Disentangling temporal associations in marine microbial networks

BACKGROUND

Microbial interactions are fundamental for Earth's ecosystem functioning and biogeochemical cycling. Nevertheless, they are challenging to identify and remain barely known. Omics-based censuses are helpful in predicting microbial interactions through the statistical inference of single (static) association networks. Yet, microbial interactions are dynamic and we have limited knowledge of how they change over time. Here, we investigate the dynamics of microbial associations in a 10-year marine time series in the Mediterranean Sea using an approach inferring a time-resolved (temporal) network from a single static network.

RESULTS

A single static network including microbial eukaryotes and bacteria was built using metabarcoding data derived from 120 monthly samples. For the decade, we aimed to identify persistent, seasonal, and temporary microbial associations by determining a temporal network that captures the interactome of each individual sample. We found that the temporal network appears to follow an annual cycle, collapsing, and reassembling when transiting between colder and warmer waters. We observed higher association repeatability in colder than in warmer months. Only 16 associations could be validated using observations reported in literature, underlining our knowledge gap in marine microbial ecological interactions.

CONCLUSIONS

Our results indicate that marine microbial associations follow recurrent temporal dynamics in temperate zones, which need to be accounted for to better understand the functioning of the ocean microbiome. The constructed marine temporal network may serve as a resource for testing season-specific microbial interaction hypotheses. The applied approach can be transferred to microbiome studies in other ecosystems. Video Abstract.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

The selection of copiotrophs may complicate biodiversity-ecosystem functioning relationships in microbial dilution-to-extinction experiments

The relationships between biodiversity-ecosystem functioning (BEF) for microbial communities are poorly understood despite the important roles of microbes acting in natural ecosystems. Dilution-to-extinction (DTE), a method to manipulate microbial diversity, helps to fill the knowledge gap of microbial BEF relationships and has recently become more popular with the development of high-throughput sequencing techniques. However, the pattern of community assembly processes in DTE experiments is less explored and blocks our further understanding of BEF relationships in DTE studies. Here, a microcosm study and a meta-analysis of DTE studies were carried out to explore the dominant community assembly processes and their potential effect on exploring BEF relationships. While stochastic processes were dominant at low dilution levels due to the high number of rare species, the deterministic processes became stronger at a higher dilution level because the microbial copiotrophs were selected during the regrowth phase and rare species were lost. From the view of microbial functional performances, specialized functions, commonly carried by rare species, are more likely to be impaired in DTE experiments while the broad functions seem to be less impacted due to the good performance of copiotrophs. Our study indicated that shifts in the prokaryotic community and its assembly processes induced by dilutions result in more complex BEF relationships in DTE experiments. Specialized microbial functions could be better used for defining BEF. Our findings may be helpful for future studies to design, explore, and interpret microbial BEF relationships using DTE.

Enhancing the structural diversity between forest patches-A concept and real-world experiment to study biodiversity, multifunctionality and forest resilience across spatial scales

Intensification of land use by humans has led to a homogenization of landscapes and decreasing resilience of ecosystems globally due to a loss of biodiversity, including the majority of forests. Biodiversity-ecosystem functioning (BEF) research has provided compelling evidence for a positive effect of biodiversity on ecosystem functions and services at the local (α-diversity) scale, but we largely lack empirical evidence on how the loss of between-patch β-diversity affects biodiversity and multifunctionality at the landscape scale (γ-diversity). Here, we present a novel concept and experimental framework for elucidating BEF patterns at α-, β-, and γ-scales in real landscapes at a forest management-relevant scale. We examine this framework using 22 temperate broadleaf production forests, dominated by Fagus sylvatica. In 11 of these forests, we manipulated the structure between forest patches by increasing variation in canopy cover and deadwood. We hypothesized that an increase in landscape heterogeneity would enhance the β-diversity of different trophic levels, as well as the β-functionality of various ecosystem functions. We will develop a new statistical framework for BEF studies extending across scales and incorporating biodiversity measures from taxonomic to functional to phylogenetic diversity using Hill numbers. We will further expand the Hill number concept to multifunctionality allowing the decomposition of γ-multifunctionality into α- and β-components. Combining this analytic framework with our experimental data will allow us to test how an increase in between patch heterogeneity affects biodiversity and multifunctionality across spatial scales and trophic levels to help inform and improve forest resilience under climate change. Such an integrative concept for biodiversity and functionality, including spatial scales and multiple aspects of diversity and multifunctionality as well as physical and environmental structure in forests, will go far beyond the current widely applied approach in forestry to increase resilience of future forests through the manipulation of tree species composition.

