Unraveling the dynamic interplay of microbial communities associated to Lupinus angustifolius in response to environmental and cultivation conditions

Microorganisms form dynamic communities with plants, providing benefits such as nutrient acquisition and stress resilience. Understanding how these microorganisms are affected by environmental factors such as growth conditions and soil characteristics are essential for harnessing these communities for sustainable agriculture practices and their response to climate change. The microbiome associated to Lupinus angustifolius, a legume native in Europe, with a high protein value and stress resilience was characterized for the first time. Using 16S rRNA gene and ITS amplicon sequencing, we characterized the compositional and temporal changes of the bacterial and fungal communities associated to the soil, rhizosphere, and plant compartments where Lupinus angustifolius grows naturally. Our results suggest that the main difference in the soil microbial communities is related to the edaphic properties, although environmental factors such as temperature, humidity or rainfall also influenced the composition of the soil microbial communities. We also characterized the bacterial communities associated with the rhizosphere, roots, nodules, and leaves of wild plants collected in the field and compared them against plants obtained under greenhouse conditions. In the plant compartments, the bacterial composition appeared to be more affected by the growing conditions (field vs greenhouse), than by soil characteristics or location. These results can be used to identify key taxa that may play crucial roles in the development and adaptation of the host plant and its associated microbiota to environmental changes and highlight the importance of characterizing the plant microbiomes in their natural habitats. Soil, influenced by climatic seasons, shapes the plant microbiome assembly. Lupinus recruits a core microbiome across rhizosphere, roots, nodules, and leaves, that is stable across locations. However, cultivation conditions may alter microbiome dynamics, impacting the adaptability of its components. Wild plants show a resilient and adaptable microbiome while germination and cultivation in greenhouse conditions alter its composition and vulnerability.

Ensemble learning algorithms to elucidate the core microbiome's impact on carbon content and degradation properties at the soil aggregate level

Soil aggregates are crucial for soil organic carbon (OC) accumulation. This study, utilizing a 32-year fertilization experiment, investigates whether the core microbiome can elucidate variations in carbon content and decomposition across different aggregate sizes more effectively than broader bacterial and fungal community analyses. Employing ensemble learning algorithms that integrate machine learning with network inference, we found that the core microbiome accounts for an average increase of 26 % and 20 % in the explained variance of PCoA and Adonis analyses, respectively, in response to fertilization. Compared to the control, inorganic and organic fertilizers decreased the decomposition index (DDI) by 31 % and 38 %, respectively. The fungal core microbiome predominantly influenced OC content and DDI in larger macroaggregates (>2000 μm), explaining over 35 % of the variance, while the bacterial core microbiome had a lesser impact, explaining <30 %. Conversely, in smaller aggregates (<2000 μm), the bacterial core microbiome significantly influenced DDI (R2 > 0.2), and the fungal core microbiome more strongly affected OC content (R2 > 0.3). Mantel tests showed that pH is the most significant environmental factor affecting core microbiome composition across all aggregate sizes (Mantel's r > 0.8, P < 0.01). Linear correlation analysis further confirmed that the core microbiome's community structure could accurately predict OC content and DDI in aggregates (R2 > 0.8, P < 0.05). Overall, our findings suggested that the core microbiome provides deeper insights into the variability of aggregate organic carbon content and decomposition, with the bacterial core microbiome playing a particularly pivotal role within the soil aggregates.

A global meta-analysis reveals a consistent reduction of soil fauna abundance and richness as a consequence of land use conversion

