Risk-appropriate regulations for gene-editing technologies

This paper explores the scope for the newly emerging technologies, based on gene editing (GE) contributing to addressing the global challenges that we face. These challenges relate to food security, climate change and biodiversity depletion. In particular, it examines the science and evidence behind the most appropriate forms of agricultural production to meet these challenges, the targets set in the Global Biodiversity Framework (GBF) agreed to at the end of 2022 and the possible role of GE technologies in contributing to meeting these targets. It then examines the most risk-appropriate regulatory environment required to best facilitate the adoption of GE technology, drawing on the experiences of the impact of regulatory systems for other innovations used in agricultural and food production systems such as genetically modified organisms (GMOs).

Bioprospecting of sourdough microbial species from artisan bakeries in the city of Valencia

This work describes the characterization of an artisanal sourdough set of bakeries located in the city of Valencia. Culture-dependent and -independent analyses detected Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Kazachstania humilis as dominant species. Nevertheless, specific technological parameters, including backslopping temperature, dough yield, or the addition of salt affected microbial counting, LAB/Yeast ratio, and gassing performance, favouring the appearance of several species of Lactobacillus sp., Limosilactobacillus pontis or Torulaspora delbrueckii as additional players. Sourdough leavening activity was affected positively by yeast counts and negatively by the presence of salt. In addition, the predominance of a particular yeast species appeared to impact the dynamics of CO2 release. Seven important flavour-active compounds (ethyl acetate, 1-hexanol, 2-penthylfuran, 3-ethyl-2-methyl-1,3-hexadiene, 2-octen-1-ol, nonanal and 1-nonanol) were detected in all samples and together with 3-methyl butanol and hexyl acetate represented more than the 53% of volatile abundancy in nine of the ten sourdoughs analysed. Even so, the specific microbial composition of each sample influenced the volatile profile. For example, the occurrence of K. humilis or S. cerevisiae as dominant yeast influenced the composition of major alcohol species, while F. sanfranciscensis and L. pontis positively correlated with aldehydes and octanoic acid content. In addition, relevant correlations could be also found among different technological parameters and between these, volatile compounds and microbial species. Overall, our study emphasises on how differences in technological parameters generate biodiversity in a relatively small set of artisan sourdoughs providing opportunities for excellence and quality baking products.

Biodiversity and antibiotic resistance profile provide new evidence for a different origin of enterococci in bovine raw milk and feces

Enterococci are widely distributed in dairy sector. They are commensals of the gastrointestinal tract of animals, thus, via fecal contamination, could reach raw milk and dairy products. The aims of this study were: 1) to investigate the enterococcal diversity in cow feces and milk samples and 2) to evaluate the antibiotic resistance (AR) of dairy-related enterococci and their ability to transfer resistance genes. E. faecalis (59.9%), E. faecium (18.6%) and E. lactis (12.4%) were prevalent in milk, while E. faecium (84.2%) and E. hirae (15.0%) were dominant in bovine feces. RAPD-PCR highlighted a high number of Enterococcus biotypes (45 from milk and 37 from feces) and none of the milk strains exhibited genetic profiles similar to those of feces biotypes. A high percentage of enterococci isolated from milk (71%) were identified as multidrug resistant and resistance against streptomycin and tetracycline were widespread among milk strains while enterococci from feces were commonly resistant to linezolid and quinupristin/dalfopristin. Only E. faecalis strains were able to transfer horizontally the tetM gene to Lb. delbrueckii subsp. lactis. Our results indicated that Enterococcus biotypes from milk and bovine feces belong to different community and the ability of these microorganisms to transfer AR genes is strain-dependent.

The human side of biodiversity: coevolution of the human niche, palaeo-synanthropy and ecosystem complexity in the deep human past

Today's biodiversity crisis fundamentally threatens the habitability of the planet, thus ranking among the primary human challenges of our time. Much emphasis is currently placed on the loss of biodiversity in the Anthropocene, yet these debates often portray biodiversity as a purely natural phenomenon without much consideration of its human dimensions and frequently lack long-term vistas. This paper offers a deep-time perspective on the key role of the evolving human niche in ecosystem functioning and biodiversity dynamics. We summarize research on past hunter-gatherer ecosystem contributions and argue that human-environment feedback systems with important biodiversity consequences are probably a recurrent feature of the Late Pleistocene, perhaps with even deeper roots. We update current understandings of the human niche in this light and suggest that the formation of palaeo-synanthropic niches in other animals proffers a powerful model system to investigate recursive interactions of foragers and ecosystems. Archaeology holds important knowledge here and shows that ecosystem contributions vary greatly in relation to different human lifeways, some of which are lost today. We therefore recommend paying more attention to the intricate relationship between biodiversity and cultural diversity, contending that promotion of the former depends on fostering the latter. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Scaling approaches and macroecology provide a foundation for assessing ecological resilience in the Anthropocene

In the Anthropocene, intensifying ecological disturbances pose significant challenges to our predictive capabilities for ecosystem responses. Macroecology-which focuses on emergent statistical patterns in ecological systems-unveils consistent regularities in the organization of biodiversity and ecosystems. These regularities appear in terms of abundance, body size, geographical range, species interaction networks, or the flux of matter and energy. This paper argues for moving beyond qualitative resilience metaphors, such as the 'ball and cup', towards a more quantitative macroecological framework. We suggest a conceptual and theoretical basis for ecological resilience that integrates macroecology with a stochastic diffusion approximation constrained by principles of biological symmetry. This approach provides an alternative novel framework for studying ecological resilience in the Anthropocene. We demonstrate how our framework can effectively quantify the impacts of major disturbances and their extensive ecological ramifications. We further show how biological scaling insights can help quantify the consequences of major disturbances, emphasizing their cascading ecological impacts. The nature of these impacts prompts a re-evaluation of our understanding of resilience. Emphasis on regularities of ecological assemblages can help illuminate resilience dynamics and offer a novel basis to predict and manage the impacts of disturbance in the Anthropocene more efficiently. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Predicting the responses of European grassland communities to climate and land cover change

European grasslands are among the most species-rich ecosystems on small spatial scales. However, human-induced activities like land use and climate change pose significant threats to this diversity. To explore how climate and land cover change will affect biodiversity and community composition in grassland ecosystems, we conducted joint species distribution models (SDMs) on the extensive vegetation-plot database sPlotOpen to project distributions of 1178 grassland species across Europe under current conditions and three future scenarios. We further compared model accuracy and computational efficiency between joint SDMs (JSDMs) and stacked SDMs, especially for rare species. Our results show that: (i) grassland communities in the mountain ranges are expected to suffer high rates of species loss, while those in western, northern and eastern Europe will experience substantial turnover; (ii) scaling anomalies were observed in the predicted species richness, reflecting regional differences in the dominant drivers of assembly processes; (iii) JSDMs did not outperform stacked SDMs in predictive power but demonstrated superior efficiency in model fitting and predicting; and (iv) incorporating co-occurrence datasets improved the model performance in predicting the distribution of rare species. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

