Embracing scale‐dependence to achieve a deeper understanding of biodiversity and its change across communities

Inter-generational consistency of the ectomycorrhizal fungal community in a mixed pine-cedar post-fire stand

The mutualistic interaction between trees and ectomycorrhizal fungi (EMF) can have a major effect on forest dynamics and specifically on seedling establishment. Here, we compared the EMF community composition associated with the roots of young saplings and mature trees of two co-habiting Pinaceae: Pinus halepensis and Cedrus deodara growing together in a post-fire forest plot, using fungal ITS metabarcoding. We found that the differences in the EMF community between the two sapling groups were mostly attributed to changes in the relative abundance of specific fungal species, with little species turnover. Specifically, Tomentella showed high abundance on pine roots, while Tuber, Russula and Sebacina were more common on the roots of cedars. The physical proximity to a specific host species was correlated with the EMF community composition of young saplings. Specifically, regardless of the sapling's own identity, the roots of saplings growing next to mature cedars had higher abundance of Tuber species, while Tomentella coerulea (Höhn. & Litsch), Russula densifolia (Secr. ex Gillet) and Tuber nitidum (Vittadini) dominated saplings next to mature pines. Cedar saplings' shoot structure was correlated with a specific EMF species. Overall, these results suggest that when germinating next to mature trees, the EMF community of saplings could be determined by extrinsic factors such as the small-scale distribution of mature trees in the forest.

Multi-scale beta-diversity patterns in testate amoeba communities: species turnover and nestedness along a latitudinal gradient

The relationship between species diversity and spatial scale is a central topic in spatial community ecology. Latitudinal gradient is among the core mechanisms driving biodiversity distribution on most scales. Patterns of β-diversity along latitudinal gradient have been well studied for aboveground terrestrial and marine communities, whereas soil organisms remain poorly investigated in this regard. The West Siberian Plain is a good model to address diversity scale-dependence since the latitudinal gradient does not overlap with other possible factors such as elevational or maritime. Here, we collected 111 samples following hierarchical sampling (sub-zones, ecosystem types, microhabitat and replicate samples) and performed multi-scale partitioning of β-diversity of testate amoeba assemblages as a model of study. We found that among-ecosystem β-diversity is a leading scale in testate amoeba assemblages variation. Rare species determine β-diversity at all scale levels especially in the northern regions, where rare taxa almost exclusively accounted for the diversity at the ecosystem level. β-Diversity is generally dominated by the turnover component at all scales in lower latitudes, whereas nestedness prevailed at among-ecosystem scale in higher latitudes. These findings indicate that microbial assemblages in northern latitudes are spatially homogeneous and constrained by historical drivers at larger scales, whereas in southern regions, it is dominated by the turnover component both at the microhabitat and ecosystem scales and therefore determined by recent vegetation and environmental heterogeneity. Overall, we have provided the evidence for the existence of negative latitudinal gradient for among-ecosystem β-diversity but not for among-microhabitat and among-sample β-diversity for terrestrial testate amoeba communities.

Land use modulates resistance of grasslands against future climate and inter-annual climate variability in a large field experiment

Climate and land-use change are key drivers of global change. Full-factorial field experiments in which both drivers are manipulated are essential to understand and predict their potentially interactive effects on the structure and functioning of grassland ecosystems. Here, we present 8 years of data on grassland dynamics from the Global Change Experimental Facility in Central Germany. On large experimental plots, temperature and seasonal patterns of precipitation are manipulated by superimposing regional climate model projections onto background climate variability. Climate manipulation is factorially crossed with agricultural land-use scenarios, including intensively used meadows and extensively used (i.e., low-intensity) meadows and pastures. Inter-annual variation of background climate during our study years was high, including three of the driest years on record for our region. The effects of this temporal variability far exceeded the effects of the experimentally imposed climate change on plant species diversity and productivity, especially in the intensively used grasslands sown with only a few grass cultivars. These changes in productivity and diversity in response to alterations in climate were due to immigrant species replacing the target forage cultivars. This shift from forage cultivars to immigrant species may impose additional economic costs in terms of a decreasing forage value and the need for more frequent management measures. In contrast, the extensively used grasslands showed weaker responses to both experimentally manipulated future climate and inter-annual climate variability, suggesting that these diverse grasslands are more resistant to climate change than intensively used, species-poor grasslands. We therefore conclude that a lower management intensity of agricultural grasslands, associated with a higher plant diversity, can stabilize primary productivity under climate change.

Abundance-diversity relationship as a unique signature of temporal scaling in the fossil record

Species diversity increases with the temporal grain of samples according to the species-time relationship (STR), impacting palaeoecological analyses because the temporal grain (time averaging) of fossil assemblages varies by several orders of magnitude. We predict a positive relation between total abundance and sample size-independent diversity (ADR) in fossil assemblages because an increase in time averaging, determined by a decreasing sediment accumulation, should increase abundance and depress species dominance. We demonstrate that, in contrast to negative ADR of non-averaged living assemblages, the ADR of Holocene fossil assemblages is positive, unconditionally or when conditioned on the energy availability gradient. However, the positive fossil ADR disappears when conditioned on sediment accumulation, demonstrating that ADR is a signature of diversity scaling induced by variable time averaging. Conditioning ADR on sediment accumulation can identify and remove the scaling effect caused by time averaging, providing an avenue for unbiased biodiversity comparisons across space and time.

Biodiversity increases resistance of grasslands against plant invasions under multiple environmental changes

Biodiversity often helps communities resist invasion. However, it is unclear whether this diversity-invasion relationship holds true under environmental changes. Here, we conduct a meta-analysis of 1010 observations from 25 grassland studies in which plant species richness is manipulated together with one or more environmental change factors to test invasibility (measured by biomass or cover of invaders). We find that biodiversity increases resistance to invaders across various environmental conditions. However, the positive biodiversity effect on invasion resistance is strengthened under experimental warming, whereas it is weakened under experimentally imposed drought. When multiple factors are imposed simultaneously, the positive biodiversity effect is strengthened. Overall, we show that biodiversity helps grassland communities resist plant invasions under multiple environmental changes. Therefore, investment in the protection and restoration of native biodiversity is not only important for prevention of invasions under current conditions but also under continued global environmental change.