Land use conversion of natural to production systems is one of the most important threats to belowground communities and to the key ecosystem processes in which they are involved. Available literature shows positive, negative, and neutral effects of land use changes on soil fauna communities; and these varying effects may be due to different characteristics of natural and production systems and soil organisms. We hypothesize that land conversion from high to low plant biomass, diversity, and structural complexity systems may have the most negative impacts on soil fauna. Here, we performed the first meta-analysis evaluating the overall effects of land use conversion on soil invertebrate communities and the influence of factors related to characteristics of natural and production systems, of soil fauna communities and methods. We compiled a dataset of 260 publications that yielded 1732 observations for soil fauna abundance and 459 for richness. Both abundance and richness showed a global decline as a consequence of natural land conversion to production systems. These negative effects were stronger, in general, when the conversion occurred in tropical and subtropical sites, and when natural systems were replaced by croplands, pastures and grazing systems. The effects of land use conversion also depended on soil property changes. In addition, the abundance of most taxa and richness of Acari and Collembola were strongly reduced by land use changes while Annelida were not affected. The highest reduction in abundance was recorded in omnivores and predators, whereas detritivores showed a reduction in richness. Our meta-analysis shows consistent evidence of soil biodiversity decline due to different land use changes and the partial dependence of those effects on the magnitude of changes in vegetation. These findings stress the need to continue developing production modes that effectively preserve soil biodiversity and ecosystem processes, without hampering food production.

Accelerated farmland bird population declines in European countries after their recent EU accession

Agricultural intensification is a major driver of global biodiversity loss. In Europe, intensification progressed over the 20th century and was accelerated by instruments of the EU's Common Agricultural Policy. Central and Eastern European (CEE) countries standing outside the EU until the beginning of the 21st century employed less intensive farming and are considered one of the continent's farmland biodiversity strongholds. Their recent EU accession might be either viewed as a threat to farmland biodiversity due to the availability of funds to increase agricultural production or as an opportunity to implement conservation measures aimed to preserve biodiversity. Here we assessed these possibilities using long-term monitoring data on farmland bird populations in seven CEE countries. We tested whether mean relative abundance and population trends changed after countries' EU accession, and whether such changes also occurred in agricultural management and conservation measures. Both agricultural intensity and spending for agri-environmental and climatic schemes increased when the CEE countries joined the EU. At the same time, farmland bird populations started to decline and their relative abundance was lower after than before EU accession. In addition, increases in fertilizer application were negatively associated with annual changes in relative farmland bird population sizes, indicating a negative impact of intensive agriculture. Taken together, these results indicate that despite the great power of the EU's environmental legislation to improve the population status of species at risk, this does not apply to farmland birds. In their case, the adverse impacts of agricultural intensification most likely overrode the possible benefits of conservation measures. To secure this region as one of the continent's farmland biodiversity strongholds, policy and management actions are urgently needed.

Potential drivers of changing ecological conditions in English and Welsh rivers since 1990

River invertebrate communities across Europe have been changing in response to variations in water quality over recent decades, but the underlying drivers are difficult to identify because of the complex stressors and environmental heterogeneity involved. Here, using data from ∼4000 locations across England and Wales, collected over 29 years, we use three approaches to help resolve the drivers of spatiotemporal variation in the face of this complexity: i) mapping changes in invertebrate richness and community composition; ii) structural equation modelling (SEM) to distinguish land cover, water quality and climatic influences; and iii) geographically weighted regression (GWR) to identify how the apparent relationships between invertebrate communities and abiotic variables change across the area. Mapping confirmed widespread increases in richness and the proportion of pollution-sensitive taxa across much of England and Wales. It also revealed regions where pollution-sensitive taxa or overall richness declined, the former primarily in the uplands. SEMs confirmed strong increases in average biochemical oxygen demand and nutrient concentrations related to urban and agricultural land cover, but only a minority of land cover's effect upon invertebrate communities was explained by average water chemistry, highlighting potential factors such as episodic extremes or emerging contaminants. GWR identified strong geographical variation in estimated relationships between macroinvertebrate communities and environmental variables, with evidence that the estimated negative impacts of nutrients and water temperature were increasing through time. Overall the results are consistent with widespread biological recovery of Britain's rivers from past gross organic pollution, whilst highlighting declines in some of the most diverse and least impacted streams. Modelling points to a complex and changing set of drivers, highlighting the multifaceted impacts of catchment land cover and the evolving role of different stressors, with the relationship to gross organic pollution weakening, whilst estimated nutrient and warming effects strengthened.