An assessment of the state of conservation planning in Europe

Expanding and managing current habitat and species protection measures is at the heart of the European biodiversity strategy. A structured approach is needed to gain insights into such issues is systematic conservation planning, which uses techniques from decision theory to identify places and actions that contribute most effectively to policy objectives given a set of constraints. Yet culturally and historically determined European landscapes make the implementation of any conservation plans challenging, requiring an analysis of synergies and trade-offs before implementation. In this work, we review the scientific literature for evidence of previous conservation planning approaches, highlighting recent advances and success stories. We find that the conceptual characteristics of European conservation planning studies likely reduced their potential in contributing to better-informed decisions. We outline pathways towards improving the uptake of decision theory and multi-criteria conservation planning at various scales, particularly highlighting the need for (a) open data and intuitive tools, (b) the integration of biodiversity-focused conservation planning with multiple objectives, (c) accounting of dynamic ecological processes and functions, and (d) better facilitation of entry-points and co-design practices of conservation planning scenarios with stakeholders. By adopting and improving these practices, European conservation planning might become more actionable and adaptable towards implementable policy outcomes. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Legacies of millennial-scale climate oscillations in contemporary biodiversity in eastern North America

The Atlantic meridional overturning circulation (AMOC) has caused significant climate changes over the past 90 000 years. Prior work has hypothesized that these millennial-scale climate variations effected past and contemporary biodiversity, but the effects are understudied. Moreover, few biogeographic models have accounted for uncertainties in palaeoclimatic simulations of millennial-scale variability. We examine whether refuges from millennial-scale climate oscillations have left detectable legacies in the patterns of contemporary species richness in eastern North America. We analyse 13 palaeoclimate estimates from climate simulations and proxy-based reconstructions as predictors for the contemporary richness of amphibians, passerine birds, mammals, reptiles and trees. Results suggest that past climate changes owing to AMOC variations have left weak but detectable imprints on the contemporary richness of mammals and trees. High temperature stability, precipitation increase, and an apparent climate fulcrum in the southeastern United States across millennial-scale climate oscillations aligns with high biodiversity in the region. These findings support the hypothesis that the southeastern United States may have acted as a biodiversity refuge. However, for some taxa, the strength and direction of palaeoclimate-richness relationships varies among different palaeoclimate estimates, pointing to the importance of palaeoclimatic ensembles and the need for caution when basing biogeographic interpretations on individual palaeoclimate simulations. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Global indicators of the environmental impacts of invasive alien species and their information adequacy

Monitoring the extent to which invasive alien species (IAS) negatively impact the environment is crucial for understanding and mitigating biological invasions. Indeed, such information is vital for achieving Target 6 of the Kunming-Montreal Global Biodiversity Framework. However, to-date indicators for tracking the environmental impacts of IAS have been either lacking or insufficient. Capitalizing on advances in data availability and impact assessment protocols, we developed environmental impact indicators to track realized and potential impacts of IAS. We also developed an information status indicator to assess the adequacy of the data underlying the impact indicators. We used data on 75 naturalized amphibians from 82 countries to demonstrate the indicators at a global scale. The information status indicator shows variation in the reliability of the data and highlights areas where absence of impact should be interpreted with caution. Impact indicators show that growth in potential impacts are dominated by predatory species, while potential impacts from both predation and disease transmission are distributed worldwide. Using open access data, the indicators are reproducible and adaptable across scales and taxa and can be used to assess global trends and distributions of IAS, assisting authorities in prioritizing control efforts and identifying areas at risk of future invasions. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Unravelling the functional and phylogenetic dimensions of novel ecosystem assemblages

Human activities are causing taxonomic rearrangements across ecosystems that often result in the emergence of novel communities (assemblies with no historical representative). It is commonly assumed that these changes in the taxonomic makeup of ecosystems also inevitably lead to changes in other aspects of biodiversity, namely functional and phylogenetic diversity. However, this assumption is not always valid, as the changes in functional and phylogenetic composition resulting from taxonomic shifts depend on the level of redundancy in the evaluated community. Therefore, we need improved theoretical frameworks to predict when we can expect coordinated or decoupled responses among these three facets of biodiversity. To advance this understanding, we discuss the conceptual and methodological issues that complicate establishing a link between taxonomic rearrangements driven by human activities and the associated functional and phylogenetic changes. Here, we show that is crucial to consider the expected changes in functional and phylogenetic composition as communities are reshaped owing to human drivers of biodiversity loss to forecast the impacts of novel assemblages on ecosystem functions and the services they provide to humanity. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Future changes in society and climate may strongly shape wild large-herbivore faunas across Europe

Restoring wild communities of large herbivores is critical for the conservation of biodiverse ecosystems, but environmental changes in the twenty-first century could drastically affect the availability of habitats. We projected future habitat dynamics for 18 wild large herbivores in Europe and the relative future potential patterns of species richness and assemblage mean body weight considering four alternative scenarios of socioeconomic development in human society and greenhouse gas emissions (SSP1-RCP2.6, SSP2-RCP4.5, SSP3-RCP7.0, SSP5-RCP8.5). Under SSP1-RCP2.6, corresponding to a transition towards sustainable development, we found stable habitat suitability for most species and overall stable assemblage mean body weight compared to the present, with an average increase in species richness (in 2100: 3.03 ± 1.55 compared to today's 2.25 ± 1.31 species/area). The other scenarios are generally unfavourable for the conservation of wild large herbivores, although under the SSP5-RCP8.5 scenario there would be increase in species richness and assemblage mean body weight in some southern regions (e.g. + 62.86 kg mean body weight in Balkans/Greece). Our results suggest that a shift towards a sustainable socioeconomic development would overall provide the best prospect of our maintaining or even increasing the diversity of wild herbivore assemblages in Europe, thereby promoting trophic complexity and the potential to restore functioning and self-regulating ecosystems. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Range and climate niche shifts in European and North American breeding birds

Species respond dynamically to climate change and exhibit time lags. Consequently, species may not occupy their full climatic niche during range shifting. Here, we assessed climate niche tracking during recent range shifts of European and United States (US) birds. Using data from two European bird atlases and from the North American Breeding Bird Survey between the 1980s and 2010s, we analysed range overlap and climate niche overlap based on kernel density estimation. Phylogenetic multiple regression was used to assess the effect of species morphological, ecological and biogeographic traits on range and niche metrics. European birds shifted their ranges north and north-eastwards, US birds westwards. Range unfilling was lower than expected by null models, and niche expansion was more common than niche unfilling. Also, climate niche tracking was generally lower in US birds and poorly explained by species traits. Overall, our results suggest that dispersal limitations were minor in range shifting birds in Europe and the USA while delayed extinctions from unfavourable areas seem more important. Regional differences could be related to differences in land use history and monitoring schemes. Comparative analyses of range and niche shifts provide a useful screening approach for identifying the importance of transient dynamics and time-lagged responses to climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Using ancient sedimentary DNA to forecast ecosystem trajectories under climate change