A new perspective on the spatial, environmental, and metacommunity controls of local biodiversity

Influential ecological research in the 1980s, elucidating that local biodiversity (LB) is a function of local ecological factors and the size of the regional species pool (γ-diversity), has prompted numerous investigations on the local and regional origins of LB. These investigations, however, have been mostly limited to single scales and target groups and centered exclusively on γ-diversity. Here we developed a unified framework including scale, environmental factors (heterogeneity and ambient levels), and metacommunity properties (intraspecific spatial aggregation, regional evenness, and γ-diversity) as hierarchical predictors of LB. We tested this framework with variance partitioning and structural equation modeling using subcontinental data on stream diatoms, insects, and fish as well as local physicochemistry, climate, and land use. Pure aggregation + regional evenness outperformed pure γ-diversity in explaining LB across groups. The covariance of the environment with aggregation + regional evenness rather than with γ-diversity generally explained a much greater proportion of the variance in diatom and insect LB, especially at smaller scales. Thus, disregarding aggregation and regional evenness, as commonly done, may lead to gross underestimation of the pure metacommunity effects and the indirect environmental effects on LB. We examined the shape of the local-regional species richness relationship, which has been widely used to infer local vs. regional effects on LB. We showed that this shape has an ecological basis, but its interpretation is not straightforward. Therefore, we advocate that the variance partitioning analysis under the proposed framework is adopted instead. In diatoms, metacommunity properties had the greatest total effects on LB, while in insects and fish, it was the environment, suggesting that larger organisms are more strongly controlled by the environment. Broader use of our framework may lead to novel biogeographical insights into the drivers of LB and improved projections of its trends along current and future environmental gradients.

Correlation between intestinal flora and GLP-1 receptor agonist dulaglutide in type 2 diabetes mellitus treatment-A preliminary longitudinal study

GLP-1 receptor agonists (GLP-1 RA) are presently used as the first-line drugs for the clinical treatment of type 2 diabetes mellitus (T2DM). It can regulate blood glucose by stimulating insulin secretion and lowering glucagon levels. We used 16S rRNA amplicon sequencing to detect structural changes in the composition of the intestinal flora of newly diagnosed T2DM after 1 and 48 weeks of dulaglutide administration. Our research found no significant changes in the intestinal flora after the administration of dulaglutide for 1 week to subjects with newly diagnosed T2DM. Nevertheless, after 48 weeks of dulaglutide administration, the composition of the intestinal flora changed significantly, with a significant reduction in the abundance of intestinal flora. Furthermore, we found that fasting glucose levels, fasting c-peptide levels, HbA1c levels, and BMI are also closely associated with intestinal flora. This reveals that intestinal flora may be one of the mechanisms by which dulaglutide treats T2DM.

How do species richness and its component dependence vary along the natural restoration in extremely heterogeneous forest ecosystems?

Giant habitat heterogeneity is an important factor contributing to the high species richness (SR) in karst forests. Yet, the driving factor behind the alterations in SR patterns during natural restoration remains unclear. In this study, we established the forest dynamics plots along the natural restoration sequence (including shrub-tree mixed forest stage (SC), secondary forest stage (SG) and old-growth forest sage (OG)) in degraded karst forests to compare the SR and the dependence on its components (including total community abundance, species abundance distribution (SAD), and conspecific spatial aggregation (CSA)) among stages of natural restoration. By evaluating the degree of contribution of the components to local SR and rarefied SR, we found that the SG exhibited the highest local SR, while the rarefied SR remained increasing along the restoration sequence after controlling the sample size. At SC-SG stage, SAD and CSA contributed negatively to the differences in SR, while abundance made a positive contribution to SR differences. At SG-OG, abundance contributed positively to the difference in SR at all scales, while SAD contributed negatively at small scales. No significant contribution of CSA was found at observed scales. In addition, local SR varied more significantly with PIE than with abundance. Our research emphasizes the importance of eliminating the influence of abundance on species richness in forest ecology and management, as well as the significance of separately evaluating the components that shape the diversity patterns.

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

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

Temporal change in urban fish biodiversity-Gains, losses, and drivers of change

Our aim was to examine temporal change in alpha and beta diversity of freshwater fish communities in rivers that have urbanized over the same period to understand the influence of changes in land use and river connectivity on community change. We used biological (2001-2018), land use (2000-2015), and connectivity data (1987-2017) from Toronto, Ontario, Canada. We used linear mixed effects models to determine the strength of upstream land use, connectivity, and their changes over time to explain temporal change in alpha and beta diversity indices. We examined beta diversity using the temporal beta diversity index (TBI) to assess site-specific community change. The TBI was partitioned into gains and losses, and species-specific changes in abundance were assessed using paired t-tests. There were more gains than losses across the study sites as measured by TBI. We found little to no significant differences in species-specific abundances at aggregated spatial scales (study region, watershed, stream order). We found different relationships between landscape and connectivity variables with the biodiversity indices tested; however, almost all estimated confidence intervals overlapped with zero and had low goodness-of-fit. More fish biodiversity gains than losses were found across the study region, as measured by TBI. We found TBI to be a useful indicator of change as it identifies key sites to further investigate. We found two high value TBI sites gained non-native species, and one site shifted from a cool-water to warm-water species dominated community, both of which have management implications. Upstream catchment land use and connectivity had poor explanatory power for change in the measured biodiversity indices. Ultimately, such spatial-temporal datasets are invaluable and can reveal trends in biodiversity useful for environmental management when considering competing interests involved with urban sprawl in the ongoing "Decade on Restoration."

Species-area relationships in microbial-mediated mutualisms

Symbioses involving microorganisms prevail in nature and are key to regulating numerous ecosystem processes and in driving evolution. A major concern in understanding the ecology of symbioses involving microorganisms arises in the effectiveness of sampling strategies to capture the contrasting size of organisms involved. In many mutualisms, including mycorrhizas and gut systems, hosts interact simultaneously with multiple smaller sized mutualists, the identity of which determines success for the host. This complicates quantifying the diversity of mutualisms because sampling techniques fail to capture effectively the diversity of each partner. Here we propose the use of species-area relationships (SARs) to explicitly consider the spatial scale of microbial partners in symbioses, which we propose will improve our understanding of the ecology of mutualisms.

Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain

Belowground bacterial communities play essential roles in maintaining ecosystem multifunction, while our understanding of how and why their distribution patterns and community compositions may change with the distinct pedogenetic conditions of different soil types is still limited. Here, we evaluated the roles of soil physiochemical properties and biotic interactions in driving belowground bacterial community composition across three typical zonal soil types, including black calcium soil (QS), typical black soil (HL) and dark brown soil (BQL), with distinct pedogenesis on the Northeast China Plain. Changes in soil bacterial diversity and community composition in these three zonal soil types were strongly correlated with soil pedogenetic features. SOC concentrations in HL were higher than in QS and BQL, but bacterial diversity was low, and the network structure revealed greater stability and connectivity. The composition of the bacterial community correlated significantly with soil pH in QS but with soil texture in BQL. The bacterial co-occurrence network of HL had higher density and clustering coefficients but lower edges, and different keystone species of networks were also detected. This work provides a basic understanding of the driving mechanisms responsible for belowground bacterial biodiversity and distribution patterns over different pedogenetic conditions in agroecosystems.

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.

Looking back on biodiversity change: lessons for the road ahead

Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

Toward a cohesive understanding of ecological complexity

Ecological systems are quintessentially complex systems. Understanding and being able to predict phenomena typical of complex systems is, therefore, critical to progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity and excessive reliance on conventional scientific approaches hamper conceptual advances and synthesis. Ecological complexity may be better understood by following the solid theoretical basis of complex system science (CSS). We review features of ecological systems described within CSS and conduct bibliometric and text mining analyses to characterize articles that refer to ecological complexity. Our analyses demonstrate that the study of complexity in ecology is a highly heterogeneous, global endeavor that is only weakly related to CSS. Current research trends are typically organized around basic theory, scaling, and macroecology. We leverage our review and the generalities identified in our analyses to suggest a more coherent and cohesive way forward in the study of complexity in ecology.

Unveiling the transition from niche to dispersal assembly in ecology

A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory^1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory^3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies^3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a 'niche detector' and a tool for assessing when communities are niche versus dispersal assembled.

Parasites indicate trophic complexity and faunal succession in restored oyster reefs over a 22-year period

Foundation species like the eastern oyster (Crassostrea virginica) create complex habitats for organisms across multiple trophic levels. Historic declines in oyster abundance have prompted decades of restoration efforts. However, it remains unclear how long it takes for restored reefs to resemble the trophic complexity of natural reefs. We used a space-for-time approach to examine community succession of restored reefs ranging in age from 3 to 22 years old in coastal North Carolina, surveying both free-living taxa and parasite communities and comparing them to natural reefs that are decades old. Trophically transmitted parasites can serve as valuable biodiversity surrogates, sometimes providing greater information about a system or question than their free-living counterparts. We found that the diversity of free-living taxa was highly variable and did not differ among new (<10 years), old (20 years), and natural reefs. Conversely, parasite diversity increased with elapsed time after restoration, and parasite communities in older restored reefs resembled those found in natural reefs. Our study also revealed that oyster toadfish (Opsanus tau) act as a key host species capable of facilitating parasite transmission and trophic ascent in oyster reef food webs. Overall, our results suggest that trophic complexity in restored oyster reefs requires at least 8 years to resemble that found in natural reefs. This work adds to a growing body of evidence demonstrating how parasites can serve as biodiversity surrogates, proxies for the presence of additional taxa that are often difficult or impractical to sample. Given the multiplicity of links formed with their hosts, parasites offer a powerful tool for quantifying diversity and trophic complexity in environmental monitoring studies.

Combining environmental niche models, multi-grain analyses, and species traits identifies pervasive effects of land use on butterfly biodiversity across Italy

Understanding how species respond to human activities is paramount to ecology and conservation science, one outstanding question being how large-scale patterns in land use affect biodiversity. To facilitate answering this question, we propose a novel analytical framework that combines environmental niche models, multi-grain analyses, and species traits. We illustrate the framework capitalizing on the most extensive dataset compiled to date for the butterflies of Italy (106,514 observations for 288 species), assessing how agriculture and urbanization have affected biodiversity of these taxa from landscape to regional scales (3-48 km grains) across the country while accounting for its steep climatic gradients. Multiple lines of evidence suggest pervasive and scale-dependent effects of land use on butterflies in Italy. While land use explained patterns in species richness primarily at grains ≤12 km, idiosyncratic responses in species highlighted "winners" and "losers" across human-dominated regions. Detrimental effects of agriculture and urbanization emerged from landscape (3-km grain) to regional (48-km grain) scales, disproportionally affecting small butterflies and butterflies with a short flight curve. Human activities have therefore reorganized the biogeography of Italian butterflies, filtering out species with poor dispersal capacity and narrow niche breadth not only from local assemblages, but also from regional species pools. These results suggest that global conservation efforts neglecting large-scale patterns in land use risk falling short of their goals, even for taxa typically assumed to persist in small natural areas (e.g., invertebrates). Our study also confirms that consideration of spatial scales will be crucial to implementing effective conservation actions in the Post-2020 Global Biodiversity Framework. In this context, applications of the proposed analytical framework have broad potential to identify which mechanisms underlie biodiversity change at different spatial scales.

Latitudinal patterns of forest ecosystem stability across spatial scales as affected by biodiversity and environmental heterogeneity

Our planet is facing a variety of serious threats from climate change that are unfolding unevenly across the globe. Uncovering the spatial patterns of ecosystem stability is important for predicting the responses of ecological processes and biodiversity patterns to climate change. However, the understanding of the latitudinal pattern of ecosystem stability across scales and of the underlying ecological drivers is still very limited. Accordingly, this study examines the latitudinal patterns of ecosystem stability at the local and regional spatial scale using a natural assembly of forest metacommunities that are distributed over a large temperate forest region, considering a range of potential environmental drivers. We found that the stability of regional communities (regional stability) and asynchronous dynamics among local communities (spatial asynchrony) both decreased with increasing latitude, whereas the stability of local communities (local stability) did not. We tested a series of hypotheses that potentially drive the spatial patterns of ecosystem stability, and found that although the ecological drivers of biodiversity, climatic history, resource conditions, climatic stability, and environmental heterogeneity varied with latitude, latitudinal patterns of ecosystem stability at multiple scales were affected by biodiversity and environmental heterogeneity. In particular, α diversity is positively associated with local stability, while β diversity is positively associated with spatial asynchrony, although both relationships are weak. Our study provides the first evidence that latitudinal patterns of the temporal stability of naturally assembled forest metacommunities across scales are driven by biodiversity and environmental heterogeneity. Our findings suggest that the preservation of plant biodiversity within and between forest communities and the maintenance of heterogeneous landscapes can be crucial to buffer forest ecosystems at higher latitudes from the faster and more intense negative impacts of climate change in the future.