Distribution patterns of reef-building corals in the Northwest Pacific and their environmental drivers

Understanding species distribution and the related driving processes is a fundamental issue in ecology. However, incomplete data on reef-building corals in the ecoregions of the South China Sea have hindered a comprehensive understanding of coral distribution patterns and their ecological drivers in the Northwest Pacific (NWP). This study investigated the coral species diversity and distribution patterns in the NWP by collecting species presence/absence data from the South China Sea and compiling an extensive species distribution database for the region, and explored their major environmental drivers. Our NWP coral database included 612 recorded coral species across 15 ecoregions. Of these, 536 coral species were recorded in the South China Sea Oceanic Islands after compilation, confirming the extraordinary coral species diversity in this ecoregion. Coral alpha diversity was found to decrease with increasing latitude in the whole NWP, while the influence of the Kuroshio Current on environmental conditions in its path results in a slower decline in species richness with latitude compared to regions within the South China Sea. Beta-diversity decomposition revealed that nestedness patterns mainly occurred between low and high latitude ecoregions, while communities within similar latitudes exhibited a turnover component, particularly pronounced at high latitudes. The impact of environmental factors on coral assemblage structure outweighed the effects of spatial distance. Temperature, especially winter temperature, and light intensity strongly influenced alpha diversity and beta diversity's nestedness component. Additionally, turbidity and winter temperature variations at high latitudes contributed to the turnover pattern observed among communities in the NWP. These findings elucidate the assembly processes and major environmental drivers shaping different coral communities in the NWP, highlighting the significant role of specific environmental filtering in coral distribution patterns and providing valuable insights for coral species conservation efforts.

Effects of industrial pollution and ambient air temperature on larval performance and population dynamics of Eriocrania leafminers (Lepidoptera)

Pollution is an integral part of global environmental change, yet the combined and interactive effects of pollution and climate on terrestrial ecosystems remain inadequately understood. This study aims to explore whether pollution alters the impacts of ambient air temperature on the population dynamics of herbivorous insects. Between 1995 and 2005, we studied populations of two closely related moths, Eriocrania semipurpurella and E. sangii, at eight sites located 1 to 64 km from a large copper‑nickel smelter in Monchegorsk, Russia. We found that pollution and temperature influence the performance of Eriocrania larvae mining in the leaves of mountain birch, Betula pubescens var. pumila, through multiple pathways. This is evident from the unconsistent changes observed in larval and frass weight, mine area, and leaf size. We found increases in both leaf quality and larval weight with decreasing pollution levels at both spatial and temporal scales and attributed these to the impact of sulphur dioxide, rather than trace elements (nickel and copper). The quality of birch leaves increased with spring (May) temperatures, enabling Eriocrania larvae to achieve greater weight while consuming less biomass. During the larval growth period (early June to early July), Eriocrania larvae increased their consumption with rising temperatures, presumably to compensate for increased metabolic expenses. Contrary to our expectations, the per capita rate of population change did not correlate with larval weight and did not vary along the pollution gradient. Nevertheless, we detected interactive effects of pollution and climate on the rate of population change. This rate decreased with rising winter temperatures in slightly polluted and unpolluted sites but remained unchanged in heavily polluted sites. We conclude that pollution disrupts mechanisms regulating the natural population dynamics of Eriocrania moths.

When does a parasite become a disease? eDNA unravels complex host-pathogen dynamics across environmental stress gradients in wild salmonid populations

Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasite's infective stages, as well as the host's ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modelling at a regional scale, we uncovered the biotic and abiotic drivers of an infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water-i.e., the propagule pressure- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts-i.e., proxies for disease emergence-were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by modulating the hosts' immune response. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on pathogen emergence.