Ecosystem response to climate change is complex. In order to forecast ecosystem dynamics, we need high-quality data on changes in past species abundance that can inform process-based models. Sedimentary ancient DNA (sedaDNA) has revolutionised our ability to document past ecosystems' dynamics. It provides time series of increased taxonomic resolution compared to microfossils (pollen, spores), and can often give species-level information, especially for past vascular plant and mammal abundances. Time series are much richer in information than contemporary spatial distribution information, which have been traditionally used to train models for predicting biodiversity and ecosystem responses to climate change. Here, we outline the potential contribution of sedaDNA to forecast ecosystem changes. We showcase how species-level time series may allow quantification of the effect of biotic interactions in ecosystem dynamics, and be used to estimate dispersal rates when a dense network of sites is available. By combining palaeo-time series, process-based models, and inverse modelling, we can recover the biotic and abiotic processes underlying ecosystem dynamics, which are traditionally very challenging to characterise. Dynamic models informed by sedaDNA can further be used to extrapolate beyond current dynamics and provide robust forecasts of ecosystem responses to future climate change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Projected future climatic forcing on the global distribution of vegetation types

Most emissions scenarios suggest temperature and precipitation regimes will change dramatically across the globe over the next 500 years. These changes will have large impacts on the biosphere, with species forced to migrate to follow their preferred environmental conditions, therefore moving and fragmenting ecosystems. However, most projections of the impacts of climate change only reach 2100, limiting our understanding of the temporal scope of climate impacts, and potentially impeding suitable adaptive action. To address this data gap, we model future climate change every 20 years from 2000 to 2500 CE, under different CO2 emissions scenarios, using a general circulation model. We then apply a biome model to these modelled climate futures, to investigate shifts in climatic forcing on vegetation worldwide, the feasibility of the migration required to enact these modelled vegetation changes, and potential overlap with human land use based on modern-day anthromes. Under a business-as-usual scenario, up to 40% of terrestrial area is expected to be suited to a different biome by 2500. Cold-adapted biomes, particularly boreal forest and dry tundra, are predicted to experience the greatest losses of suitable area. Without mitigation, these changes could have severe consequences both for global biodiversity and the provision of ecosystem services. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

The importance of regeneration processes on forest biodiversity in old-growth forests in the Pacific Northwest

Forest diversity is the outcome of multiple species-specific processes and tolerances, from regeneration, growth, competition and mortality of trees. Predicting diversity thus requires a comprehensive understanding of those processes. Regeneration processes have traditionally been overlooked, due to high stochasticity and assumptions that recruitment is not limiting for forests. Thus, we investigated the importance of seed production and seedling survival on forest diversity in the Pacific Northwest (PNW) using a forest gap model (ForClim). Equations for regeneration processes were fit to empirical data and added into the model, followed by simulations where regeneration processes and parameter values varied. Adding regeneration processes into ForClim improved the simulation of species composition, compared to Forest Inventory Analysis data. We also found that seed production was not as important as seedling survival, and the time it took for seedlings to grow into saplings was a critical recruitment parameter for accurately capturing tree species diversity in PNW forest stands. However, our simulations considered historical climate only. Due to the sensitivity of seed production and seedling survival to weather, future climate change may alter seed production or seedling survival and future climate change simulations should include these regeneration processes to predict future forest dynamics in the PNW. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Soil properties constrain forest understory plant distributions along an elevation gradient

Projections of spatial biodiversity dynamics under climate warming are often based on models including only climate variables, and when non-climatic factors (e.g. soil) are included, data are often at much coarser spatial resolutions than those experienced by plants. Field studies along elevation gradients permit the gathering of detailed soil data, while still covering a wide climatic gradient. Here, an intensive field survey of four spring forest herbs along an elevation gradient showed that soil properties had substantial impacts on the occurrence/abundance of all species, and that soil effects were more pronounced at higher elevations. For Trillium erectum and Claytonia caroliniana, very infrequent occurrences at high elevation were strongly associated with rare microsites with high pH or nutrients. In a seven-year transplant experiment with T. erectum, we found that individuals grew to much smaller sizes at high than low elevation, suggesting that environmental factors rather than dispersal limitation constrain the species' upper range limit, despite substantial warming in recent decades. Our study demonstrates that soil factors interact strongly with climate to determine plant range limits along climatic gradients. Unsuitable soils for plants at high elevations or latitudes may represent an important constraint on future plant migration and biodiversity change. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

A nature-positive future with biological invasions: theory, decision support and research needs

In 2050, most areas of biodiversity significance will be heavily influenced by multiple drivers of environmental change. This includes overlap with the introduced ranges of many alien species that negatively impact biodiversity. With the decline in biodiversity and increase in all forms of global change, the need to envision the desired qualities of natural systems in the Anthropocene is growing, as is the need to actively maintain their natural values. Here, we draw on community ecology and invasion biology to (i) better understand trajectories of change in communities with a mix of native and alien populations, and (ii) to frame approaches to the stewardship of these mixed-species communities. We provide a set of premises and actions upon which a nature-positive future with biological invasions (NPF-BI) could be based, and a decision framework for dealing with uncertain species movements under climate change. A series of alternative management approaches become apparent when framed by scale-sensitive, spatially explicit, context relevant and risk-consequence considerations. Evidence of the properties of mixed-species communities together with predictive frameworks for the relative importance of the ecological processes at play provide actionable pathways to a NPF in which the reality of mixed-species communities are accommodated and managed. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Towards a novel biosphere in 2300: rapid and extensive global and biome-wide climatic novelty in the Anthropocene

Recent climate change has effectively rewound the climate clock by approximately 120 000 years and is expected to reverse this clock a further 50 Myr by 2100. We aimed to answer two essential questions to better understand the changes in ecosystems worldwide owing to predicted climate change. Firstly, we identify the locations and time frames where novel ecosystems could emerge owing to climate change. Secondly, we aim to determine the extent to which biomes, in their current distribution, will experience an increase in climate-driven ecological novelty. To answer these questions, we analysed three perspectives on how climate changes could result in novel ecosystems in the near term (2100), medium (2200) and long term (2300). These perspectives included identifying areas where climate change could result in new climatic combinations, climate isoclines moving faster than species migration capacity and current environmental patterns being disaggregated. Using these metrics, we determined when and where novel ecosystems could emerge. Our analysis shows that unless rapid mitigation measures are taken, the coverage of novel ecosystems could be over 50% of the land surface by 2100 under all change scenarios. By 2300, the coverage of novel ecosystems could be above 80% of the land surface. At the biome scale, these changes could mean that over 50% of locations could shift towards novel ecosystems, with the majority seeing these changes in the next few decades. Our research shows that the impact of climate change on ecosystems is complex and varied, requiring global action to mitigate and adapt to these changes. This article is part of the theme issue 'Biodiversity dynamics and stewardship in a transforming biosphere'. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