Introduction of non-native Douglas fir reduces leaf damage on beech saplings and mature trees in European beech forests

Recent ecological research suggests that, in general, mixtures are more resistant to insect herbivores and pathogens than monocultures. However, we know little about mixtures with non-native trees, where enemy release could lead to patterns that differ from commonly observed relationships among native species. This becomes particularly relevant when considering that adaptation strategies to climate change increasingly promote a larger share of non-native tree species, such as North American Douglas fir in Central Europe. We studied leaf damage on European beech (Fagus sylvatica) saplings and mature trees across a wide range of site conditions in monocultures and mixtures with phylogenetically distant conifers native Norway spruce (Picea abies) and non-native Douglas fir (Pseudotsuga menziesii). We analyzed leaf herbivory and pathogen damage in relation to tree diversity and composition effects, as well as effects of environmental factors and plant characteristics. We observed lower sapling herbivory and tree sucking damage on beech in non-native Douglas fir mixtures than in beech monocultures, probably due to a lower herbivore diversity on Douglas fir trees, and higher pathogen damage on beech saplings in Norway spruce than Douglas fir mixtures, possibly because of higher canopy openness. Our findings suggest that for low diversity gradients, tree diversity effects on leaf damage can strongly depend on tree species composition, in addition to modifications caused by feeding guild and tree ontogeny. Moreover, we found that nutrient capacity modulated the effects of tree diversity, composition, and environmental factors, with different responses in sites with low or high nutrient capacity. The existence of contrasting diversity effects based on tree species composition provides important information on our understanding of the relationships between tree diversity and plant-herbivore interactions in light of non-native tree species introductions. Especially with recent Norway spruce die-off, the planting of Douglas fir as replacement is likely to strongly increase in Central Europe. Our findings suggest that mixtures with Douglas fir could benefit the survival or growth rates of beech saplings and mature trees due to lower leaf damage, emphasizing the need to clearly identify and compare the potential benefits and ecological trade-offs of non-native tree species in forest management under ongoing environmental change.

Two dominant forms of multisite similarity decline - Their origins and interpretation

The number of species shared by two or more sites is a fundamental measure of spatial variation in species composition. As more sites are included in the comparison of species composition, the average number of species shared across them declines, with a rate increasingly dependent on only the most widespread species. In over 80% of empirical communities, models of decline in shared species across multiple sites (multisite similarity decline) follow one of two distinct forms. An exponential form is assumed to reflect stochastic assembly and a power law form niche-based sorting, yet these explanations are largely untested, and little is known of how the two forms arise in nature. Using simulations, we first show that the distribution of the most widespread species largely differentiates the two forms, with the power law increasingly favored where such species occupy more than ~75% of sites. We reasoned the less cosmopolitan distribution of widespread species within exponential communities would manifest as differences in community biodiversity properties, specifically more aggregated within-species distributions, less even relative abundance distributions, and weaker between-species spatial associations. We tested and largely confirmed these relationships using 80 empirical datasets, suggesting that the form of multisite similarity decline offers a basis to predict how landscape-scale loss or gain of widespread species is reflected in different local-scale community structures. Such understanding could, for example, be used to predict changes in local-scale competitive interactions following shifts in widespread species' distributions. We propose multiple explanations for the origin of exponential decline, including high among-site abiotic variation, sampling of highly specialized (narrow niche width) taxa, and strong dispersal limitation. We recommend these are evaluated as alternative hypotheses to stochastic assembly.

Abundance trends for river macroinvertebrates vary across taxa, trophic group and river typology

There is mounting evidence that terrestrial arthropods are declining rapidly in many areas of the world. It is unclear whether freshwater invertebrates, which are key providers of ecosystem services, are also declining. We addressed this question by analysing a long-term dataset of macroinvertebrate abundance collected from 2002 to 2019 across 5009 sampling sites in English rivers. Patterns varied markedly across taxonomic groups. Within trophic groups we detected increases in the abundance of carnivores by 19% and herbivores by 14.8%, while we estimated decomposers have declined by 21.7% in abundance since 2002. We also found heterogeneity in trends across rivers belonging to different typologies based on geological dominance and catchment altitude, with organic lowland rivers having generally higher rates of increase in abundance across taxa and trophic groups, with siliceous lowland rivers having the most declines. Our results reveal a complex picture of change in freshwater macroinvertebrate abundance between taxonomic groups, trophic levels and river typologies. Our analysis helps with identifying priority regions for action on potential environmental stressors where we discover macroinvertebrate abundance declines.

The Rise of Gastrointestinal Cancers as a Global Phenomenon: Unhealthy Behavior or Progress?

The overall burden of cancer is rapidly increasing worldwide, reflecting not only population growth and aging, but also the prevalence and spread of risk factors. Gastrointestinal (GI) cancers, including stomach, liver, esophageal, pancreatic, and colorectal cancers, represent more than a quarter of all cancers. While smoking and alcohol use are the risk factors most commonly associated with cancer development, a growing consensus also includes dietary habits as relevant risk factors for GI cancers. Current evidence suggests that socioeconomic development results in several lifestyle modifications, including shifts in dietary habits from local traditional diets to less-healthy Western diets. Moreover, recent data indicate that increased production and consumption of processed foods underlies the current pandemics of obesity and related metabolic disorders, which are directly or indirectly associated with the emergence of various chronic noncommunicable conditions and GI cancers. However, environmental changes are not restricted to dietary patterns, and unhealthy behavioral features should be analyzed with a holistic view of lifestyle. In this review, we discussed the epidemiological aspects, gut dysbiosis, and cellular and molecular characteristics of GI cancers and explored the impact of unhealthy behaviors, diet, and physical activity on developing GI cancers in the context of progressive societal changes.

