A new conceptual and methodological framework for exploring and explaining pattern in presence - absence data

Fish beta diversity associated with hydrologic and anthropogenic disturbance gradients in contrasting stream flow regimes

Understanding the role of hydrologic variation in structuring aquatic communities is crucial for successful conservation and sustainable management of native freshwater biodiversity. Partitioning beta diversity into the additive components of spatial turnover and nestedness can provide insight into the forces driving variability in fish assemblages across stream flow regimes. We examined stream fish beta diversity across hydrologic and anthropogenic disturbance gradients using long-term (1916-2016) site occurrence records (n = 17,375) encompassing 252 species. We assessed total beta diversity (Sørensen dissimilarity), spatial turnover, and nestedness of fish assemblages in contrasting stream flow regimes across a gradient of decreasing flow stability: groundwater stable (n = 77), groundwater (n = 67), groundwater flashy (n = 175), perennial runoff (n = 141), runoff flashy (n = 255), and intermittent (n = 63) streams. Differences in total beta diversity among the stream flow regimes were driven predominantly (>86 %) by spatial turnover (i.e. species replacement) as opposed to nestedness (i.e. species loss or gain). Total fish beta diversity and spatial turnover were highest in streams with intermediate flow stability (groundwater flashy), while more flow-stable streams (groundwater stable and groundwater) had lower turnover and higher nestedness. Species turnover was also strongly associated with seasonal variation in hydrology across all flow regimes, but these relationships were most evident for assemblages in intermittent streams. Distance-based statistical comparisons showed significant correlations between beta diversity and anthropogenic disturbance variables, including dam density, dam storage volume and water withdrawals in catchments of groundwater stable streams, while hydrologic variables were more strongly correlated with beta diversity in streams with runoff-dominated and flashy flow regimes. The high spatial turnover of species implies that fish conservation actions would benefit from watershed-focused approaches targeting multiple streams with wide spatial distribution, as opposed to simply focusing on preserving sites with the greatest number of species.

Rainfall seasonality shapes microbial assembly and niche characteristics in Yunnan Plateau lakes, China

Microorganisms are crucial components of freshwater ecosystems. Understanding the microbial community assembly processes and niche characteristics in freshwater ecosystems, which are poorly understood, is crucial for evaluating microbial ecological roles. The Yunnan Plateau lakes in China represent a freshwater ecosystem that is experiencing eutrophication due to anthropogenic activities. Here, variation in the assembly and niche characteristics of both prokaryotic and microeukaryotic communities was explored in Yunnan Plateau lakes across two seasons (dry season and rainy season) to determine the impacts of rainfall and environmental conditions on the microbial community and niche. The results showed that the environmental heterogeneity of the lakes decreased in the rainy season compared to the dry season. The microbial (bacterial and microeukaryotic) α-diversity significantly decreased during the rainy season. Deterministic processes were found to dominate microbial community assembly in both seasons. β-Diversity decomposition analysis revealed that microbial community compositional dissimilarities were dominated by species replacement processes. The co-occurrence networks indicated reduced species complexity for microbes and a destabilized network for prokaryotes prior to rainfall, while the opposite was found for microeukaryotes following rainfall. Microbial niche breadth decreased significantly in the rainy season. In addition, lower prokaryotic niche overlap, but greater microeukaryotic niche overlap, was observed after rainfall. Rainfall and environmental conditions significantly affected the microbial community assembly and niche characteristics. It can be concluded that rainfall and external pollutant input during the seasonal transition alter the lake environment, thereby regulating the microbial community and niche in these lakes. Our findings offer new insight into microbiota assembly and niche patterns in plateau lakes, further deepening the understanding of freshwater ecosystem functioning.

Shallow tillage mitigates plant competition by increasing diversity and altering plant community assembly process

Introduction

Understanding how human activities affect biodiversity is needed to inform systemic policies and targets for achieving sustainable development goals. Shallow tillage to remove Artemisia ordosica is commonly conducted in the Mu Us Desert. However, the impacts of shallow tillage on plant community species diversity, phylogenetic structure, and community assembly processes remain poorly understood.

Methods

This study explores the effects of shallow tillage on species diversity including three a-diversity and two b-diversity indicators, as well as phylogenetic structure [phylogenetic diversity (PD), net relatedness index (NRI), and nearest taxon index (NTI)]. Additionally, this research analyzes the effects of shallow tillage on the community assembly process.

Results and discussion

The results showed that the a-diversity index, b-diversity index, and PD of the shallow tillage (ST) communities were significantly higher than those of the non-shallow tillage (NT) communities, and the phylogenetic structures of both the ST and NT communities tended to be differentiated, with competitive exclusion being the main mechanism of plant assembly. However, shallow tillage increased the relative importance of the stochastic processes dominated by dispersal limitation, mitigating plant competition in the communities. This conclusion was supported by the Raup-Crick difference index-based analysis.

Conclusion

Therefore, for the ecological restoration of the Mu Us Desert, species with adaptability and low niche overlap should be selected to increase the utilization efficiency of the environmental resources. The results of this study provide a foundation for policy development for ecosystem management and restoration in the Mu Us Desert.

Combined effects of climate and land-use changes on the alpha and beta functional diversities of terrestrial mammals in China

Climate and land-use changes are predicted to impact biodiversity, threatening ecosystem services and functions. However, their combined effects on the functional diversity of mammals at the regional scale remain unclear, especially at the beta level. Here, we use projected climate and land-use changes in China to investigate their potential effects on the alpha and beta functional diversities of terrestrial mammals under low- and high-emission scenarios. In the current projection, we showed strong positive spatial correlations between functional richness and species richness. Functional evenness (FEve), functional specialization (FSpe), and functional originality (FOri) decreased with species richness, and functional divergence (FDiv) increased first and then plateaued. Functional beta diversity was dominated by its nestedness component, in contrast to the taxonomic facet. Potential changes in species richness are more strongly influenced by land-use change under the low-emission scenario, while under the high-emission scenario, they are more strongly influenced by climate change. Changes in functional richness (FRic) were inconsistent with those in species richness, with a magnitude of decreases greater than predicted from species richness. Moreover, mammal assemblages showed potential functional differentiation (FD) across the country, and the trends exceeded those towards taxonomic differentiation (TD). Our findings help us understand the processes underlying biodiversity responses to global changes on multiple facets and provide new insight for conservation plans.