Navigating ecological novelty towards planetary stewardship: challenges and opportunities in biodiversity dynamics in a transforming biosphere

Human-induced global changes, including anthropogenic climate change, biotic globalization, trophic downgrading and pervasive land-use intensification, are transforming Earth's biosphere, placing biodiversity and ecosystems at the forefront of unprecedented challenges. The Anthropocene, characterized by the importance of Homo sapiens in shaping the Earth system, necessitates a re-evaluation of our understanding and stewardship of ecosystems. This theme issue delves into the multifaceted challenges posed by the ongoing ecological planetary transformation and explores potential solutions across four key subthemes. Firstly, it investigates the functioning and stewardship of emerging novel ecosystems, emphasizing the urgent need to comprehend the dynamics of ecosystems under uncharted conditions. The second subtheme focuses on biodiversity projections under global change, recognizing the necessity of predicting ecological shifts in the Anthropocene. Importantly, the inherent uncertainties and the complexity of ecological responses to environmental stressors pose challenges for societal responses and for accurate projections of ecological change. The RAD framework (resist-accept-direct) is highlighted as a flexible yet nuanced decision-making tool that recognizes the need for adaptive approaches, providing insights for directing and adapting to Anthropocene dynamics while minimizing negative impacts. The imperative to extend our temporal perspective beyond 2100 is emphasized, given the irreversible changes already set in motion. Advancing methods to study ecosystem dynamics under rising biosphere novelty is the subject of the third subtheme. The fourth subtheme emphasizes the importance of integrating human perspectives into understanding, forecasting and managing novel ecosystems. Cultural diversity and biological diversity are intertwined, and the evolving relationship between humans and ecosystems offers lessons for future stewardship. Achieving planetary stewardship in the Anthropocene demands collaboration across scales and integration of ecological and societal perspectives, scalable approaches fit to changing, novel ecological conditions, as well as cultural innovation. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

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.

To what extent can we predict variation of bryophyte and tracheophyte community composition at fine spatial scale along an elevation gradient?

Mounting evidence points to the need for high-resolution climatic data in biodiversity analyses under global change. As we move to finer resolution, other factors than climate, including other abiotic variables and biotic interactions play, however, an increasing role, raising the question of our ability to predict community composition at fine scales. Focusing on two lineages of land plants, bryophytes and tracheophytes, we determine the relative contribution of climatic, non-climatic environmental drivers, spatial effects, community architecture and composition of one lineage to predict community composition of the other lineage, and how our ability to predict community composition varies along an elevation gradient. The relationship between community composition of one lineage and 68 environmental variables at 2-25 m spatial resolution, architecture and composition of the other lineage, and spatial factors, was investigated by hierarchical and variance partitioning across 413 2x2m plots in the Swiss Alps. Climatic data, although significant, contributed less to the model than any other variable considered. Community composition of one lineage, reflecting both direct interactions and unmeasured (hidden) abiotic factors, was the best predictor of community composition of the other lineage. Total explained variance substantially varied with elevation, underlining the fact that the strength of the species composition-environment relationship varies depending on environmental conditions. Total variance explained increased towards high elevation up to 50 %, with an increasing importance of spatial effects and vegetation architecture, pointing to increasing positive interactions and aggregated species distribution patterns in alpine environments. In tracheophytes, an increase of the contribution of non-climatic environmental factors was also observed at high elevation, in line with the hypothesis of a stronger environmental control under harsher conditions. Further improvements of our ability to predict changes in plant community composition may involve the implementation of historical variables and higher-resolution climatic data to better describe the microhabitat conditions actually experienced by organisms.

Fostering biodiversity research in post-fire biology

The impacts of wildfire on vegetation and soil erosion have been studied for decades aiming to bring back ecosystems after fire perturbance. However, the influence of fires on above and belowground biodiversity remains far less understood. Biodiversity is critical for supporting ecosystem function, and this data scarcity is hampering managers in adopting effective practices for a proper restoration of burned ecosystems. This limitation could be overcome by future research that should focus post-fire diversity of plants and soil biota, by (i) analysing the environmental factors driving post-fire evolutionary trends; (ii) exploring their interrelations across different spatial and temporal scales; (iii) identifying the variability across fires of different severities and frequency; (iv) ascertaining the post-fire response of individual plant species and soil taxa to fire with or without application of post-fire restoration actions.

Environmental DNA methods for biosecurity and invasion biology in terrestrial ecosystems: Progress, pitfalls, and prospects

Analysis of environmental DNA (eDNA) enables indirect detection of species without the need to directly observe and sample them. For biosecurity and invasion biology, eDNA-based methods are useful to address biological invasions at all phases, from detecting arrivals to confirming eradication of past invasions. We conducted a systematic review of the literature and found that in biosecurity and invasion biology, eDNA has primarily been used to detect new incursions and monitor spread in marine and freshwater ecosystems, with much slower uptake in terrestrial ecosystems, reflecting a broader trend common to the usage of eDNA tools. In terrestrial ecosystems, eDNA research has mostly focussed on the use of eDNA metabarcoding to characterise biodiversity, rather than targeting biosecurity threats or non-native populations. We discuss how eDNA-based methods are being applied to terrestrial ecosystems for biosecurity and managing non-native populations at each phase of the invasion continuum: transport, introduction, establishment, and spread; across different management options: containment, control, and eradication; and for detecting the impact of non-native organisms. Finally, we address some of the current technical issues and caveats of eDNA-based methods, particularly for terrestrial ecosystems, and how these might be solved. As eDNA-based methods improve, they will play an increasingly important role in the early detection and adaptive management of biological invasions, and the implementation of effective biosecurity controls.

Local environmental factors are the main drivers of phytoplankton biovolume in subtropical streams of Brazil

The ecological attributes of phytoplankton in freshwater environments are strongly influenced by limnological factors and temporal variability. In this study, we investigated the importance of local environmental and regional (spatial and landscape) predictors in structuring stream phytoplankton from the perspective of metacommunity theory. We seasonally sampled phytoplankton and abiotic variables from nine streams in three subtropical basins. Variation partitioning was used to investigate the influence of environmental, landscape, and spatial predictors on phytoplankton biovolume. Independent of the hydrological period (dry and rainy), the phytoplankton communities were predominantly structured by local environmental factors. In addition, the different land uses considered (landscape) showed weak significance during the dry season, with emphasis on the rural category. Biovolume values remained low, and diatoms and green algae were the most representative groups. Our findings are consistent with recognized ecological patterns for potamoplankton and emphasize local environmental filters as a fundamental regulator of phytoplankton biodiversity in lotic environments.