Landscape-scale habitat fragmentation is positively related to biodiversity, despite patch-scale ecosystem decay

Positive effects of habitat patch size on biodiversity are often extrapolated to infer negative effects of habitat fragmentation on biodiversity at landscape scales. However, such cross-scale extrapolations typically fail. A recent, landmark, patch-scale analysis (Chase et al., 2020, Nature 584, 238-243) demonstrates positive patch size effects on biodiversity, that is, 'ecosystem decay' in small patches. Other authors have already extrapolated this result to infer negative fragmentation effects, that is, higher biodiversity in a few large than many small patches of the same cumulative habitat area. We test whether this extrapolation is valid. We find that landscape-scale patterns are opposite to their analogous patch-scale patterns: for sets of patches with equal total habitat area, species richness and evenness decrease with increasing mean size of the patches comprising that area, even when considering only species of conservation concern. Preserving small habitat patches will, therefore, be key to sustain biodiversity amidst ongoing environmental crises.

The supply of multiple ecosystem services requires biodiversity across spatial scales

The impact of local biodiversity loss on ecosystem functioning is well established, but the role of larger-scale biodiversity dynamics in the delivery of ecosystem services remains poorly understood. Here we address this gap using a comprehensive dataset describing the supply of 16 cultural, regulating and provisioning ecosystem services in 150 European agricultural grassland plots, and detailed multi-scale data on land use and plant diversity. After controlling for land-use and abiotic factors, we show that both plot-level and surrounding plant diversity play an important role in the supply of cultural and aboveground regulating ecosystem services. In contrast, provisioning and belowground regulating ecosystem services are more strongly driven by field-level management and abiotic factors. Structural equation models revealed that surrounding plant diversity promotes ecosystem services both directly, probably by fostering the spill-over of ecosystem service providers from surrounding areas, and indirectly, by maintaining plot-level diversity. By influencing the ecosystem services that local stakeholders prioritized, biodiversity at different scales was also shown to positively influence a wide range of stakeholder groups. These results provide a comprehensive picture of which ecosystem services rely most strongly on biodiversity, and the respective scales of biodiversity that drive these services. This key information is required for the upscaling of biodiversity-ecosystem service relationships, and the informed management of biodiversity within agricultural landscapes.

Individual species and site dynamics are the main drivers of spatial scaling of stability in aquatic communities

Introduction

Any measure of ecological stability scales with the spatial and temporal extent of the data on which it is based. The magnitude of stabilization effects at increasing spatial scale is determined by the degree of synchrony between local and regional species populations.

Methods

We applied two recently developed approaches to quantify these stabilizing effects to time series records from three aquatic monitoring data sets differing in environmental context and organism type.

Results and Discussion

We found that the amount and general patterns of stabilization with increasing spatial scale only varied slightly across the investigated species groups and systems. In all three data sets, the relative contribution of stabilizing effects via asynchronous dynamics across space was higher than compensatory dynamics due to differences in biomass fluctuations across species and populations. When relating the stabilizing effects of individual species and sites to species and site-specific characteristics as well as community composition and aspects of spatial biomass distribution patterns, however, we found that the effects of single species and sites showed large differences and were highly context dependent, i.e., dominant species can but did not necessarily have highly stabilizing or destabilizing effects on overall community biomass. The sign and magnitude of individual contributions depended on community structure and the spatial distribution of biomass and species in space. Our study therefore provides new insights into the mechanistic understanding of ecological stability patterns across scales in natural species communities.

Applying landscape metrics to species distribution model predictions to characterize internal range structure and associated changes

Distributional shifts in species ranges provide critical evidence of ecological responses to climate change. Assessments of climate-driven changes typically focus on broad-scale range shifts (e.g. poleward or upward), with ecological consequences at regional and local scales commonly overlooked. While these changes are informative for species presenting continuous geographic ranges, many species have discontinuous distributions-both natural (e.g. mountain or coastal species) or human-induced (e.g. species inhabiting fragmented landscapes)-where within-range changes can be significant. Here, we use an ecosystem engineer species (Sabellaria alveolata) with a naturally fragmented distribution as a case study to assess climate-driven changes in within-range occupancy across its entire global distribution. To this end, we applied landscape ecology metrics to outputs from species distribution modelling (SDM) in a novel unified framework. SDM predicted a 27.5% overall increase in the area of potentially suitable habitat under RCP 4.5 by 2050, which taken in isolation would have led to the classification of the species as a climate change winner. SDM further revealed that the latitudinal range is predicted to shrink because of decreased habitat suitability in the equatorward part of the range, not compensated by a poleward expansion. The use of landscape ecology metrics provided additional insights by identifying regions that are predicted to become increasingly fragmented in the future, potentially increasing extirpation risk by jeopardising metapopulation dynamics. This increased range fragmentation could have dramatic consequences for ecosystem structure and functioning. Importantly, the proposed framework-which brings together SDM and landscape metrics-can be widely used to study currently overlooked climate-driven changes in species internal range structure, without requiring detailed empirical knowledge of the modelled species. This approach represents an important advancement beyond predictive envelope approaches and could reveal itself as paramount for managers whose spatial scale of action usually ranges from local to regional.

The community ecology perspective of omics data

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.

How does invasion degree shape alpha and beta diversity of freshwater fish at a regional scale?