Local environment and fragmentation by drought and damming shape different components of native and non-native fish beta diversity across pool refuges

Pool refuges are critical for maintaining stream fish diversity in increasingly intermittent streams. Yet, the patterns and drivers of beta diversity of native and non-native fish in pool refuges remain poorly known. Focusing on Mediterranean streams, we decomposed beta diversity of native and non-native fish into richness difference (RichDiff) and species replacement (Repl), and local (LCBD, LCBDRichDiff and LCBDRepl) and species (SCBD) contributions. We assessed the influence of environmental and spatial factors associated with drought and damming fragmentations on beta diversity components and LCBDs, and of local species richness and occupancy on LCBDs and SCBD, respectively. Overall, non-native species showed a more limited occupancy of pool refuges than native fish. RichDiff dominated beta diversity, though it was influenced by drought and damming fragmentations for native fish and local environment for non-native fish. Repl for native fish was slightly influenced by local environment, but for non-native fish was largely driven by drought and damming, albeit with a contribution of local environment as well. LCBD and LCBDRichDiff increased in pools in low order streams for native fish and at low elevations for non-native fish, and with high or low species richness. SCBD was higher for native species with intermediated pool occupancy, but for non-native species with low occupancy. Our results suggest that stream fragmentation may drive native species loss and non-native species replacement in pool refuges, and that environmental filtering may shape non-native species loss. Pools in lower order streams harbouring unique species-rich or species-poor assemblages should be prioritize for conservation and restoration, respectively, and pools at low elevation with unique non-native assemblages should deserve control efforts. We encourage the partitioning of beta diversity and individual analysis of native and non-native fish in intermittent streams, which may be key in stressing the importance of pool refuges in safeguarding native fish diversity.

Taxonomic and functional β-diversity patterns reveal stochastic assembly rules in microbial communities of seagrass beds

Microorganisms are important members of seagrass bed ecosystems and play a crucial role in maintaining the health of seagrasses and the ecological functions of the ecosystem. In this study, we systematically quantified the assembly processes of microbial communities in fragmented seagrass beds and examined their correlation with environmental factors. Concurrently, we explored the relative contributions of species replacement and richness differences to the taxonomic and functional β-diversity of microbial communities, investigated the potential interrelation between these components, and assessed the explanatory power of environmental factors. The results suggest that stochastic processes dominate community assembly. Taxonomic β-diversity differences are governed by species replacement, while for functional β-diversity, the contribution of richness differences slightly outweighs that of replacement processes. A weak but significant correlation (p < 0.05) exists between the two components of β-diversity in taxonomy and functionality, with almost no observed significant correlation with environmental factors. This implies significant differences in taxonomy, but functional convergence and redundancy within microbial communities. Environmental factors are insufficient to explain the β-diversity differences. In conclusion, the assembly of microbial communities in fragmented seagrass beds is governed by stochastic processes. The patterns of taxonomic and functional β-diversity provide new insights and evidence for a better understanding of these stochastic assembly rules. This has important implications for the conservation and management of fragmented seagrass beds.

Damming exacerbates the discontinuities of phytoplankton in a subtropical river in China

Phytoplankton is sensitive to changes in river ecosystems. Increasing dams disrupt the continuity of river ecosystems. However, the spatial impacts of dams on phytoplankton have not been well documented. In this study, using multiple statistical analyses, the relationships between environmental drivers and phytoplankton community structures in natural background reaches, reservoirs, and corresponding post-dam reaches were explored in the Jiulong River with multiple cascaded dams, which encountered eutrophication and algal blooms in the past 15 years. Results illustrated that damming exacerbated longitudinal discontinuities of phytoplankton communities. The relative abundance of phytoplankton varied in three types of river sections. The average phytoplankton abundance in the reservoirs (1.62 × 105 cell·L-1) was higher than those in the natural background reaches (5.15 × 104 cell·L-1) and the corresponding downstream reaches (4.55 × 104 cell·L-1). The total β diversity ranged from 0.38 to 0.89 with an average of 0.64 and dominated by species replacement and least by species richness. The water environmental factors and hydraulic parameters rather than nutrients were more attributable to phytoplankton community variability in three river sections. These findings facilitate the management of rivers with multiple cascade dams by releasing environmental flows, jointly operating cascade hydropower stations, and developing nutrient reduction schemes to mitigate the negative impacts of damming in the river.

Upstream cascade reservoirs drive temporal beta diversity increases through species loss in a dammed river

Changes in the biodiversity of aquatic environments over time and space due to human activities are a topic of theoretical and conservational interest in ecology. Thus, variation in taxonomic beta diversity of the planktonic ciliates community was investigated along a temporal and spatial gradient in two subsystems of a Neotropical floodplain, one impacted by dams (Paraná) and the other free of them along its course (Ivinhema). For the spatial analysis, the Paraná subsystem did not show a significant decrease in beta diversity, presenting a pattern like that observed for the Ivinhema subsystem. Therefore, biotic homogenization was not observed for the ciliate's community downstream of the dams. It was noted that there was a fluctuation in the relevance of the components of beta diversity, regardless of the subsystem analyzed. For the temporal analysis there was a significant change in species composition from the first to the last year investigated, essentially for the subsystem impacted by dams, and that this was determined mainly by species loss. Although spatial beta diversity remained high without a clear process of biotic homogenization, dams promoted remarkable changes in ciliate species composition over the years mainly by continuous loss of species.

eDNA metabarcoding reveals the role of habitat specialization and spatial and environmental variability in shaping diversity patterns of fish metacommunities

Information is scarce on how environmental and dispersal processes interact with biological features of the organisms, such as their habitat affinity, to influence patterns in biodiversity. We examined the role of habitat specialist vs. generalist species, and the spatial configuration, connectivity, and different environmental characteristics of river-floodplain habitats to get a more mechanistic understanding of alpha and beta diversity of fish metacommunities. We used environmental DNA metabarcoding to characterize species (taxa) richness and composition in two separate floodplains of the river Danube (Austria and Hungary) during two different hydrological conditions. Results showed that differences in the number of generalist and specialist species and their responses to connectivity and environmental gradients influenced patterns in alpha and beta diversity. Of the components of beta diversity, richness difference (nestedness) showed consistently higher values than replacement (turnover), mainly due to the decrease of specialist species along the connectivity gradient (i.e., from the mainstem to the most isolated oxbows). Variance in both alpha and beta diversity could be well predicted by a set of local and regional variables, despite high environmental variability, which characterizes river-floodplain ecosystems. Of these, the joint or shared variance fractions proved to be the most important, which indicates that the effects of local and regional processes cannot be unambiguously separated in these river-floodplain systems. Local scale environmental variables were more important determinants of both alpha and beta diversity in the low water period than in the high water period. These results indicate the differential role of local and regional processes in community organization during different hydrological conditions. Maintenance of both local and regional scale processes are thus important in the preservation of alpha and beta diversity of floodplain fish metacommunities, which should be considered by environmental management.

Maternal transmission of bacterial microbiota during embryonic development in a viviparous lizard

IMPORTANCE

We investigated the presence and diversity of bacteria in the embryos of the viviparous lizard Sceloporus grammicus and their amniotic environment. We compared this diversity to that found in the maternal intestine, mouth, and cloaca. We detected bacterial DNA in the embryos, albeit with a lower bacterial species diversity than found in maternal tissues. Most of the bacterial species detected in the embryos were also found in the mother, although not all of them. Interestingly, we detected a high similarity in the composition of bacterial species among embryos from different mothers. These findings suggest that there may be a mechanism controlling the transmission of bacteria from the mother to the embryo. Our results highlight the possibility that the interaction between maternal bacteria and the embryo may affect the development of the lizards.