Evidence for a survival-driven traveling wave in a keystone boreal predator population

Cyclical population dynamics are a common phenomenon in populations worldwide, yet the spatial organization of these cycles remains poorly understood. In this study, we investigated the spatial form and timing of a population collapse from 2018 to 2022 in Canada lynx (Lynx canadensis) across the northwest boreal forest. We analyzed survival, reproduction, and dispersal data from 143 individual global positioning system (GPS) collared lynx from populations across five study sites spanning interior Alaska to determine whether lynx displayed characteristics of a population wave following a concurrent wave in snowshoe hare (Lepus americanus) abundance. Reproductive rates declined across the study sites; however, site-level reproduction declined first in our easternmost study sites, supporting the idea of a population wave. Despite a clear increase in percent of dispersing lynx, there was no evidence of directional bias in dispersal following a hare population wave. Analysis did show increasingly poor survival for lynx dispersing to the east compared to combined resident and westward dispersal. This pattern is consistent with a survival-mediated population wave in lynx as the driver of the theorized population wave. The combination of these factors supports the idea of a hierarchical response to snowshoe hare population declines with a drop in lynx reproduction followed by increased dispersal, and finally reduced survival. All of this evidence is consistent with the expected characteristics of a population undergoing a traveling wave and supports the hypothesis that lynx presence may facilitate and mirror the underlying wave patterns in snowshoe hare.

Unravelling the influence of microplastics with/without additives on radish (Raphanus sativus) and microbiota in two agricultural soils differing in pH

Here we investigated the effects of three types of microplastics (MPs), i.e., PS (P), ABS (B), PVC (V), and each with additive (MPAs) (PA, BA, and VA), on soil health, microbial community, and plant growth in two acidic and slightly alkaline soils. Incubation experiment revealed that although MPs and MPAs consistently stimulated soil nutrients and heavy metals (e.g., Mn, Cu) in weakly alkaline soils, only BA and VA led to increase in soil nutrients and heavy metals in acidic soils. This suggests distinct response patterns in the two soils depending on their initial pH. Concerning microorganisms, MPs and MPAs reduced the assembly degree of bacteria in acidic soils, with a reduction of Chloroflexi and Acidobacteriota but an increase of WPS-2 in VA. Culture experiment showed consistent positive or negative responses in radish seed germination, roots, and antioxidant activity across MPs and MPAs types in both soils, while the responses of seed heavy metals (e.g., Cr, Cd) were consistent in acidic soils but dependent on MPs and MPAs types in alkaline soils. Therefore, our study strongly suggests that the effects of MPs on soil-microbial-plant systems were highly dependent on initial soil characteristics and the types of MPs with plastic additives.

Source apportionment of organic carbon and nitrogen in sediments from river and lake in the highly urbanized Changjiang Delta

While the impact of human activities on organic matter pollution is recognized, how these impacts vary seasonally in the Changjiang Delta needs further investigation. This study addresses this gap by investigating seasonal variations in organic matter sources and ecological responses to human activities in Changjiang Delta sediments. Total organic carbon (TOC), total nitrogen (TN), and carbon (δ13C) and nitrogen (δ15N) isotopic compositions of surface sediments collected from the Taipu River and Dalian Lake wetland were analyzed. Both water bodies exhibited similar seasonal trends for TOC and TN, with the Taipu River containing an average of 0.46% and 0.03% higher concentrations of TOC and TN, respectively, compared to Dalian Lake. Additionally, the organic index (OI) and organic nitrogen (ON) index were elevated in both water bodies during the wet season. Sediments from Dalian Lake remained uncontaminated to moderately contaminated, while those from the Taipu River were generally classified as moderately to heavily contaminated. Stable isotope analysis identified terrestrial C3 plants (averaging 25.5%), C4 plants (averaging 16.0%), and municipal wastewater (averaging 16.0%) as the main contributors to organic matter in the sediments. These findings suggest that terrestrial plant material and municipal wastewater are key targets for managing organic matter contamination in the Changjiang Delta. Implementing strategic land-use planning and targeted interventions to minimize these inputs can significantly improve water quality and ecosystem health.

Fungal community determines soil multifunctionality during vegetation restoration in metallic tailing reservoir

Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals.