Freshwater ecosystems appear more vulnerable to biodiversity loss due to several anthropogenic disturbances and freshwater fish are particularly vulnerable to these impacts. We aimed to (1) identify the contribution of land use, spatial variables, and invasion degree in determining freshwater fish alpha (i.e., species richness) and beta (i.e., local contributions to beta diversity, LCBD) diversity, evaluating also the relationship between invasion degree and nestedness (β nes) and turnover (β sim) components of beta diversity. (2) Investigate the relationship between alpha diversity and LCBD, under the hypothesis that alpha diversity and LCBD correlate negatively and (3) investigate the relationship between species contributions to beta diversity (SCBD) and species occurrence, hypothesizing that non-native species show a lower contribution to beta diversity. The linear mixed models and the partition of R 2 retained the invasion degree as the most important variables explaining alpha and beta diversity, having a positive relationship with both diversity components. Furthermore, land use related to human impacts had a positive influence on alpha diversity, whereas it showed a negative effect on LCBD. Regression model further showed that invasion degree related positively withβ sim, but negatively withβ nes, suggesting that non-native species were involved in the replacement of native species in the fish community. Alpha diversity and LCBD showed a weak positive correlation, meaning that sites with low species richness have higher LCBD. SCBD scaled positively with species occurrence highlighting that rarer species contribute less to SCBD. Finally, native and exotic species contributed similarly to beta diversity. These results suggest that invasion degree plays a central role in shaping alpha and beta diversity in stream fish, more than land use features reflecting habitat alteration or other geospatial variables. Furthermore, it is important to evaluate separately the native and the non-native components of biotic communities to identify linkages between invasion dynamics and biodiversity loss.

Beta diversity as a driver of forest biomass across spatial scales

Despite the importance of biodiversity-ecosystem functioning (BEF) relationships in ecology and conservation, relatively little is known about how BEF relationships change across spatial scales. Theory predicts that change in BEF relationships with increasing spatial scale will depend on variation in species composition across space (β-diversity), but empirical evidence for this is limited. Moreover, studies have not quantified the direct and indirect role the environment plays in costructuring ecosystem functioning across spatial scales. We used 14 temperate-forest plots 1.4 ha in size containing 18,323 trees to quantify scale-dependence between aboveground tree biomass and three components of tree-species diversity-α-diversity (average local diversity), γ-diversity (total diversity), and β-diversity. Using structural-equation models, we quantified the direct effects of each diversity component and the environment (soil nutrients and topography), as well as indirect effects of the environment, on tree biomass across 11 spatial extents ranging from 400 to 14,400 m² . Our results show that the relationship between β-diversity and tree biomass strengthened with increasing spatial extent. Moreover, β-diversity appeared to be a stronger predictor of biomass than α-diversity and γ-diversity at intermediate to large spatial extents. The environment had strong direct and indirect effects on biomass, but, in contrast to diversity, these effects did not strengthen with increasing spatial extent. This study provides some of the first empirical evidence that β-diversity underpins the scaling of BEF relationships in naturally complex ecosystems.

Species accumulation in small–large vs large–small order: more species but not all species?

Although groups of small habitat patches often support more species than large patches of equal total area, their biodiversity value remains controversial. An important line of evidence in this debate compares species accumulation curves, where patches are ordered from small–large and large–small (aka ‘SLOSS analysis’). However, this method counts species equally and is unable to distinguish patch size dependence in species’ occupancies. Moreover, because of the species–area relationship, richness differences typically only contribute to accumulation in small–large order, maximizing the probability of adding species in this direction. Using a null model to control for this, I tested 202 published datasets from archipelagos, habitat islands and fragments for patch size dependence in species accumulation and compared conclusions regarding relative species accumulation with SLOSS analysis. Relative to null model expectations, species accumulation was on average 2.7% higher in large–small than small–large order. The effect was strongest in archipelagos (5%), intermediate for fragments (1.5%) and smallest for habitat islands (1.1%). There was no difference in effect size among taxonomic groups, but each shared this same trend. Results suggest most meta-communities include species that either prefer, or depend upon, larger habitat patches. Relative to SLOSS analysis, null models found lower frequency of greater small-patch importance for species representation (e.g., for fragments: 69 vs 16% respectively) and increased frequency for large patches (fragments: 3 vs 25%). I suggest SLOSS analysis provides unreliable inference on species accumulation and the outcome largely depends on island species–area relationships, not the relative diversity value of small vs large patches.

The Role of Habitat Amount and Vegetation Density for Explaining Loss of Small-Mammal Diversity in a South American Woodland Savanna

The focus of research and conservation in tropical regions is mainly devoted to forest ecosystems, usually neglecting the processes underlying widespread, more open biomes, like savannas. Here we test a wide range of sampled woodland sites across the South American savanna for the direct and indirect effects of habitat loss and vegetation density on the diversity of small-mammal species. We quantify the direction and magnitude of the effects of habitat amount (habitat loss), vegetation density (tree or foliage density), and patch size (species-area effect) on species composition and richness. We also test whether the relative effect sizes of landscape and patch-related metrics predict a persistence gradient from habitat specialist to generalist species across 54 sites. We used structural equation models (SEM) to test our predictions. After 22,032 trap-nights considering all sampled sites and 20 small-mammal species identified, the structural equation model explained 23.5% of the variance in the richness of small-mammal species. Overall, we found that landscape-level metrics were more important in explaining species richness, with a secondary role of patch-level metrics such as vegetation density. The direct effect of local landscape was significant for explaining species richness variation, but a strong positive association between regional and local landscapes was also present. Furthermore, considering the direct and indirect paths, SEM explained 46.2% of the species composition gradient. In contrast to species richness, we recorded that the combined landscape-level and patch-level metrics are crucial to determining small-mammal species composition at savanna patches. The small mammals from the South American woodland savanna exhibit clear ecological gradients on their species composition and richness, driven by habitat specialist (e.g., Thrichomys fosteri, Monodelphis domestica, and Thylamys macrurus) and generalist (e.g., Didelphis albiventris, Rhipidomys macrurus, and Calomys callosus) species’ responses to habitat amount and/or vegetation density, as seen in dense-forest Neotropical biomes.

How does variation in total and relative abundance contribute to gradients of species diversity?

Patterns of biodiversity provide insights into the processes that shape biological communities around the world. Variation in species diversity along biogeographical or ecological gradients, such as latitude or precipitation, can be attributed to variation in different components of biodiversity: changes in the total abundance (i.e., more-individual effects) and changes in the regional species abundance distribution (SAD). Rarefaction curves can provide a tool to partition these sources of variation on diversity, but first must be converted to a common unit of measurement. Here, we partition species diversity gradients into components of the SAD and abundance using the effective number of species (ENS) transformation of the individual-based rarefaction curve. Because the ENS curve is unconstrained by sample size, it can act as a standardized unit of measurement when comparing effect sizes among different components of biodiversity change. We illustrate the utility of the approach using two data sets spanning latitudinal diversity gradients in trees and marine reef fish and find contrasting results. Whereas the diversity gradient of fish was mostly associated with variation in abundance (86%), the tree diversity gradient was mostly associated with variation in the SAD (59%). These results suggest that local fish diversity may be limited by energy through the more-individuals effect, while species pool effects are the larger determinant of tree diversity. We suggest that the framework of the ENS-curve has the potential to quantify the underlying factors influencing most aspects of diversity change.