Multidimensional beta-diversity across local and regional scales in a Chinese subtropical forest: The role of forest structure

Beta-diversity, or the spatio-temporal variation in community composition, can be partitioned into turnover and nestedness components in a multidimensional framework. Forest structure, including comprehensive characteristics of vertical and horizontal complexity, strongly affects species composition and its spatial variation. However, the effects of forest structure on beta-diversity patterns in multidimensional and multiple-scale contexts are poorly understood. Here, we assessed beta-diversity at local (a 20-ha forest dynamics plot) and regional (a plot network composed of 19 1-ha plots) scales in a Chinese subtropical evergreen broad-leaved forest. We then evaluated the relative importance of forest structure, topography, and spatial structure on beta-diversity and its turnover and nestedness components in taxonomic, functional, and phylogenetic dimensions at local and regional scales. We derived forest structural parameters from both unmanned aerial vehicle light detection and ranging (UAV LiDAR) data and plot inventory data. Turnover component dominated total beta-diversity for all dimensions at the two scales. With the exception of some components (taxonomic and functional turnover at the local scale; functional nestedness at the regional scale), environmental factors (i.e., topography and forest structure) contributed more than pure spatial variation. Explanations of forest structure for beta-diversity and its component patterns at the local scale were higher than those at the regional scale. The joint effects of spatial structure and forest structure influenced component patterns in all dimensions (except for functional turnover) to some extent at the local scale, while pure forest structure influenced taxonomic and phylogenetic nestedness patterns to some extent at the regional scale. Our results highlight the importance and scale dependence of forest structure in shaping multidimensional beta-diversity and its component patterns. Clearly, further studies need to link forest structure directly to ecological processes (e.g., asymmetric light competition and disturbance dynamics) and explore its roles in biodiversity maintenance.

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.

Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties

Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.

Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest

Background

Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific?

Methods

We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific.

Results

Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana).

Discussion

Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort to evaluate and link the soil microenvironmental effect on tree α and β-diversity, finding a high replacement in a small-fragment of Neotropical montane oak forest from eastern Mexico.

Covariation of taxonomic and functional facets of β-diversity in Chilean freshwater fish assemblages: Implications for current and future processes of biotic homogenization

The biodiversity of assemblages that experience the introduction and extinction of species may lead to responses in two important facets: The taxonomic and functional diversity. The way in which these facets are associated may reveal important implications and consequences for the conservation of those assemblages. Considering the critical situation of freshwater fishes in continental Chile (30° - 56° S), we analyzed how the taxonomic (TDβ) and functional (FDβ) facets of β-diversity, and their components of turnover and nestedness, are associated. We evaluated changes in β-diversity (ΔTDβ and ΔFDβ), turnover (ΔTDtur and ΔFDtur), and nestedness (ΔTDnes and ΔFDnes) in 20 fish assemblages from their historical (pre-European) to current composition. We also simulated future trends of these changes, assuming that native species with conservation issues would become extinct. Our results show that the fish assemblages studied are in a process of loss of β-diversity, both in taxonomic and functional facets (ΔTDβ = -3.9%; ΔFDβ = -30.4%); also, that these facets are positively correlated in the assemblages studied (r = 0.617; P < 0.05). Both components showed by loss in nestedness (ΔTDnes = -36.9%; ΔFDnes = -60.9%) but gain in turnover (ΔTDtur = 9.2%; ΔFDtur = 12.3%). The functional β-diversity decreased more than the taxonomic (ΔFDβ > ΔTDβ), which was caused chiefly by six exotic species of Salmonidae, whose geographical spread was wider and that at the same time shared several morpho-functional traits. Our forecasts, assuming an intensification in the extinction of Endangered and Vulnerable native species, indicate that the process of homogenization will continue, though at a lower rate. Our study shows that the freshwater ichthyofauna of continental Chile is undergoing biotic homogenization, and that this process involves the facets of taxonomic and functional β-diversity, which are show high correlation between historical and current compositions. Both facets show that process is influenced by nestedness, and while turnover contributes to differentiation (both taxonomic and functional), its importance is overshadowed by nestedness.

Structure and impact of root-associated fungi in treatment wetland mesocosms

Root fungal endophytes have been shown to play a positive role in soil phytoremediation by immobilizing or degrading contaminants. In comparison, little is known about their ecological functions and possible role in improving plant performance in treatment wetlands. In a greenhouse study, we compared the structure of fungal communities associated with Phragmites australis roots in treatment wetland mesocosms fed with pre-treated wastewater to mesocosms fed with drinking water. We evaluated the role of water source as an environmental filter structuring fungal communities, and correlated the relative abundances of fungal taxa with key services delivered by the wetlands (i.e., biomass production and nutrient removal). Mesocosms fed with wastewater had higher fungal alpha-diversity. Contrary to expectations, many fungi were unique to drinking water-fed mesocosms, suggesting that the oligotrophic conditions prevailing in these mesocosms benefited specific fungal taxa. On the other hand, wastewater-fed mesocosms had a slightly higher proportion of sequence reads belonging to fungal species recognized as potential endophytes and phytopathogens, highlighting the potential role of wastewater as a source of plant-associated fungi. Interestingly, we found contrasted association patterns between fungal species' relative abundances and different treatment wetland services (e.g., N vs P removal), such that some fungi were positively associated with N removal but negatively associated with P removal. This suggests that fungal endophytes may be functionally complementary in their contribution to distinct mesocosm services, thus supporting arguments in favor of microbial diversity in phytotechnologies. Because of the wide alpha-diversity of fungal communities, and the fact that with current databases, most species remained unassigned to a specific function (or even guild), further investigation is needed to link fungal community structure and service delivery in treatment wetlands.

Understanding the taxonomic homogenization of road-influenced plant assemblages in the Qionglai mountain range: A functional and phylogenetic perspective

As an increasingly prevalent form of human activity, roads drive the taxonomic homogenization of mountain plant assemblages, threatening global biodiversity. However, little is known about how mountain roads impact functional and phylogenetic beta diversity and how these effects are related to taxonomic homogenization. To understand the mechanism of taxonomic homogenization triggered by mountain roads, we used species absence/presence data from 76 plots (2 m*50 m) and values for 12 traits measured on 978 species from the interior and roadside communities in the Qionglai mountain range, one of the temperate regions with the highest plant species richness in the world. We used a structural equation modeling approach (SEM) to consider several surrogates of road disturbance (changes in soil physicochemical properties and the presence or absence of roads) and the causal relationship between three facets of beta diversity (taxonomic beta diversity, TBD; functional beta diversity, FBD and phylogenetic beta diversity, PBD). The results suggest that TBD, FBD and PBD respond inconsistently to mountain roads, despite strong positive correlations between the three facets of plant beta diversity in the study area. Compared with the interior community, the βtotal.tax and βtotal.func of the roadside community decreased by 2.54% and 2.22%, respectively, which were related to the reduction of species and trait richness differences and replacements; however, we did not find the same results when assessing the changes in βtotal.phy, which represents tip-weighted PBD (twPBD). Furthermore, the largest effect of roads on beta diversity was reflected in basal-weighted PBD (bwPBD), which decreased by 9.97%, indicating that those species with fewer extant relatives and longer evolutionary histories are more sensitive to mountain roads. Therefore, it is necessary to take targeted protection measures for ancient species in roadside communities. In addition, we believe that it is still necessary to take measures to prevent the further dispersal of nonnative species, although the presence of non-native species in roadside plots has led to small changes in three facets of beta diversity. There were causal relationships between the three facets of beta diversity, but their intensity and sign different in the SEM of different components of beta diversity (i.e., richness difference and replacement). Our findings suggest that the homogenization of community species composition at the landscape scale arises by a combination of adaptive responses of the functional traits of organisms to environmental consistency (e.g., reduced the differences in soil variables) caused by roads and resorting or reassembly of community clades composition due to environmental filtering. These results contribute to our comprehensive understanding of the impact of mountain roads on plant diversity, which highlights the complex relationship between human pressure and biodiversity loss.