Biodiversity drives ecosystem multifunctionality in sandy grasslands?

Plant communities and soil microbiomes play a crucial role in regulating ecosystem multifunctionality (EMF). However, whether and how aboveground plant diversity, belowground soil microbial diversity and interactions with environmental factors affect EMF in sandy grasslands under climate change conditions is unclear. Here, we selected 15 typical grassland communities from the Horqin sandy grassland along temperature and precipitation gradients, using the mean annual temperature (AMT), mean annual precipitation (AP), soil temperature (ST), soil water content (SW) and pH as abiotic factors, and plant diversity (PD) and soil microbial diversity (SD) as biodiversity indicators. The effects of biodiversity and abiotic factors on individual ecosystem functions and EMF were studied. We found that PD and its components, plant species richness (SR), species diversity (PR) and genetic diversity (GD), had significant effects on aboveground biomass (AGB) and major factors involved in ecosystem nitrogen cycling (plant leaf nitrogen content (PLN) and soil total nitrogen content (STN)) (P < 0.05). Soil fungal diversity (FR) has a greater impact on ecosystem function than soil bacteria (BR) and archaea (ABR) in sandy grasslands and mainly promotes the accumulation of soil microbial carbon and nitrogen (MBC, MBN) (P < 0.05), STC and STN (P < 0.01). PD and two types of SD (FR and ABR) significantly regulated EMF (P < 0.01). Among the abiotic factors, soil pH and SW regulated EMF (P < 0.05), and SW and ST directly drove EMF (P < 0.05). PD drove EMF significantly and indirectly (positively) through soil pH and ST (P < 0.001), while SD drove EMF weakly and indirectly (negatively) through AP and PD (P > 0.05). PD was a stronger driving force on EMF than SD. These results improve our understanding of the drivers of multifunctionality in sandy grassland ecosystems.

Understanding the role of biodiversity in the climate, food, water, energy, transport and health nexus in Europe

Biodiversity underpins the functioning of ecosystems and the diverse benefits that nature provides to people, yet is being lost at an unprecedented rate. To halt or reverse biodiversity loss, it is critical to understand the complex interdependencies between biodiversity and key drivers and sectors to inform the development of holistic policies and actions. We conducted a literature review on the interlinkages between biodiversity and climate change, food, water, energy, transport and health ("the biodiversity nexus"). Evidence extracted from 194 peer-reviewed articles was analysed to assess how biodiversity is being influenced by and is influencing the other nexus elements. Out of the 354 interlinkages between biodiversity and the other nexus elements, 53 % were negative, 29 % were positive and 18 % contained both positive and negative influences. The majority of studies provide evidence of the negative influence of other nexus elements on biodiversity, highlighting the substantial damage being inflicted on nature from human activities. The main types of negative impacts were land or water use/change, land or water degradation, climate change, and direct species fatalities through collisions with infrastructure. Alternatively, evidence of biodiversity having a negative influence on the other nexus elements was limited to the effects of invasive alien species and vector-borne diseases. Furthermore, a range of studies provided evidence of how biodiversity and the other nexus elements can have positive influences on each other through practices that promote co-benefits. These included biodiversity-friendly management in relevant sectors, protection and restoration of ecosystems and species that provide essential ecosystem services, green and blue infrastructure including nature-based solutions, and sustainable and healthy diets that mitigate climate change. The review highlighted the complexity and context-dependency of interlinkages within the biodiversity nexus, but clearly demonstrates the importance of biodiversity in underpinning resilient ecosystems and human well-being in ensuring a sustainable future for people and the planet.

Socio-economic variables improve accuracy and change spatial predictions in species distribution models

In an era marked by increasing anthropogenic pressure, understanding the relations between human activities and wildlife is crucial for understanding ecological patterns, effective conservation, and management strategies. Here, we explore the potential and usefulness of socio-economic variables in species distribution modelling (SDM), focusing on their impact on the occurrence of wild mammals in Poland. Beyond the environmental factors commonly considered in SDM, like land-use, the study tests the importance of socio-economic characteristics of local human societies, such as age, income, working sector, gender, education, and village characteristics for explaining distribution of diverse mammalian groups, including carnivores, ungulates, rodents, soricids, and bats. The study revealed that incorporating socio-economic variables enhances the predictive power for >60 % of species and overall for most groups, with the exception being carnivores. For all the species combined, among the 10 predictors with highest predictive power, 6 belong to socio-economic group, while for specific species groups, socio-economic variables had similar predictive power as environmental variables. Furthermore, spatial predictions of species occurrence underwent changes when socio-economic variables were included in the model, resulting in a substantial mismatch in spatial predictions of species occurrence between environment-only models and models containing socio-economic variables. We conclude that socio-economic data has potential as useful predictors which increase prediction accuracy of wildlife occurrence and recommend its wider usage. Further, to our knowledge this is a first study on such a big scale for terrestrial mammals which evaluates performance based on presence or absence of socio-economic predictors in the model. We recognise the need for a more comprehensive approach in SDMs and that bridging the gap between human socio-economic dynamics and ecological processes may contribute to the understanding of the factors influencing biodiversity.

Four decades of region- and species-specific trends in lowland stream Ephemeroptera abundance

Lowland stream ecosystems are under threat from climate change, industrialization, urbanization, and intensive agriculture. Since the 1980s, improvements in water quality have led to an increase in lowland stream biodiversity. Despite restoration efforts, however, further recovery is often hampered by the presence of region-specific (combinations of) stressors, and species-specific stressor responses. Identification of these stressors may not be achieved by the analysis of abundance data over large areas for entire communities or species assemblages. Therefore, our study introduces an alternative in-depth approach, selecting Ephemeroptera as a model organism group and analyzing 41 years of species abundance data across distinct geographical regions. Our findings revealed that 15 Ephemeroptera species had already disappeared before 1985, emphasizing the importance of evaluating an extended historical period when analyzing biodiversity trends. While biodiversity was generally characterized by an initial recovery that stagnated over time, the analysis of the past 41 years of Ephemeroptera abundance data revealed strong differences in species' abundance trends between periods, regions, and species. Certain species were likely to have benefitted from local restoration measures in specific geographical regions, while others may have declined due to the presence of region-specific stressors. Our approach underscores the importance of studying the development of region- and species-specific stream biodiversity trends over time to aid the selection of the appropriate restoration measures to recover lowland stream biodiversity.