Tree Species Biodiversity in Small Ukrainian Towns

Biodiversity is one of the important indicators of ecosystem sustainability, which is less studied in relation to urban areas, particularly Ukraine, and even more so in small towns. Taking the example of three small Ukrainian towns, the biodiversity of tree species is compared in the article. The studied small towns are located in two geographic zones, mixed forests (Polissya) and forest-steppe, and administratively, in Chernihiv and Kyiv regions. An inventory of trees in the residential area of Ukrainka, in the central streets of Novhorod-Siverskyi, as well as in the central part and all streets of Vyshhorod was conducted. Thus, the species richness of trees both between the studied towns and between its central part and the whole territory of the town was compared. The species structure of tree plantings in terms of richness, diversity, dominance, alignment, and similarity was assessed. The obtained results were subjected to cluster and correlation analysis. It was found that the greatest diversity is characteristic for the dendroflora of the whole territory of Vyshhorod, which is the fastest growing town, located closest to the capital. The dendrofloras of small towns were quite similar to each other. The values of similarity indices varied in a wide range: Jacquard’s index from 0.26 to 0.56 and Sørensen index from 0.41 to 0.66. The lowest degree of similarity was found with the dendroflora of the most distant Novgorod-Siverskyi town. Mainly the urban plantings require enrichment of the tree species composition, taking into account their resistance to anthropogenic impacts and climate change.

The relative influence of history, climate, topography and vegetation structure on local animal richness varies among taxa and spatial grains

1. Understanding the spatial scales at which environmental factors drive species richness patterns is a major challenge in ecology. Due to the trade-off between spatial grain and extent, studies tend to focus on a single spatial scale, and the effects of multiple environmental variables operating across spatial scales on the pattern of local species richness have rarely been investigated. 2. Here, we related variation in local species richness of ground beetles, landbirds, and small mammals to variation in vegetation structure and topography, regional climate, biome diversity, and glaciation history for 27 sites across the USA at two different spatial grains. 3. We studied the relative influence of broad-scale (landscape) environmental conditions using variables estimated at the site level (climate, productivity, biome diversity, and glacial era ice cover) and fine-scale (local) environmental conditions using variables estimated at the plot level (topography and vegetation structure) to explain local species richness. We also examined whether plot-level factors scale up to drive continental scale richness patterns. We used Bayesian hierarchical models and quantified the amount of variance in observed richness that was explained by environmental factors at different spatial scales. 4. For all three animal groups, our models explained much of the variation in local species richness (85-89%), but site-level variables explained a greater proportion of richness variance than plot-level variables. Temperature was the most important site-level predictor for explaining variance in landbirds and ground beetles richness. Some aspects of vegetation structure were the main plot-level predictors of landbird richness. Environmental predictors generally had poor explanatory power for small mammal richness, while glacial era ice cover was the most important site-level predictor. 5. Relationships between plot-level factors and richness varied greatly among geographical regions and spatial grains, and most relationships did not hold when predictors were scaled up to continental scale. Our results suggest that the factors that determine richness may be highly dependent on spatial grain, geography, and animal group. We demonstrate that instead of artificially manipulating the resolution to study multi-scale effects, a hierarchical approach that uses fine grain data at broad extents could help solve the issue of scale selection in environment-richness studies.

Metagenomics uncovers the effect of nitrogen-doped graphene on anammox consortia and microbial function

The effect of 50 mg/L nitrogen-doped graphene (N-G) on anammox microbial guild was studied by metagenomics in this paper. The continuous experiment results showed the average NRE improved by 17.57% with N-G addition. The metagenomic analysis revealed N-G significantly increased the relative abundance of dominant AnAOB (Candidatus Kuenenia) from 18.10% to 28.30%. And the FISH assay further manifested N-G promoted the growth of AnAOB biomass. Meanwhile, metagenomics indicated that N-G enriched the abundance of genes (Hzs, Hdh, NosZ, NorB, NirK, NirS and NrfA) involved in nitrogen metabolism to varying degrees. Furthermore, N-G not only improved the microbial functionality in terms of "Metabolism", but markedly upregulated the abundance of c-di-GMP synthesized genes and genes related to quinolone signal molecule, which contributed to more EPS content and better sludge settleability. In brief, this study provided a novel perspective for anammox biomass enrichment, which may be valuable for practical engineering applications of anammox.

Food web rewiring drives long-term compositional differences and late-disturbance interactions at the community level

Multiple anthropogenic disturbances affect the structure and functioning of communities. Recent evidence highlighted that, after pulse disturbance, the functioning a community performs may be recovered fast due to functional redundancy, whereas community multivariate composition needs a longer time. Yet, the mechanisms that drive the different community recovery times have not been quantified empirically. We use quantitative food-web analysis to assess the influence of species interactions on community recovery. We found species-interactions strength to be the main mechanism driving differences between structural and functional recovery. Additionally, we show that interactions between multiple disturbances appear in the long term only when both species-interaction strength and food-web architecture change significantly.

Ecological communities are constantly exposed to multiple natural and anthropogenic disturbances. Multivariate composition (if recovered) has been found to need significantly more time to be regained after pulsed disturbance compared to univariate diversity metrics and functional endpoints. However, the mechanisms driving the different recovery times of communities to single and multiple disturbances remain unexplored. Here, we apply quantitative ecological network analyses to try to elucidate the mechanisms driving long-term community-composition dissimilarity and late-stage disturbance interactions at the community level. For this, we evaluate the effects of two pesticides, nutrient enrichment, and their interactions in outdoor mesocosms containing a complex freshwater community. We found changes in interactions strength to be strongly related to compositional changes and identified postdisturbance interaction-strength rewiring to be responsible for most of the observed compositional changes. Additionally, we found pesticide interactions to be significant in the long term only when both interaction strength and food-web architecture are reshaped by the disturbances. We suggest that quantitative network analysis has the potential to unveil ecological processes that prevent long-term community recovery.