High taxonomic turnover and functional homogenization of rotifer communities in an amazonian river

Patterns of beta diversity of plankton communities in rivers have been mainly determined by hydrological factors that alter the dispersion and composition of species and traits. Rotifers in the Guamá River (eastern Amazonian River) were sampled (monthly between October 2017 and June 2019) to analyze the temporal variation of taxonomic and functional beta diversity and its partitions (turnover and nestedness) as well as the effects of temporal, environmental, and seasonal dissimilarities. Taxonomic turnover and functional nestedness over time were observed as well as functional homogenization, which was arguably due to the hypereutrophic condition of the river. There were no seasonal differences in taxonomic and functional beta diversity probably due the low environmental dissimilarity. This study demonstrated that this Guamá River stretch presented low environmental dissimilarity and hypereutrophic waters, which benefited the establishment of a community of species with high taxonomic turnover over time, but with low functional dissimilarity and loss of some functions related to the functional traits evaluated in the ecosystem. It is important to point out that temporal studies should evaluate both taxonomic and functional aspects of communities, mainly because the effect of environmental changes may be more noticeable at the functional level of communities.

Avifaunal diversity in Indian Institute of Technology Guwahati Campus, Assam, India

Indian Institute of Technology - Guwahati (IITG), Assam, is an ecologically rich campus hosting different species of birds, butterflies and mammals. It accommodates several migratory and resident species of birds across different seasons. However, information is scanty on avian diversity with respect to the different habitats of the campus. Therefore, the present study attempts to gain insight into avian diversity with respect to habitat heterogeneity by considering the species presence-absence dataset collected for three years (2017–2020). A multivariate Beta (β) diversity analysis is carried out for the IITG campus constituted of five primary habitats, viz., secondary growth, eco–forest, water bodies, swampy-marshy area, and constructions. Of 152 bird species observed in the IITG campus, the highest number is reported from secondary growth, followed by eco-forest. The multivariate analysis shows that the average β–diversity for the IITG campus is approximately equal to 79%, which is in accordance with another published study. These observations are examined in light of hypotheses and phenomena documented in the literature, such as habitat heterogeneity hypothesis, niche-based hypothesis and anthropogenic impact on habitats. The study also establishes that the IITG is among the educational institutes and campuses that host many migratory bird species. Lastly, based on the outcomes of β–diversity analysis, it is suggested that the conservation effort for avian species in the campus should be directed towards individual habitats uniformly.

Comparative diversity of vascular plants in black alder floodplain and swamp forests of Central European biogeographical regions

Plant species diversity of black alder-dominated forests was studied in three biogeographical regions (Alpine, Continental and Pannonian) of Central Europe. They were represented by regions of the Polish Plain (Continental), the High Western Carpathians and Matricum of the Western Carpathians (Alpine) and the Pannonian lowland (Pannonian). We analysed 35 plots per region in order to identify: i) local alpha (α) diversity defined as the counted number of plant taxa occurring in a single sampling plot, ii) amongst-site beta (β) diversity, iii) regional (γ) diversity defined as the total species richness of all sampling plots and iv) zeta diversity (ζ) as a generalisation of beta diversity. We recorded a total of 432 vascular plant taxa in all bioregions; more than 13% were alien plants. Statistically significant differences in species richness (α) of both native and alien plants were found between assemblages of the regions. The High Western Carpathians showed the highest native and the lowest alien plant species richness. Total β-diversity was high in all regions, but significantly differed amongst regions only for alien plant species. Cumulative native and alien species richness (γ) was the highest and lowest in the High Western Carpathians and Matricum of Western Carpathians, respectively. Our results identified the High Western Carpathians as a hotspot for diversity of native plants in Central European black alder-dominated forests.

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa

Green roofs are unique ecosystems combining two major community assembly filters, namely stress and spatial isolation. As such, they represent an interesting model ecosystem in community ecology. In this study, we characterized the microbiome structure on 19 green roofs and 5 urban parks as a benchmark comparison (i.e. non-isolated, non-stressful habitats). Green roofs were not species depauperate, showing similar α-diversity compared to surrounding parks. We also did not find an overrepresentation of bacterial phyla typically recognized as oligotrophs, which calls into question the notion of green roofs as highly stressful habitats for bacteria, and/or the conservatism of nutritional ecophysiology at the phylum level. The geographical position of a roof, or its degree of spatial isolation (assessed through its height and area) were not important predictors of microbiome diversity and structure, suggesting that dispersal limitations impose little constraints on green roof microbiome assembly. Finally, key microbial groups (e.g. archaeal nitrifiers, Actinobacteria) were much less frequent and/or abundant on green roofs, which may have important implications for nutrient cycling and urban biogeochemistry. More work will be required to phenotype the microorganisms overrepresented on green roofs and specifically measure key soil processes in these unique urban ecosystems.

Ecological drivers of macroinvertebrate metacommunity assembly in a subtropical river basin in the Yangtze River Delta, China

Identifying the underlying ecological drivers of macroinvertebrate community assembly is fundamental to metacommunity ecology. Comparably, determining the influence of different drivers on beta diversity patterns can provide insight into processes governing community organization. Exploring the ecological drivers of metacommunity and beta diversity are major avenues to improve bioassessment, restoration, and river management, which are still poorly explored in China, especially in subtropical highly developed river networks. To address this gap, we use a dataset (macroinvertebrate communities and environmental variables) collected from the Yangtze River Delta, China to test the above ideas. We used the K-means clustering method to divide 405 river sites into three anthropogenic impacted groups, nearly pristine sites, moderately impacted sites, and heavily impacted sites, and subsequently used partial Mantel tests to investigate how species sorting and dispersal shaped the metacommunity that varied with the levels of anthropogenic impacts and to explore the responses of different components of beta diversity to environmental and spatial distances among sites for each group. Our results revealed that both species sorting and dispersal shape communities, but the importance of species sorting and dispersal varied with the levels of anthropogenic impacts. Nearly pristine sites were mostly shaped only by species sorting, while heavily impacted sites were shaped by dispersal. We also found that turnover was by far the dominant component of beta diversity across all levels of impact. Therefore, we encourage that environmental variables and spatial processes should be considered in bioassessment approaches. In addition, it is essential to focus on maintaining habitat heterogeneity and identifying and protecting regional species pools that could improve local biodiversity through dispersal for ecosystem management of the Yangtze River Delta of China.