Phages in different habitats and their ability to carry antibiotic resistance genes

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Diversity response of necrophagous dipteran communities and their functional groups to an anthropization gradient

The anthropization process exerts a profound effect on ecosystems, causing alterations in biodiversity, habitat structure, and species composition, ultimately disrupting the delicate balance of natural environments. The aim of the present study was to explore the ecological dynamics of necrophagous Sarcophagidae and Calliphoridae flies along an anthropization gradient. This research investigated alpha and beta diversity patterns to unravel the impact of human-induced environmental changes on these insect communities and also assesses the dynamics of functional groups in relation to their impact on medical and forensic fields. Five distinct habitats, ranging from urban to forested areas, were surveyed in two Departments in the Province of Chaco, Argentina. Necrophagous flies were collected using van Someren-Rydon canopy traps across three seasons. Two main functional groups were analyzed: oviparous flies (Calliphoridae) and larviparous flies (Sarcophagidae). Results indicated a significant negative correlation between Sarcophagidae species richness and anthropization, whereas Calliphoridae showed increased abundance in highly anthropized sites. The combined assemblage of Calliphoridae+Sarcophagidae exhibited significant relationships across all community parameters evaluated. Beta diversity analysis revealed turnover as the main process shaping dipteran communities along the anthropization gradient, with spatial species replacement dominating. This underscores the importance of interspecific spatial segregation in dipteran community composition. In conclusion, this study enhances our understanding of the ecological adaptations of necrophagous dipterans to anthropogenic disturbances. The observed shifts in diversity and abundance have implications for forensic investigations and public health, emphasizing the need for nuanced monitoring and conservation strategies. This research contributes valuable insights into the intricate ecological interactions of these insect communities within changing ecosystems.

Diversity of forest structures important for biodiversity is determined by the combined effects of productivity, stand age, and management

In forests, the amount and diversity of structural features with high value for biodiversity, such as large trees and dead wood, are affected by productivity, stand age, and forest management. For efficient conservation of forest biodiversity, it is essential to understand the combined effects of these drivers. We used data from the Swedish National Forest Inventory to study the combined effects of productivity, stand age, and management for wood production on structures with high value for biodiversity: tree species richness, large living trees, dead wood volume, and specific dead wood types. Forest management changed the relationship between productivity and amount or diversity of some of the structures. Most structures increased with productivity and stand age, but decreased due to management. The negative effect of management was greatest for structures occurring mainly in high-productivity forests, such as deciduous dead wood. Thus, biodiversity conservation should target high-productivity forests to preserve these structures.

Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool

The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.

Irrigation dams threaten Brazilian biodiversity

Brazil is among the main contributors to global biodiversity, which, in turn, provides extensive ecosystem services. Agriculture is an activity that benefits greatly from these ecosystem services, but at the same time is degrading aquatic and terrestrial ecosystems and eroding Brazilian biodiversity. This conflict is growing, as emerging unsustainable legislative proposals that will benefit the agricultural sector are likely to accelerate the decline of biodiversity. One such initiative (Bill 1282/2019) would change Brazil's "Forest Code" (Law 12,651/2012) to facilitate construction of irrigation dams in Permanent Preservation Areas, a category that includes strips (with or without vegetation) along the edges of watercourses. Two other similar bills are advancing through committees in the Chamber of Deputies. Here we provide details of these three bills and discuss their consequences for Brazil's biodiversity if they are approved. Expected negative impacts with changes in the legislation include: increased deforestation; siltation; habitat fragmentation; introduction of non-native species; reduction in the availability of aquatic habitats; and changes in biogeochemical process. These proposals jeopardize biodiversity and may compromise the negotiations for an agreement between Mercosur and the European Union.

Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems

Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.

From DNA to diagnostics: A case study using macroinvertebrate metabarcoding to assess the effectiveness of restoration measures in a Dutch stream

Stream ecosystems are under pressure due to multiple stressors. Restoration measures can halt further degradation and improve their ecological status. However, assessment of the effectiveness of the implemented measures is often insufficient because of logistic and financial constraints. DNA-metabarcoding has been proposed to scale up sample processing, although its application as a diagnostic tool has received less attention. The aim of our study was to evaluate if DNA-metabarcoding of stream macroinvertebrates can be used to compute a stressor-specific index to assess the effectiveness of a stream restoration project. For this purpose, we sampled the upstream, restored, and downstream section of a recently restored lowland stream in the Netherlands. At each site, we applied three different methods of macroinvertebrate identification: morphological identification of bulk samples (morphology), DNA-metabarcoding of the same bulk samples (DNA) and metabarcoding of eDNA extracted from the water (eDNA). First, we compared the community composition identified by each method. The communities identified by morphology and DNA were highly similar, whereas the communities generated by the eDNA differed. Second, we analysed whether the identification methods could be used to assess the effectiveness of the restoration project, focussing on a stressor-specific index for flow as the restoration measures aimed at improving flow conditions. Both the morphology and bulk DNA samples indicated improved flow conditions in the restored section of the stream (i.e., less stress from the reduction or absence of flow than in the unrestored sections). Contrary, the eDNA-water samples did not differentiate the amount of stress throughout the catchment, although applying recent developments in eDNA sampling could lead to more robust results. In conclusion, this study forms proof of concept that DNA from bulk samples can be utilized to assess the effectiveness of restoration measures, showing the added value of this approach for water managers.

Climate change market-driven poleward shifts in cropland production create opportunities for tropical biodiversity conservation and habitat restoration

Although the impacts of climate change on the yields of crops have been studied, how these changes will result in the eventual realized crop production through market feedbacks has received little attention. Using a combination of attainable yield predictions for wheat, rice, maize, soybean and sugarcane, computable general equilibrium and land rent models, we project market impacts and crop-specific land-use change up to 2100 and the resulting implications for carbon and biodiversity. The results show a general increase in crop prices in tropical regions and a decrease in sub-tropical and temperate regions. Land-use change driven by market feedbacks generally amplify the effects of climate change on yields. Wheat, maize and sugarcane are projected to experience the most expansion especially in Canada and Russia, which also present the highest potential for habitat conversion-driven carbon emissions. Conversely, Latin America presents the highest extinction potential for birds, mammals and amphibians due to cropland expansion. Climate change is likely to redistribute agricultural production, generating market-driven land-use feedback effects which could, counterintuitively, protect global biodiversity by shifting global food production towards less-biodiverse temperate regions while creating substantial restoration opportunities in the tropics.

Collaboration and engagement with decision-makers are needed to reduce evidence complacency in wildlife management

There exists an extensive, diverse, and robust evidence base to support complex decisions that address the planetary biodiversity crisis. However, it is generally not sought or used by environmental decision-makers, who instead draw on intuition, experience, or opinion to inform important decisions. Thus, there is a need to examine evidence exchange processes in wildlife management to understand the multiple inputs to decisions. Here, we adopt a novel approach, fuzzy cognitive mapping (FCM), to examine perceptions of individuals from Indigenous and Western governments on the reliability of evidence which may influence freshwater fisheries management decisions in British Columbia, Canada. We facilitated four FCM workshops participants representing Indigenous or Western regulatory/governance groups of fisheries managers. Our results show that flows of evidence to decision-makers occur within a relatively closed governance network, constrained to the few well-connected decision-making organizations (i.e., wildlife management agencies) and their close partners. This implies that increased collaboration (i.e., knowledge co-production) and engagement (i.e., knowledge brokerage) with wildlife managers and decision-makers are needed to produce actionable evidence and increase evidence exchange.