Genetic diversity and connectivity of the Ostreid herpesvirus 1 populations in France: A first attempt to phylogeographic inference for a marine mollusc disease

The genetic diversity of viral populations is a key driver of the spatial and temporal diffusion of viruses; yet, studying the diversity of whole genomes from natural populations still remains a challenge. Phylodynamic approaches are commonly used for RNA viruses harboring small genomes but have only rarely been applied to DNA viruses with larger genomes. Here, we used the Pacific oyster mortality syndrome (a disease that affects oyster farms around the world) as a model to study the genetic diversity of its causative agent, the Ostreid herpesvirus 1 (OsHV-1) in the three main French oyster-farming areas. Using ultra-deep sequencing on individual moribund oysters and an innovative combination of bioinformatics tools, we de novo assembled twenty-one OsHV-1 new genomes. Combining quantification of major and minor genetic variations, phylogenetic analysis, and ancestral state reconstruction of discrete traits approaches, we assessed the connectivity of OsHV-1 viral populations between the three oyster-farming areas. Our results suggest that the Marennes-Oléron Bay represents the main source of OsHV-1 diversity, from where the virus has dispersed to other farming areas, a scenario consistent with current practices of oyster transfers in France. We demonstrate that phylodynamic approaches can be applied to aquatic DNA viruses to determine how epidemiological, immunological, and evolutionary processes act and potentially interact to shape their diversity patterns.

Detecting patterns of vertebrate biodiversity across the multidimensional urban landscape

Explicit characterisation of the complexity of urban landscapes is critical for understanding patterns of biodiversity and for detecting the underlying social and ecological processes that shape them. Urban environments exhibit variable heterogeneity and connectivity, influenced by different historical contingencies, that affect community assembly across scales. The multidimensional nature of urban disturbance and co-occurrence of multiple stressors can cause synergistic effects leading to nonlinear responses in populations and communities. Yet, current research design of urban ecology and evolutionary studies typically relies on simple representation of the parameter space that can be observed. Sampling approaches apply simple urban gradients such as linear transects in space or comparisons of urban sites across the urban mosaic accounting for a few variables. This rarely considers multiple dimensions and scales of biodiversity, and proves to be inadequate to explain observed patterns. We apply a multidimensional approach that integrates distinctive social, ecological and built characteristics of urban landscapes, representing variations along dimensions of heterogeneity, connectivity and historical contingency. Measuring species richness and beta diversity across 100 US metropolitan areas at the city and 1-km scales, we show that distinctive signatures of urban biodiversity can result from interactions between socioecological heterogeneity and connectivity, mediated by historical contingency.

Random placement models explain species richness and dissimilarity of frog assemblages within Atlantic Forest fragments

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

Decay of similarity across tropical forest communities: integrating spatial distance with soil nutrients

Understanding the mechanisms that drive the change of biotic assemblages over space and time is the main quest of community ecology. Assessing the relative importance of dispersal and environmental species selection in a range of organismic sizes and motilities has been a fruitful strategy. A consensus for whether spatial and environmental distances operate similarly across spatial scales and taxa, however, has yet to emerge. We used censuses of four major groups of organisms (soil bacteria, fungi, ground insects, and trees) at two observation scales (1-m² sampling point vs. 2,500-m² plots) in a topographically standardized sampling design replicated in two tropical rainforests with contrasting relationships between spatial distance and nutrient availability. We modeled the decay of assemblage similarity for each taxon set and site to assess the relative contributions of spatial distance and nutrient availability distance. Then, we evaluated the potentially structuring effect of tree composition over all other taxa. The similarity of nutrient content in the litter and topsoil had a stronger and more consistent selective effect than did dispersal limitation, particularly for bacteria, fungi, and trees at the plot level. Ground insects, the only group assessed with the capacity of active dispersal, had the highest species turnover and the flattest nonsignificant distance-decay relationship, suggesting that neither dispersal limitation nor nutrient availability were fundamental drivers of their community assembly at this scale of analysis. Only the fungal communities at one of our study sites were clearly coordinated with tree composition. The spatial distance at the smallest scale was more important than nutrient selection for the bacteria, fungi, and insects. The lower initial similarity and the moderate variation in composition identified by these distance-decay models, however, suggested that the effects of stochastic sampling were important at this smaller spatial scale. Our results highlight the importance of nutrients as one of the main environmental drivers of rainforest communities irrespective of organismic or propagule size and how the overriding effect of the analytical scale influences the interpretation, leading to the perception of greater importance of dispersal limitation and ecological drift over selection associated with environmental niches at decreasing observation scales.

A cloud-based toolbox for the versatile environmental annotation of biodiversity data

A vast range of research applications in biodiversity sciences requires integrating primary species, genetic, or ecosystem data with other environmental data. This integration requires a consideration of the spatial and temporal scale appropriate for the data and processes in question. But a versatile and scale flexible environmental annotation of biodiversity data remains constrained by technical hurdles. Existing tools have streamlined the intersection of occurrence records with gridded environmental data but have remained limited in their ability to address a range of spatial and temporal grains, especially for large datasets. We present the Spatiotemporal Observation Annotation Tool (STOAT), a cloud-based toolbox for flexible biodiversity–environment annotations. STOAT is optimized for large biodiversity datasets and allows user-specified spatial and temporal resolution and buffering in support of environmental characterizations that account for the uncertainty and scale of data and of relevant processes. The tool offers these services for a growing set of near global, remotely sensed, or modeled environmental data, including Landsat, MODIS, EarthEnv, and CHELSA. STOAT includes a user-friendly, web-based dashboard that provides tools for annotation task management and result visualization, linked to Map of Life, and a dedicated R package (rstoat) for programmatic access. We demonstrate STOAT functionality with several examples that illustrate phenological variation and spatial and temporal scale dependence of environmental characteristics of birds at a continental scale. We expect STOAT to facilitate broader exploration and assessment of the scale dependence of observations and processes in ecology.

In ecology and evolution, processes, data collection, and inference or prediction usually occur at different scales in space and time. This study introduces a cloud-based toolbox for the flexible fusion of biodiversity records with remotely sensed and other environmental information that supports an assessment and accounting of such scale dependencies.