Species richness and turnover patterns for tropical and temperate plants on the elevation gradient of the eastern Himalayan Mountains

Understanding species’ elevational distributions in mountain ecosystems is needed under climate change, but remote biodiverse mountain areas may be poorly documented. National Forest Inventories (NFIs) offer a potential source of data. We used NFI records from Bhutan to ask three questions about elevational richness patterns of Himalayan woody plant species. First, does the mean elevation for all species differ from those species whose entire elevational distribution is recorded in the survey? Second, how does the elevation of maximum richness differ when combining species originating from temperate and tropical regions vs. analyzing them separately? And third, do the highest species turnover rates adjoin elevation zones of maximum species richness? We used 32,198 species records from 1685 forest plots along a 7570 m gradient to map species elevation ranges. Species whose entire range was documented were those whose lowest records are located above 400 m, while bare rock defined all species’ upper limits. We calculated species richness and turnover using 400 m elevation bands. Of 569 species, 79% of temperate and 61% of tropical species’ elevation ranges were fully sampled within the NFI data. Mean elevation of tree and shrub species differed significantly for temperate and tropical species. Maximum combined species richness is from 1300 to 1700 m (277 species), differing significantly from maximum tropical (900–1300 m, 169) and temperate species richness (2500–2900 m, 92). Temperate tree turnover rate was highest in the bands adjoining its maximum species richness (2500–2900 m). But turnover for tropical trees was highest several bands above their maximum species richness, where turnover and decrease in richness interact. Shrub species turnover patterns are similar, but rates were generally higher than for trees. Bhutan’s NFI records show that woody plant species are arrayed on the Himalaya in part according to floristic origins, and that combining temperate- and tropical-originating floras for gradient-based studies such as species richness and turnover obscures actual elevational patterns. In addition, species whose ranges extend below the Himalayan elevation gradient should be accounted for in future studies that correlate climate and environment factors with elevational species richness patterns.

How do distribution mapping methods perform in estimating beta diversity at macroecological scales? A case study with Neotropical anurans

Species distribution mapping methods have their advantages and limitations concerning their use on theoretical and/or applied macroecological approaches. However, it remains underexplored how the estimates of community ecology metrics vary across the distributions generated by different mapping methods. Here, we mapped the distribution patterns of the anuran beta diversity in the Atlantic Forest and Cerrado hotspots generated by three mapping methods: point-to-grid (PTG), extent-of-occurrence (EOO), and ecological niche modelling (ENM) maps, so we were able to compare the congruence of the local contribution to beta diversity index (LCBD) among them, as well as their turnover and nestedness components. PTGs generated the most divergent LCBD values probably due to the more resolved spatial scale in which species' presence are considered, so EEO and ENM generated similar beta diversity estimates for both hotspots. High LCBD values in the Cerrado were recorded in ecotone regions, whereas in the Atlantic Forest the highest beta diversity values were found along the Atlantic coast. The structure of beta diversity of PTG showed way too high values of importance for the turnover component compared to the EEO and ENM maps, which also recorded higher importance for the turnover than for the nestedness component.

Generalists and Specialists Determine the Trend and Rate of Soil Fungal Distance Decay of Similarity in a 20-ha Subtropical Forest

Fungi are an important component of microbial communities that serve a variety of important roles in nutrient cycling and are essential for plant nutrient uptake in forest soils. Distance decay of similarity (DDS) is one of the few ubiquitous phenomena in community ecology. However, the contribution of specialist and generalist fungal species in shaping DDS remains poorly investigated. Through removing operational taxonomic units (OTU) with low or high frequencies, we rigorously quantified the impact of specialists or generalists on the change in slope, initial similarity, and halving distance of DDS of undefined saprotroph, plant mutualist, and plant putative pathogen communities in a 20-ha subtropical evergreen forest plot in Yunnan Province, Southwest China. We hypothesized that (1) the soil fungal co-occurrence networks are different between the three fungal guilds; (2) specialists and generalists contribute to the spatial turnover and nestedness of beta diversity, respectively; and (3) the removal of specialists or generalists will have opposite effects on the change of slope, initial similarity, and halving distance of DDS. Co-occurrence network analysis showed that the undefined saprotroph network had a much more complicated structure than mutualist and pathogen networks. Ascomycota and Basidiomycota were the two most abundant phyla in soil fungal communities. We found that partly in line with our expectations, the change in initial similarity increased and decreased when removing specialists and generalists, respectively, but there was always one exception guild of out of the three communities for the change in slope and halving distance. We identified that such change was mainly due to the change in turnover and nestedness of beta diversity. Furthermore, the results show that species turnover rather than species nestedness drove fungal beta diversity across functional guilds for both specialists and generalists.

Land conversion induced by urbanization leads to taxonomic and functional homogenization of a river macroinvertebrate metacommunity

Conversion of forests to urban land-use in the processes of urbanization is one of the major causes of biotic homogenization (i.e., decline in beta diversity) in freshwater ecosystems, threating ecosystem functioning and services. However, empirical studies exploring urban land-use shaping patterns of taxonomic and functional beta diversities and their components in subtropical urban rivers are limited. Here, by leveraging data for 43 sampling sites from urban and forest rivers in Shenzhen, a megacity showing rapid urbanization, we determined the spatio-temporal dynamics and associated drivers of taxonomic and functional beta diversities of river macroinvertebrates. Our results showed that, from the forest to urban rivers, taxonomic beta diversity (wet: 32.9%; dry: 17.1%) declined more significantly than functional beta diversity (wet: 17.4%; dry: 9.5%) in different seasons. We further found that these compositional changes were largely driven by decreased roles of species/traits replacement. Although replacement was also dominant for taxonomic beta diversity (60.4%-68.4%) in two sets of rivers, richness difference contributed more to functional beta diversity in the urban river (52.6%-60.5%). Both deterministic and stochastic processes simultaneously affected beta diversity, with stochastic processes being more important in the urban (3.0-19.0%) than forest rivers (0.0%-3.0%). Besides, db-RDA and variation partitioning results showed that local-scale environmental variables explained considerably large fractions of variation in beta diversity. We hence recommended that biodiversity conservation should focus on improving and restoring local environmental conditions. Despite no significant seasonal differences in beta diversity were detected in this study, we found that the roles of deterministic (i.e., local-scale and land-use variables) and stochastic processes varied considerately across seasons. This result highlights the viewpoint that urban river biodiversity monitoring should go beyond one-season snapshot surveys. As the ongoing trend of urbanization in developing countries, the findings of this study are relevant in guiding urban river environmental monitoring, biodiversity conservation and land-use planning.