β-diversity in temperate grasslands is driven by stronger environmental filtering of plant species with large genomes

Elucidating mechanisms underlying community assembly and biodiversity patterns is central to ecology and evolution. Genome size (GS) has long been hypothesized to potentially affect species' capacity to tolerate environmental stress and might therefore help drive community assembly. However, its role in driving β-diversity (i.e., spatial variability in species composition) remains unclear. We measured GS for 161 plant species and community composition across 52 sites spanning a 3200-km transect in the temperate grasslands of China. By correlating the turnover of species composition with environmental dissimilarity, we found that resource filtering (i.e., environmental dissimilarity that includes precipitation, and soil nitrogen and phosphorus concentrations) affected β-diversity patterns of large-GS species more than small-GS species. By contrast, geographical distance explained more variation of β-diversity for small-GS than for large-GS species. In a 10-year experiment manipulating levels of water, nitrogen, and phosphorus, adding resources increased plant biomass in species with large GS, suggesting that large-GS species are more sensitive to the changes in resource availability. These findings highlight the role of GS in driving community assembly and predicting species responses to global change.

Deterministic Assembly Processes Strengthen the Effects of β-Diversity on Community Biomass of Marine Bacterioplankton

The presence of more species in the community of a sampling site (α diversity) typically increases ecosystem functions via nonrandom processes like resource partitioning. When considering multiple communities, we hypothesize that higher compositional difference (β diversity) increases overall functions of these communities. Further, we hypothesize that the β diversity effect is more positive when β diversity is increased by nonrandom assembly processes. To test these hypotheses, we collected bacterioplankton along a transect of 6 sampling sites in the southern East China Sea in 14 cruises. For any pairs of the 6 sites within a cruise, we calculated the Bray-Curtis index to represent β diversity and summed bacterial biomass as a proxy to indicate the overall function of the two communities. We then calculated deviation of observed mean pairwise phylogenetic similarities among species in two communities from random to represent the influences of nonrandom processes. The bacterial β diversity was found to positively affect the summed bacterial biomass; however, the effect varied among cruises. Cross-cruise comparison indicated that the β diversity effect increased with the nonrandom processes selecting for phylogenetically dissimilar species. This study extends biodiversity-ecosystem functioning research to the scale of multiple sites and enriches the framework by considering community assembly processes. IMPORTANCE The implications of our analyses are twofold. First, we emphasize the importance of studying β diversity. We expanded the current biodiversity-ecosystem functioning framework from single to multiple sampling sites and investigated the influences of species compositional differences among sites on the overall functioning of these sites. Since natural ecological communities never exist alone, our analyses allow us to more holistically perceive the role of biodiversity in natural ecosystems. Second, we took community assembly processes into account to attain a more mechanistic understanding of the impacts of biodiversity on ecosystem functioning.

Universal beta-diversity-functioning relationships are neither observed nor expected

Widespread evidence shows that local species richness (α-diversity) loss hampers the biomass production and stability of ecosystems. β-Diversity, namely the variation of species compositions among different ecological communities, represents another important biodiversity component, but studies on how it drives ecosystem functioning show mixed results. We argue that to better understand the importance of β-diversity we need to consider it across contexts. We focus on three scenarios that cause gradients in β-diversity: changes in (i) abiotic heterogeneity, (ii) habitat isolation, and (iii) species pool richness. We show that across these scenarios we should not expect universally positive relationships between β-diversity, production, and ecosystem stability. Nevertheless, predictable relationships between β-diversity and ecosystem functioning do exist in specific contexts, and can reconcile seemingly contrasting empirical relationships.