Emerging threat of marine microplastics: Cigarette butt contamination on Yellow Sea beaches and the potential toxicity risks to rotifer growth and reproduction

Cigarette butts have become one of the most common and persistent forms of debris in marine coastal areas, where they pose significant toxicity risks. This study investigated cigarette butt pollution along beaches of the Yellow Sea and used laboratory experiments to assess the toxicity of their leachate and fibers on the euryhaline rotifer Brachionus plicatilis. A pollution index confirmed pollution by this debris across all eight beaches surveyed, where the density of cigarette butts averaged 0.23 butts/m2. In controlled laboratory experiments, both the fibers and leachates from cigarette butts exhibited negative impacts on the development, reproduction, and population growth of rotifers. Unique abnormalities observed under different exposure treatments indicated toxicity specific to certain chemicals and particles. Continuous exposure to cigarette butts initially reduced rotifer fecundity, but this effect diminished over successive generations. However, the exposure induced transgenerational reproductive toxicity in the rotifers. Adaptive responses in rotifers after repeated exposure led to relative reduction in reproductive inhibition in the F3 and F4 generations. Furthermore, rotifers were capable of ingesting and accumulating cigarette butts, and maternal transfer emerged as an alternative pathway for uptake of this material in the offspring. These results increase our understanding of the ecological risks posed by cigarette butts in aquatic environments.

An integrated fast-slow plant and nematode economics spectrum predicts soil organic carbon dynamics during natural restoration

Aboveground and belowground attributes of terrestrial ecosystems interact to shape carbon (C) cycling. However, plants and soil organisms are usually studied separately, leading to a knowledge gap regarding their coordinated contributions to ecosystem C cycling. We explored whether integrated consideration of plant and nematode traits better explained soil organic C (SOC) dynamics than plant or nematode traits considered separately. Our study system was a space-for-time natural restoration chronosequence following agricultural abandonment in a subtropical region, with pioneer, early, mid and climax stages. We identified an integrated fast-slow trait spectrum encompassing plants and nematodes, demonstrating coordinated shifts from fast strategies in the pioneer stage to slow strategies in the climax stage, corresponding to enhanced SOC dynamics. Joint consideration of plant and nematode traits explained more variation in SOC than by either group alone. Structural equation modeling revealed that the integrated fast-slow trait spectrum influenced SOC through its regulation of microbial traits, including microbial C use efficiency and microbial biomass. Our findings confirm the pivotal role of plant-nematode trait coordination in modulating ecosystem C cycling and highlight the value of incorporating belowground traits into biogeochemical cycling under global change scenarios.

Reviving collapsed plant-pollinator networks from a single species

Mutualistic ecological networks can suddenly transition to undesirable states due to small changes in environmental conditions. Recovering from such a collapse can be difficult as restoring the original environmental conditions may be infeasible. Additionally, such networks can also exhibit a phenomenon known as hysteresis, whereby the system could exhibit multiple states under the same environmental conditions, implying that ecological networks may not recover. Here, we attempted to revive collapsed mutualistic networks to a high-functioning state from a single species, using concepts from signal propagation theory and an eco-evolutionary model based on network structures of 115 empirical plant-pollinator networks. We found that restoring the environmental conditions rarely aided in recovery of collapsed networks, but a positive relationship between recovering pollinator density and network nestedness emerged, which was qualitatively supported by empirical plant-pollinator restoration data. In contrast, network resurrection from a collapsed state in undesirable environmental conditions where restoration has minimal impacts could be readily achieved by perturbing a single species or a few species that controls the response of the dynamical networks. Additionally, nestedness in networks and a moderate amount of trait variation could aid in the revival of networks even in undesirable environmental conditions. Our work suggests that focus should be applied to a few species whose dynamics could be steered to resurrect entire networks from a collapsed state and that network architecture could play a crucial role in reviving collapsed plant-pollinator networks.

Warming and trophic structure tightly control phytoplankton bloom amplitude, composition and succession