Small Run-of-River Dams Affect Taxonomic and Functional β-Diversity, Community Assembly Process of Benthic Diatoms

Being increasingly constructed worldwide, dams are a main driver of flow regime change and biodiversity decline. Although small run-of-river dams have exceeded the number of large dams, their impacts on taxonomic and functional β-diversity as well as community assembly process of aquatic organisms have been largely neglected. Ninety sites within twenty three small run-of-river dams in the Xiangxi River were selected, and the hydrological and physicochemical variables for each site were measured. We analyzed the traits and β-diversity of benthic diatoms, and explored the key driving mechanism of benthic diatom community assembly. Our results indicated that the construction of small run-of-river dams could affect the β-diversity of benthic diatoms and the mechanism of community assembly. Specifically, we found that small run-of-river dams could change the relative contribution of nestedness components to the trait-based β-diversity of benthic diatoms, but generally the taxonomy-based β-diversity was relatively higher than the trait-based β-diversity. Furthermore, the community assembly process of benthic diatoms was also affected. In areas affected directly by small run-of-river dams, dispersal assembly was the key mechanism for community assembly. Compared to unregulated habitats, the dispersal assembly process between the impacted and the unregulated habitats has been enhanced. We advocate that this study can be expanded to other organisms (such as macroinvertebrates, phytoplankton, fish) in future to fully understand impacts of small run-of-river dams on biodiversity from a multi-trophic level aspect. Based on our results, we suggest that maintaining genetic and ecological connectivity based on an effective impact assessment in dry seasons is a potential solution to mitigate the impacts of such dams, as key to adaptive management and sustainability.

Mapping differences in mammalian distributions and diversity using environmental DNA from rivers

Finding more efficient ways to monitor and estimate the diversity of mammalian communities is a major step towards their management and conservation. Environmental DNA (eDNA) from river water has recently been shown to be a viable method for biomonitoring mammalian communities. Most of the studies to date have focused on the potential for eDNA to detect individual species, with little focus on describing patterns of community diversity and structure. Here, we first focus on the sampling effort required to reliably map the diversity and distribution of semi-aquatic and terrestrial mammals and allow inferences of community structure surrounding two rivers in southeastern England. Community diversity and composition was then assessed based on species richness and β-diversity, with differences between communities partitioned into nestedness and turnover, and the sampling effort required to rapidly detect semi-aquatic and terrestrial species was evaluated based on species accumulation curves and occupancy modelling. eDNA metabarcoding detected 25 wild mammal species from five orders, representing the vast majority (82%) of the species expected in the area. The required sampling effort varied between orders, with common species (generally rodents, deer and lagomorphs) more readily detected, with carnivores detected less frequently. Measures of species richness differed between rivers (both overall and within each mammalian order) and patterns of β-diversity revealed the importance of species replacement in sites within each river, against a pattern of species loss between the two rivers. eDNA metabarcoding demonstrated its capability to rapidly detect mammal species, allowing inferences of community composition that will better inform future sampling strategies for this Class. Importantly, this study highlights the potential use of eDNA data for investigating mammalian community dynamics over different spatial scales.

Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches

Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that despite differences in the number and identity of taxa recorded, both approaches may retrieve comparable patterns of community change, and detect similar ecological gradients influencing such changes. We compared results obtained with morphological identification at family level of macroinvertebrates collected at 80 streams under a Water Framework Directive biomonitoring program in Portugal, with results obtained with metabarcoding from the ethanol preserving the bulk samples, using either single (COI-M19BR2, 16S-Inse01, 18S-Euka02) or multiple markers. Metabarcoding recorded less families and different communities compared to morphotaxonomy, but community sensitivities to disturbance estimated with the IASPT index were more similar across approaches. Spatial variation in local community metrics and the factors influencing such variation were significantly correlated between morphotaxonomy and metabarcoding. After reducing random noise in the dissimilarity matrices, the spatial variation in community composition was also significantly correlated across methods. A dominant gradient of community change was consistently retrieved, and all methods identified a largely similar set of anthropogenic stressors strongly influencing such gradient. Overall, results confirm our initial hypothesis, suggesting that morphotaxonomy and metabarcoding can estimate consistent spatial patterns of community variation and their main drivers. These results are encouraging for macroinvertebrate biomonitoring using metabarcoding approaches, suggesting that they can be intercalibrated with morphotaxonomic approaches to recover equivalent spatial and temporal gradients of ecological change.

Resilience of spider communities affected by a range of silvicultural treatments in a temperate deciduous forest stand

To secure the ecosystem services forests provide, it is important to understand how different management practices impact various components of these ecosystems. We aimed to uncover how silvicultural treatments affected the ground-dwelling spider communities during the first five years of a forest ecological experiment. In an oak-hornbeam forest stand, five treatments, belonging to clear-cutting, shelterwood and continuous cover forestry systems, were implemented using randomised complete block design. Spiders were sampled by pitfall traps, and detailed vegetation, soil and microclimate data were collected throughout the experiment. In the treatment plots spider abundance and species richness increased marginally. Species composition changes were more pronounced and treatment specific, initially diverging from the control plots, but becoming more similar again by the fifth year. These changes were correlated mostly to treatment-related light intensity and humidity gradients. The patchy implementation of the treatments induced modest increase in both gamma and beta diversity of spiders in the stand. Overall, spiders gave a prompt and species specific response to treatments that was by the fifth year showing signs of relatively quick recovery to pre-treatment state. At the present fine scale of implementation the magnitude of changes was not different among forestry treatments, irrespective of their severity.

Beta diversity differs among hydrothermal vent systems: Implications for conservation

Deep-sea hydrothermal vent habitats are small, rare and support unique species through chemosynthesis. As this vulnerable ecosystem is increasingly threatened by human activities, management approaches should address biodiversity conservation. Diversity distribution data provide a useful basis for management approaches as patterns of β-diversity (the change in diversity from site to site) can guide conservation decisions. Our question is whether such patterns are similar enough across vent systems to support a conservation strategy that can be deployed regardless of location. We compile macrofaunal species occurrence data for vent systems in three geological settings in the North Pacific: volcanic arc, back-arc and mid-ocean ridge. Recent discoveries in the Mariana region provide the opportunity to characterize diversity at many vent sites. We examine the extent to which diversity distribution patterns differ among the systems by comparing pairwise β-diversity, nestedness and their additive components. A null model approach that tests whether species compositions of each site pair are more or less similar than random provides insight into community assembly processes. We resolve several taxonomic uncertainties and find that the Mariana arc and back-arc share only 8% of species despite their proximity. Species overlap, species replacement and richness differences create different diversity distributions within the three vent systems; the arc system exhibits much greater β-diversity than both the back-arc and mid-ocean ridge systems which, instead, show greater nestedness. The influence of nestedness on β-diversity also increased from the arc to back-arc to ridge. Community assembly processes appear more deterministic in the arc and ridge systems while back-arc site pairs deviate little from the null expectation. These analyses reflect the need for a variety of management strategies that consider the character of diversity distribution to protect hydrothermal vents, especially in the context of mining hydrothermal deposits.