Light at the end of the tunnel: Innovative opportunities for saving tropical biodiversity

The expansion of roads into wilderness areas and biodiversity hotspots in the Global South seems inevitable and is predicted to bring about significant biodiversity loss. Even so, existing widespread strategies aiming to mitigate the direct and indirect impacts of roads on the environment have been of limited effectiveness. These tactics, including construction of fencing, wildlife crossings on paved roads, and establishment of protected areas along the roads, are unlikely to be sufficient for protecting diverse species assemblages from roadkill, habitat fragmentation, and anthropogenic activity in tropics. This indicates the need for integration of more ambitious approaches into the conservation toolkit, such as the constructing tunnels, covered ways, and elevated roads. Although these tools could significantly support conservation efforts to save tropical biodiversity, to date, they are rarely considered. Here, we discuss factors which determine the need for application of these approaches in the Global South. We highlight the often-overlooked long-term benefits associated with the application of the proposed tools. We also discuss the potential challenges and risks, and the ways to minimise them. Hopefully this article will encourage practitioners to integrate these strategies into conservation toolkits and allow policy-makers and investors to make informed decisions on sustainable road infrastructure development in the Global South.

natural habitats: Higher microbial biodiversity pays the trade-off of lower connectivity

Climate change and anthropogenic disturbances are known to influence soil biodiversity. The objectives of this study were to compare the community composition, species coexistence patterns, and ecological assembly processes of soil microbial communities in a paired setting featuring a natural and an anthropogenic ecosystem facing each other at identical climatic, pedological, and vegetational conditions. A transect gradient from forest to seashore allowed for sampling across different habitats within both sites. The field survey was carried out at two adjacent strips of land within the Po River delta lagoon system (Veneto, Italy) one of which is protected within a natural preserve and the other has been converted for decades into a tourist resort. The anthropogenic pressure interestingly led to an increase in the α-diversity of soil microbes but was accompanied by a reduction in β-diversity. The community assembly mechanisms of microbial communities differentiate in natural and anthropic ecosystems: for bacteria, in natural ecosystems deterministic variables and homogeneous selection play a main role (51.92%), while stochastic dispersal limitation (52.15%) is critical in anthropized ecosystems; for fungi, stochastic dispersal limitation increases from 38.1% to 66.09% passing from natural to anthropized ecosystems. We are on calcareous sandy soils and in more natural ecosystems a variation of topsoil pH favors the deterministic selection of bacterial communities, while a divergence of K availability favors stochastic selection. In more anthropized ecosystems, the deterministic variable selection is influenced by the values of SOC. Microbial networks in the natural system exhibited higher numbers of nodes and network edges, as well as higher averages of path length, weighted degree, clustering coefficient, and density than its equivalent sites in the more anthropically impacted environment. The latter on the other hand presented a stronger modularity. Although the influence of stochastic processes increases in anthropized habitats, niche-based selection also proves to impose constraints on communities. Overall, the functionality of the relationships between groups of microorganisms co-existing in communities appeared more relevant to the concept of functional biodiversity in comparison to the plain number of their different taxa. Fewer but functionally more organized lineages displayed traits underscoring a better use of the resources than higher absolute numbers of taxa when those are not equally interconnected in their habitat exploitation. However, considering that network complexity can have important implications for microbial stability and ecosystem multifunctionality, the extinction of complex ecological interactions in anthropogenic habitats may impair important ecosystem services that soils provide us.

A case study on the application of spore sampling for the monitoring of macrofungi

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

Wildlife Conservation on Private Land: A Social-Ecological Systems Study

As human activity accelerates the global crisis facing wildlife populations, private land conservation provides an example of wildlife management challenges in social-ecological systems. This study reports on the research phase of 'WildTracker' - a co-created citizen science project, involving 160 landholders across three Tasmanian regions. This was a transdisciplinary collaboration between an environmental organisation, university researchers, and local landholders. Focusing on mammal and bird species, the project integrated diverse data types and technologies: social surveys, quantitative ecology, motion sensor cameras, acoustic recorders, and advanced machine-learning analytics. An iterative analytical methodology encompassed Pearson and point-biserial correlation for interrelationships, Non-Metric Multidimensional Scaling (NMDS) for clustering, and Random Forest machine learning for variable importance and prediction. Taken together, these analyses revealed complex relationships between wildlife populations and a suite of ecological, socio-economic, and land management variables. Both site-scale habitat characteristics and landscape-scale vegetation patterns were useful predictors of mammal and bird activity, but these relationships were different for mammals and birds. Four focal mammal species showed variation in their response to ecological and land management drivers. Unexpectedly, threatened species, such as the eastern quoll (Dasyurus viverrinus), favoured locations where habitat was substantially modified by human activities. The research provides actionable insights for landowners, and highlights the importance of 'messy,' ecologically heterogeneous, mixed agricultural landscapes for wildlife conservation. The identification of thresholds in habitat fragmentation reinforced the importance of collaboration across private landscapes. Participatory research models such as WildTracker can complement efforts to address the wicked problem of wildlife conservation in the Anthropocene.

Optimizing waterborne eDNA capture from waterholes in savanna systems under remote field conditions

Environmental DNA (eDNA) is used for biodiversity assessments in a variety of ecosystems across the globe, whereby different eDNA concentration, preservation and extraction methods can outperform others depending on the sampling conditions and environment. Tropical and subtropical ecosystems in Africa are among the less studied systems concerning eDNA-based monitoring. Waterholes in arid parts of southern Africa represent important agglomeration points for terrestrial mammals, and the eDNA shed into such waterbodies provides a powerful source of information for monitoring mammalian biodiversity in the surrounding area. However, the applied methods for eDNA sampling, preservation and filtering in different freshwater systems vary greatly, and rigorous protocol testing in African freshwater systems is still lacking. This study represents the first attempt to examine variations in eDNA concentration, preservation and extraction methods under remote field conditions using waterborne eDNA in a savanna system. Collected samples were heavily affected by microalgal and bacterial growth, impeding eDNA capture and PCR success. We demonstrate clear effects of the methodological choices, which also depend on the state of eDNA. A preliminary metabarcoding run showed little taxonomic overlap in mammal species detection between two metabarcoding primers tested. We recommend water filtering (using filters with pore sizes >1 μm) over centrifugation for eDNA concentration, Longmire's solution for ambient temperature sample preservation and Qiagen's DNeasy PowerSoil Pro Kit for DNA extraction of these inhibitor-prone samples. Furthermore, at least two independent metabarcoding markers should be utilized in order to maximize species detections in metabarcoding studies.