To better identify the responses of phytoplankton blooms to warming conditions as expected in a climate change context, an in situ mesocosm experiment was carried out in a coastal Mediterranean lagoon (Thau Lagoon, South of France) in April 2018. Our objective was to assess both the direct and indirect effects of warming on phytoplankton, particularly those mediated by top-down control. Four treatments were applied: 1) natural planktonic community with ambient water temperature (C); 2) natural planktonic community at +3°C elevated temperature (T); 3) exclusion of larger zooplankton (> 200 μm; mesozooplankton) leaving microzooplankton predominant with ambient water temperature (MicroZ); and 4) exclusion of larger zooplankton (> 200 μm; mesozooplankton) at +3°C elevated temperature (TMicroZ). Warming strongly depressed the amplitude of the phytoplankton bloom as the chlorophyll a concentration was twice lower in the T treatment. This decline under warmer conditions was most likely imputed to increase top-down control by zooplankton. However, removal of mesozooplankton resulted in an opposite trend, with a higher bloom amplitude observed under warmer conditions (MicroZ vs. TMicroZ) pointing at a strong interplay between micro- and mesozooplankton and the effect of warming for the spring phytoplankton blooms. Furthermore, both warming and mesozooplankton exclusion induced shifts in phytoplankton community composition during bloom and post-bloom periods, favoring dinoflagellates and small green algae at the expense of diatoms and prymnesiophytes. Moreover, warming altered phytoplankton succession by promoting an early bloom of small green flagellates, and a late bloom of diatoms. Our findings clearly highlighted the sensitivity of phytoplankton blooms amplitudes, community composition and succession patterns to temperature increases, as well as the key role of initial zooplankton community composition to elicit opposite response in bloom dynamics. It also points out that warmer conditions might favor dinoflagellates and small green algae, irrespective of zooplankton community composition, with potential implications for food web dynamics and energy transfer efficiency under future ocean condition.

Species traits, landscape quality and floral resource overlap with honeybees determine virus transmission in plant-pollinator networks

Emerging infectious diseases pose a threat to pollinators. Virus transmission among pollinators via flowers may be reinforced by anthropogenic land-use change and concomitant alteration of plant-pollinator interactions. Here, we examine how species' traits and roles in flower-visitation networks and landscape-scale factors drive key honeybee viruses-black queen cell virus (BQCV) and deformed wing virus-in 19 wild bee and hoverfly species, across 12 landscapes varying in pollinator-friendly (flower-rich) habitat. Viral loads were on average more than ten times higher in managed honeybees than in wild pollinators. Viral loads in wild pollinators were higher when floral resource use overlapped with honeybees, suggesting these as reservoir hosts, and increased with pollinator abundance and viral loads in honeybees. Viral prevalence decreased with the amount of pollinator-friendly habitat in a landscape, which was partly driven by reduced floral resource overlap with honeybees. Black queen cell virus loads decreased with a wild pollinator's centrality in the network and the proportion of visited dish-shaped flowers. Our findings highlight the complex interplay of resource overlap with honeybees, species traits and roles in flower-visitation networks and flower-rich pollinator habitat shaping virus transmission.

The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions

Humans have been driving a global erosion of species richness for millennia, but the consequences of past extinctions for other dimensions of biodiversity-functional and phylogenetic diversity-are poorly understood. In this work, we show that, since the Late Pleistocene, the extinction of 610 bird species has caused a disproportionate loss of the global avian functional space along with ~3 billion years of unique evolutionary history. For island endemics, proportional losses have been even greater. Projected future extinctions of more than 1000 species over the next two centuries will incur further substantial reductions in functional and phylogenetic diversity. These results highlight the severe consequences of the ongoing biodiversity crisis and the urgent need to identify the ecological functions being lost through extinction.

Drivers of urban biodiversity in Mexico and joint risks from future urban expansion, climate change, and urban heat island effect

Urbanization is a phenomenon where humans concentrate in high densities and consume more per capita energy than in rural areas, imposing high pressures on biodiversity and ecosystem services. Although Mexico is recognized as a megadiverse country and there is an understanding of ecological and evolutionary processes underlying this high diversity, only some efforts have been devoted to understanding how urban biodiversity has been shaped. Here, we compiled a set of socioeconomic and ecological variables to explore macroecological patterns in urban biodiversity across Mexican municipalities. Specifically, we tested the species-area relationships (SAR) between rural and urban areas across municipalities and evaluated the relative role of different socioeconomic and ecological variables driving urban species richness for terrestrial vertebrates. Finally, we explored the exposure of Mexican municipalities to future urban expansion, the urban heat island (UHI) effect, and climate change. Urban and rural settlements show differences in the shape of SAR models. We found that urban area, size of the network of urban protected areas, the number of ecoregions, and GDP explained the urban total species richness relatively well. Mexican cities in the northeast region may be at a higher risk than others. Based on our analyses, policymakers should identify priority urban conservation sites in cities with high species richness and low urbanization development. These actions would alleviate future urban biodiversity loss in these growing cities.