Decomposing Spatial β-Diversity in the temperate forests of Northeastern China

β-Diversity, which describes the extent of change in species composition in a given region, has become a core issue in ecology in recent years. However, it is hard to understand the underlying mechanisms of β-diversity by using indices that yield identical values under species replacement and nestedness pattern. Partitioning β-diversity into turnover (caused by species replacement among plots) and nestedness components (caused by species loss or gain among plots) may provide improved understanding of the variation in species composition. Here, we collected presence-absence data of 456 one-tenth ha circular plots in the temperate forests of Northeastern China spanning a latitudinal range of 12° (41-53°N). We decomposed β-diversity to assess the relative contribution of the turnover and nestedness components across latitudinal gradients. We used regression analysis to assess the relationship between spatial distance and β-diversity. We applied variation partitioning to evaluate the importance of the measured environmental and spatial variables in explaining β-diversity. We used the Tukey honest significant difference test to test the differences of β-diversity along latitudinal gradients. Pearson correlations (r) and significance (p-value) were computed using the Mantel tests to verify the relationship between distance and β-diversity. The ANOVA test was used to verify whether the variation of β-diversity explained by the environment and distance was significant. Our results showed that (1) β-diversity and the turnover component were higher at low latitudes (zones A and B) than at high latitudes (zones C and D), while there was no relationship between the nestedness component and latitude. (2) The turnover component was dominant. (3) The spatial distance explained more variation of β-diversity than the measured environmental factors. Therefore, we conclude that β-diversity is mainly a product of species turnover in our temperate forests, suggesting that different localities harbor different species. We find that decomposing β-diversity into the turnover and nestedness components is a useful approach to explore the variation of community composition and their causes.

Different patterns in root and soil fungal diversity drive plant productivity of the desert truffle Terfezia claveryi in plantation

The desert truffle Terfezia claveryi is one of the few mycorrhizal fungi currently in cultivation in semiarid and arid areas. Agroclimatic parameters seem to affect its annual yield, but there is no information on the influence of biotic factors. In this study, fungal diversity was analysed by high-throughput sequencing of the ITS2 rDNA region from soil and root samples to compare productive and non-productive mycorrhizal plants in a 4-years old plantation (Murcia, Spain). The fungal metaprofile was dominated by Ascomycota phylum. Desert truffle productivity was driven by different patterns of fungal species composition in soil (species replacement) and root (species richness differences). Moreover, positive associations for ectomycorrhizal and negative for arbuscular mycorrhizal guilds were found in productive roots, and positive associations for fungal parasite-plant pathogen guild in non-productive ones. Soil samples were dominated by pathotroph and saprotroph trophic modes, showing positive associations for Aureobasidium pullulans and Alternaria sp. in productive areas, and positive associations for Fusarium sp. and Mortierella sp. were found in non-productive soils. Finally, some significant OTUs were identified and associated to ascocarp producing patches, which could serve as predictive and location markers of desert truffle production.

Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic

Although microorganisms are the very first colonizers of recently deglaciated soils even prior to plant colonization, the drivers and patterns of microbial community succession at early-successional stages remain poorly understood. The successional dynamics and assembly processes of bacterial and fungal communities were compared on a glacier foreland in the maritime Antarctic across the ~10-year soil-age gradient from bare soil to sparsely vegetated area. Bacterial communities shifted more rapidly than fungal communities in response to glacial retreat; species turnover (primarily the transition from glacier- to soil-favouring taxa) contributed greatly to bacterial beta diversity, but this pattern was less clear in fungi. Bacterial communities underwent more predictable (more deterministic) changes along the soil-age gradient, with compositional changes paralleling the direction of changes in soil physicochemical properties following deglaciation. In contrast, the compositional shift in fungal communities was less associated with changes in deglaciation-induced changes in soil geochemistry and most fungal taxa displayed mosaic abundance distribution across the landscape, suggesting that the successional dynamics of fungal communities are largely governed by stochastic processes. A co-occurrence network analysis revealed that biotic interactions between bacteria and fungi are very weak in early succession. Taken together, these results collectively suggest that bacterial and fungal communities in recently deglaciated soils are largely decoupled from each other during succession and exert very divergent trajectories of succession and assembly under different selective forces.

Does taxonomic and numerical resolution affect the assessment of invertebrate community structure in New World freshwater wetlands?

The efficiency of biodiversity assessments and biomonitoring studies is commonly challenged by limitations in taxonomic identification and quantification approaches. In this study, we assessed the effects of different taxonomic and numerical resolutions on a range of community structure metrics in invertebrate compositional data sets from six regions distributed across North and South America. We specifically assessed the degree of similarity in the metrics (richness, equitability, beta diversity, heterogeneity in community composition and congruence) for data sets identified to a coarse resolution (usually family level) and the finest taxonomic resolution practical (usually genus level, sometimes species or morphospecies) and by presence-absence and relative abundance numerical resolutions. Spearman correlations showed highly significant and positive associations between univariate metrics (richness and equitability) calculated for coarse- and finest-resolution datasets. Procrustes analysis detected significant congruence between composition datasets. Higher correlation coefficients were found for datasets with the same numerical resolutions regardless of the taxonomic level (about 90%), while the correlations for comparisons across numerical resolutions were consistently lower. Our findings indicate that family-level resolution can be used as a surrogate of finer taxonomic resolutions to calculate a range of biodiversity metrics commonly used to describe invertebrate community structure patterns in New World freshwater wetlands without significant loss of information. However, conclusions on biodiversity patterns derived from datasets with different numerical resolutions should be critically considered in studies on wetland invertebrates.

The value of novel ecosystems: Disclosing the ecological quality of quarry lakes

Intense sand and gravel mining has created numerous man-made lakes around the world in the past century. These small quarry lakes (1-50 ha) are usually hydrologically isolated, often deep (6-40 m) and stratify during summer and in cold winters. Due to their small size, these deep man-made lakes are usually not included in the regular monitoring campaigns, e.g. as required for the European Water Framework Directive (WFD). Therefore, not much is known about the ecological functioning of these novel ecosystems. During two summers, we determined the macrophyte diversity and measured a range of physico-chemical and biological parameters in 51 quarry lakes in the catchment area of the rivers Meuse and Rhine. We compared the results of this campaign to the chemical and macrophyte sampling as performed for the WFD in the immediate surrounding shallow standing waters. Alpha (local) and beta diversity (regional), and local contribution to beta diversity were calculated for the whole region of which beta diversity was further partitioned into a true species replacement and richness difference component. Quarry lakes contain higher water quality reflected by lower nutrient and chlorophyll-a concentration compared with shallow water bodies. Additionally, quarry lakes contribute significantly to the regional macrophyte diversity pool by harboring distinctly different macrophyte communities (beta diversity - replacement). Specifically quarry lakes with a total phosphorus concentration in the water column below 35 μg P/l contribute most to beta diversity among quarry lakes. Novel ecosystems such as deep quarry lakes are often perceived as less valuable ecosystems, with strong implications regarding their management. Our results show that quarry lakes are in general of better chemical and biological quality compared with shallow standing waters. We therefore call for a more integrated assessment of the quality of quarry lakes and corresponding management strategy of these waters by water managers.