Wilder rangelands as a natural climate opportunity: Linking climate action to biodiversity conservation and social transformation

Rangelands face threats from climate and land-use change, including inappropriate climate change mitigation initiatives such as tree planting in grassy ecosystems. The marginalization and impoverishment of rangeland communities and their indigenous knowledge systems, and the loss of biodiversity and ecosystem services, are additional major challenges. To address these issues, we propose the wilder rangelands integrated framework, co-developed by South African and European scientists from diverse disciplines, as an opportunity to address the climate, livelihood, and biodiversity challenges in the world's rangelands. More specifically, we present a Theory of Change to guide the design, monitoring, and evaluation of wilder rangelands. Through this, we aim to promote rangeland restoration, where local communities collaborate with regional and international actors to co-create new rangeland use models that simultaneously mitigate the impacts of climate change, restore biodiversity, and improve both ecosystem functioning and livelihoods.

Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species

Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.

Proceed with Caution: Social Acceptability of Forestry Practices in Puerto Rico among Members of Local Environmental Organizations, Academia and Professional Associations

Social acceptability of forestry practices plays a key role in defining sustainable forestry policies and strategies. In this study an online survey was distributed among members of environmental, non-governmental, professional, and academic organizations to assess the acceptability of forestry practices in Puerto Rico among members of civic society interested in environmental management issues. Participants were asked about their perception of forest uses, their preference of tree harvesting technologies, methods that may apply in small scale wood production settings, and trust in organizations providing forest information. We also inquired about attitudes towards economic activity in forests and the impact of such activity on recreation and biodiversity. The results show that even though participants do not place a high priority on economic development through forestry activities, acceptance of forest management for wood harvesting will be possible by considering adherence to particular forestry technologies and methods to safeguard current recreation activities and biodiversity conservation. Social acceptability information would be worthwhile when seeking consensus among a broader group of local stakeholders. As a next step we suggest the creation of a council constituted by diverse forestry sector stakeholders that would engage in a strategic planning exercise to delineate a clear road map that can guide short and long-term sustainable forest management, including wood industry development.

Interplay between Livestock Grazing and Aridity on the Ecological and Nutritional Value of Forage in Semi-arid Mediterranean Rangelands (NE Spain)

Rangeland-based livestock production constitutes a primary source of livelihood for many inhabitants of dryland regions. Their subsistence relies heavily on maintaining the productivity, biodiversity and services of these ecosystems. Harsh environmental conditions (e.g., drought) combined with land use intensification (e.g., overgrazing) make dryland ecosystems vulnerable and prone to degradation. However, the interplay between livestock grazing intensity and aridity conditions in driving the conservation and nutritional value of forage in arid and semi-arid rangelands is still not fully understood. In this study, we performed structural equation models (SEM) to assess the simultaneous direct and indirect effects of livestock grazing intensity and aridity level on community structure, diversity, biomass, forage production, forage C:N ratio and forage fiber composition in two semi-arid Mediterranean rangelands, NE Spain. Not surprisingly, we found that higher livestock grazing intensity led to lower community plant cover, especially when combined with higher aridity. However, both increasing grazing intensity and aridity were associated with higher forage production after one year of grazing exclusion. We did not find any adverse effect of livestock grazing on plant diversity, although plant species composition differed among grazing intensity levels. On the other hand, we found an aridity-driven trade-off in regard of the nutritional value of forage. Specifically, higher aridity was associated with a decrease in the least digestible fiber fraction (i.e., lignin) and an increase in forage C:N ratio. More interestingly, we found that livestock grazing modulated this trade-off by improving the overall forage nutritional value. Altogether, our results provide further insights into the management of semi-arid Mediterranean rangelands, pointing out that maintaining traditional rangeland-based livestock production may be a sustainable option as long as rangeland conservation (e.g., community plant cover) is not severely compromised.

Long-term recovery of benthic food webs after stream restoration

The assessment of restoration success often neglects trophic interactions within food webs, focusing instead on biodiversity and community structure. Here, we analysed the long-term recovery of food web structure based on stable isotopes (δ13C and δ15N) of benthic invertebrates and quantified responses of food web metrics to time since restoration. The samples derived from twelve restored sites with different restoration ages, sampled annually from 2012 to 2021, and covering an investigation period of up to 28 years after restoration for the whole catchment. Temporal developments of the restored sites were compared to the development of two near-natural sites. The restoration measures consisted of the cessation of sewage inflow and morphological restoration of the channels. As a clear and consistent result over almost all sites, trophic similarity (proportion of co-existing species occupying similar trophic niches) increased with time since restoration, and reached values of near-natural sites, suggesting an increase in the stability and resilience of the food webs. Surprisingly, resource diversity decreased at most restored sites within 10 years after restoration, probably due to the removal of wastewater-derived resources, and a shift towards leaf litter as the dominant resource following the regrowth of the riparian vegetation. Food chain length showed no consistent pattern over time at the different sites both increasing and decreasing with time since restoration. Overall, restoration had clear effects on the food web structure of stream ecosystems. While some effects such as the increase in trophic similarity were consistent at almost all sites, others such as response of the food chain length were context dependent. The study demonstrates the potential of utilizing food web metrics, particularly trophic similarity, in restoration research to achieve a more holistic understanding of ecosystem recovery.

Revealing population demographics with environmental RNA

The analyses of environmental DNA (eDNA) and environmental RNA (eRNA) released by organisms into their surrounding environment (water, soil and air) have emerged as powerful tools for monitoring biodiversity. While eDNA has been widely adopted for the non-invasive detection of species and characterization of community composition, the utilization of eRNA is still in its infancy. Due to its functional nature, eRNA holds intriguing potential for biodiversity monitoring offering new avenues of research beyond species detection. For example, conspecifics that are almost genetically identical can exhibit distinct transcriptomic differences depending on their life stage. In this issue of Molecular Ecology Resources, Parsley and Goldberg (2024) demonstrate, through a lab-validated field study, that eRNA can be used to detect distinct life stages of amphibians. This study elegantly demonstrates that eRNA can be used not only to detect invasive or endangered species but also to reveal population demographic information important for guiding effective conservation strategies.

Upsetting offsetting? Nathan the Wise's Ring Parable and three reasons why not to adopt the carbon offsetting logic to biodiversity

The climate crisis and the alarming loss of biodiversity require urgent action. One of the most popular tools to tackle these crises is offsetting, an accounting logic through which environmental damages can be compensated elsewhere with environmental benefits. Developed to help address the climate crisis, the carbon offsetting logic has also been transposed to address biodiversity loss. Biodiversity offsets permit the compensation of residual environmental damages through equivalent gains undertaken elsewhere. This article identifies three arguments that show why such a transposition is problematic. To explain the fundamental problem with biodiversity offsetting, the famous Lessing's "Nathan the Wise" Ring Parable (Ringparabel) is proposed as an allegoric interpretation of the biodiversity offsetting logic, stressing that unique entities lose their uniqueness and power once people try to replicate them.

Predicting downstream transport distance of fish eDNA in lotic environments

Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.