Aridity drives the response of soil total and particulate organic carbon to drought in temperate grasslands and shrublands

The increasing prevalence of drought events in grasslands and shrublands worldwide potentially has impacts on soil organic carbon (SOC). We leveraged the International Drought Experiment to study how SOC, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) concentrations, responds to extreme drought treatments (1-in-100-year) for 1 to 5 years at 19 sites worldwide. In more mesic areas (aridity index > 0.65), SOC and POC concentrations decreased by 7.9% (±3.9) and 15.9% (±6.2) with drought, respectively, but there were no impacts on MAOC concentrations. However, drought had no impact on SOC, POC, or MAOC concentrations in drylands (aridity index < 0.65). The response of SOC to drought varied along an aridity gradient, concomitant with interannual precipitation variability and standing SOC concentration gradients. These findings highlight the differing response magnitudes of POC and MAOC concentrations to drought and the key regulating role of aridity.

Resource availability enhances positive tree functional diversity effects on carbon and nitrogen accrual in natural forests

Forests harbor extensive biodiversity and act as a strong global carbon and nitrogen sink. Although enhancing tree diversity has been shown to mitigate climate change by sequestering more carbon and nitrogen in biomass and soils in manipulative experiments, it is still unknown how varying environmental gradients, such as gradients in resource availability, mediate the effects of tree diversity on carbon and nitrogen accrual in natural forests. Here, we use Canada's National Forest Inventory data to explore how the relationships between tree diversity and the accumulation of carbon and nitrogen in tree biomass and soils vary with resource availability and environmental stressors in natural forests. We find that the positive relationship between tree functional diversity (rather than species richness) and the accumulation of carbon in tree biomass strengthens with increasing light and soil nutrient availability. Moreover, the positive relationship between tree functional diversity and the accumulation of carbon and nitrogen in both organic and mineral soil horizons is more pronounced at sites with greater water and nutrient availabilities. Our results highlight that conserving and promoting functionally diverse forests in resource-rich environments could play a greater role than in resource-poor environments in enhancing carbon and nitrogen sequestration in Canada's forests.

Droughts reshape apex predator space use and intraguild overlap

Droughts are increasing in frequency and severity globally due to climate change, leading to changes in resource availability that may have cascading effects on animal ecology. Resource availability is a key driver of animal space use, which in turn influences interspecific interactions like intraguild competition. Understanding how climate-induced changes in resource availability influence animal space use, and how species-specific responses scale up to affect intraguild dynamics, is necessary for predicting broader community-level responses to climatic changes. Although several studies have demonstrated the ecological impacts of drought, the behavioural responses of individuals that scale up to these broader-scale effects are not well known, particularly among animals in top trophic levels like large carnivores. Furthermore, we currently lack understanding of how the impacts of climate variability on individual carnivore behaviour are linked to intraguild dynamics, in part because multi-species datasets collected at timescales relevant to climatic changes are rare. Using 11 years of GPS data from four sympatric large carnivore species in southern Africa-lions (Panthera leo), leopards (Panthera pardus), African wild dogs (Lycaon pictus) and cheetahs (Acinonyx jubatus)-spanning 4 severe drought events, we test whether drought conditions impact (1) large carnivore space use, (2) broad-scale intraguild spatial overlap and (3) fine-scale intraguild interactions. Drought conditions expanded space use across species, with carnivores increasing their monthly home range sizes by 35% (wild dogs) to 66% (leopards). Drought conditions increased the amount of spatial overlap between lions and subordinate felids (cheetahs and leopards) by up to 119%, but only lion-cheetah encounter rates were affected by these changes, declining in response to drought. Our findings reveal that drought has a clear signature on the space use of multiple sympatric large carnivore species, which can alter spatiotemporal partitioning between competing species. Our study thereby illuminates the links between environmental change, animal behaviour and intraguild dynamics. While fine-scale avoidance strategies may facilitate intraguild coexistence during periodic droughts, large carnivore conservation may require considerable expansion of protected areas or revised human-carnivore coexistence strategies to accommodate the likely long-term increased space demands of large carnivores under projected increases in drought intensity.