A multi-faceted comparative perspective on elevational beta-diversity: the patterns and their causes

The observed patterns and underlying mechanisms of elevational beta-diversity have been explored intensively, but multi-dimensional comparative studies remain scarce. Herein, across distinct beta-diversity components, dimensions and species groups, we designed a multi-faceted comparative framework aiming to reveal the general rules in the observed patterns and underlying causes of elevational beta-diversity. We have found that: first, the turnover process dominated altitudinal patterns of species beta-diversity (β_sim > β_sne), whereas the nestedness process appeared relatively more important for elevational trait dissimilarity (β_funcsim < β_funcsne); second, the taxonomic turnover was relative higher than its phylogenetic and functional analogues (β_sim > β_phylosim/β_funcsim), conversely, nestedness-resultant trait dissimilarity tended to be higher than the taxonomic and phylogenetic measures (β_funcsne > β_sne/β_phylosne); and third, as elevational distance increased, the contradicting dynamics of environmental filtering and limiting similarity have jointly led the elevational patterns of beta-diversity, especially at taxonomic dimension. Based on these findings, we infer that the species turnover among phylogenetic relatives sharing similar functional attributes appears to be the main cause of shaping the altitudinal patterns of multi-dimensional beta-diversity. Owing to the methodological limitation in the randomization approach, currently, it remains extremely challenging to distinguish the influence of the neutral process from the offset between opposing niche-based processes. Despite the complexities and uncertainties during species assembling, with a multi-dimensional comparative perspective, this work offers us several important commonalities of elevational beta-diversity dynamics.

Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Damming affects riverine macroinvertebrate metacommunity dynamics: Insights from taxonomic and functional beta diversity

Understanding ecological processes that drive metacommunity dynamics is essential for elucidating the mechanisms of community assembly and for guiding biodiversity conservation. This is especially important in dammed rivers. Here, we examined the taxonomic and functional beta diversity of macroinvertebrates and their underlying drivers in a dammed tropical river and compared the patterns with those in an adjacent undammed river. We found that both taxonomic and functional beta diversities were higher in the dammed river than in the undammed river across wet and dry seasons. The replacement component contributed most to the overall beta diversity for both taxonomic and functional facets, and this component was higher in the dammed river than in the undammed river. In addition, the taxonomic richness difference component was significantly higher in the dammed river in the dry season, but the functional richness difference component showed no difference between the two rivers and between the two seasons. Environmental filtering was the primary driver of total beta diversity and its replacement component, whereas the richness difference component was mainly explained by spatial factors, but these drivers varied in the dammed river in different seasons. Overall, our results indicated that damming induced changes in physiochemical variables (e.g., temperature, conductivity, and nutrients), accompanied by alterations in flow regime and longitudinal connectivity, increased replacement and loss of taxa or traits. These changes have consequently led to alteration of macroinvertebrate taxonomic and functional community dissimilarity and affected the relative effects of environmental and spatial factors on beta diversity and its components. Our study helps understand the ecological processes associated with dam impacts on macroinvertebrate biodiversity and the conservation potential of undammed rivers. In addition, our results showed that taxonomic and functional beta diversities can provide complementary information about dam impacts on riverine biodiversity.

Effects of long-term floodplain disconnection on multiple facets of lake fish biodiversity: Decline of alpha diversity leads to a regional differentiation through time

Hydrological disconnection is increasingly threatening biodiversity in river floodplain ecosystems worldwide, but studies reporting long-term change of aquatic biodiversity in relation to floodplain disconnection are seldom, especially from multifaceted biodiversity perspectives. Here, we examined how loss of river-lake connectivity affected multifaceted (taxonomic, functional and phylogenetic) alpha and beta diversity of fish assemblages in 11 Yangtze River floodplain lakes over the past 70 years. We found that all three facets of alpha diversity significantly decreased through time, but the decrease rate was highest (31.4%) in taxonomic richness, second in functional (26.4%) and lowest in phylogenetic facet (4.7%). Nevertheless, taxonomic, functional and phylogenetic structures of fish fauna all exhibited differentiation. The taxonomic and phylogenetic differentiations were due to the joint increases in their turnover and nestedness-resultant component, whereas the functional differentiation was mainly driven by the increase in its turnover component. Such distinct results were because of the imbalanced extirpations of fish species (especially from species-poor orders and families) in disconnected lakes and connected lakes. With few exceptions of strong correlations between changes in taxonomic dissimilarities and phylogenetic dissimilarities, we generally found weak correlations between changes in different facets of both alpha and beta diversity. This discrepancy highlights that measuring different biodiversity facets offer distinct information about biodiversity dynamics and can enhance our ability to detect and evaluate the impacts of floodplain disconnection on biodiversity. We therefore recommend an integrative approach embracing taxonomic, functional and phylogenetic diversity is essential to effective biodiversity assessment and conservation in large river floodplains.

Distance decay of benthic macroinvertebrate communities in a mountain river network: Do dispersal routes and dispersal ability matter?

Environmental heterogeneity and dispersal limitation are important drivers of beta diversity; however, their relative influence on the two fundamental components of beta diversity (i.e., species replacement and richness difference) has not been fully examined in montane streams. Here, we examined the relative importance of local environmental gradients and three physical distance matrices (i.e., overland, watercourse and cost distances) on beta diversity and its two components for a macroinvertebrate metacommunity in a stream network. To provide additional insights into community assembly, we also analysed variation in two deconstructed sub-communities based on dispersal ability (i.e., weak and strong dispersers). Both environmental filters and physical distances (dispersal limitation) drove patterns of overall beta diversity, with the former generally prevailing over the latter. Species replacement components showed stronger correlations with environmental gradients than physical distances, while the opposite is true for the richness difference components. Overland distances were generally more important than cost and watercourse distances for community dissimilarity of stream macroinvertebrates, implying that lateral dispersal out of stream corridors through flight was the major dispersal route in the studied steam network. As expected, community dissimilarity of strong dispersers was primarily shaped by environmental filtering, while community dissimilarity of weak dispersers was associated with the joint effects of environmental filtering and dispersal limitation. Our findings demonstrate that partitioning overall dissimilarity into species replacement and richness difference provides more insights into the processes driving spatial variability in biological communities compared with the utilization of total beta diversity alone. Our results support the notion that maintaining environmental heterogeneity and natural connectivity of stream networks should be effective measures to conserve regional biodiversity.

Seasonal Patterns Contribute More Towards Phyllosphere Bacterial Community Structure than Short-Term Perturbations

Phyllosphere microorganisms are sensitive to fluctuations in wind, temperature, solar radiation, and rain. However, recent explorations of patterns in phyllosphere communities across time often focus on seasonal shifts and leaf senescence without measuring the contribution of environmental drivers and leaf traits. Here, we focus on the effects of rain on the phyllosphere bacterial community of the wetland macrophyte broadleaf cattail (Typha latifolia) across an entire year, specifically targeting days before and 1, 3, and 5 days after rain events. To isolate the contribution of precipitation from other factors, we covered a subset of plants to shield them from rainfall. We used targeted Illumina sequencing of the V4 region of the bacterial 16S rRNA gene to characterize phyllosphere community composition. Rain events did not have a detectable effect on phyllosphere community richness or evenness regardless of whether the leaves were covered from rain or not, suggesting that foliar microbial communities are robust to such disturbances. While climatic and leaf-based variables effectively modeled seasonal trends in phyllosphere diversity and composition, they provided more limited explanatory value at shorter time scales. These findings underscore the dominance of long-term seasonal patterns related to climatic variation as the main factor influencing the phyllosphere community.