Environment-independent distribution of mutational effects emerges from microscopic epistasis

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, in which the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.

The pace of life for forest trees

Tree growth and longevity trade-offs fundamentally shape the terrestrial carbon balance. Yet, we lack a unified understanding of how such trade-offs vary across the world's forests. By mapping life history traits for a wide range of species across the Americas, we reveal considerable variation in life expectancies from 10 centimeters in diameter (ranging from 1.3 to 3195 years) and show that the pace of life for trees can be accurately classified into four demographic functional types. We found emergent patterns in the strength of trade-offs between growth and longevity across a temperature gradient. Furthermore, we show that the diversity of life history traits varies predictably across forest biomes, giving rise to a positive relationship between trait diversity and productivity. Our pan-latitudinal assessment provides new insights into the demographic mechanisms that govern the carbon turnover rate across forest biomes.

A bird's-eye view of avian extinctions

Conservation should consider species' functional and phylogenetic traits.

Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany

Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.

Testing the sequence of successional processes in miniature ecosystems

Dispersal, environmental filtering, and biotic interactions define the species inventory of local communities. Along successional gradients, these assembly processes are predicted to sequentially vary in their relative importance with dispersal as the dominating process early in succession, followed by environmental filtering and biotic interactions at later stages. While observational data from field studies supported this prediction, controlled experiments confirming a sequence of successional processes are still lacking. We designed miniature ecosystems to explicitly test these assumptions under controlled laboratory conditions. Our "Ecosystems on a Plate" (EsoaP) are 3D-printed customized microplates with 24 connected wells allowing us to track dispersal, niche filtering, and biotic interactions among bacteria and plants in time and space. Within EsoaPs, we created heterogeneous habitat landscapes by well-specific nutrient levels or by providing plant seedlings as mutualistic partners in a checkerboard pattern. Bacteria of a single strain were released in one well and subsequently distributed themselves within the plates. We measured the spatial distribution of bacterial abundances at two time points as a function of abiotic or biotic heterogeneity. Bacterial abundance distribution confirmed a shift from initial dispersal-dominated processes to later niche filtering and biotic interactions as more important processes. Our approach follows the principles of open science as the affordable availability of 3D printers as well as shared STL files makes EsoaPs disseminatable and accessible to all levels of society, facilitating future experimental research.

IMPORTANCE

Hypotheses regarding the underlying processes of ecological successions have primarily emerged from and have been tested in observational studies, lacking substantial support through controlled experiments. The design of such experiments should focus on testing contemporary ecological theories at the intersection of community assembly and successional research. To achieve this, we developed and employed 3D-printed "Ecosystems on a Plate" (EsoaP) within controlled laboratory settings. EsoaPs surmount several limitations of nanoscale instruments that had hindered their application in ecologically meaningful research. By sharing 3D printing designs, experimental protocols, and data openly, we facilitate reproducibility of our experiments by researchers across diverse ecological disciplines. Moreover, our approach facilitates cost-effective replication of experiments, democratizing access to tools for ecological research, and thus holds the potential to serve as a model for future studies and educational purposes.

Stem Growth and Dehydration Responses of Mediterranean Tree Species to Atmospheric and Soil Drought

Stem growth responses to soil and atmospheric drought are critical to forecasting the tree carbon sink strength. Yet, responses of drought-prone forests remain uncertain despite global aridification trends. Stem diameter variations at an hourly resolution were monitored in five Mediterranean tree species from a mesic and a xeric site for 6 and 12 years. Stem growth and dehydration responses to soil (REW) and atmospheric (VPD) drought were explored at different timescales. Annually, growth was determined by the number of growing days and hours. Seasonally, growth was bimodal (autumn growth ≈ 8%-18% of annual growth), varying among species and sites across the hydrometeorological space, while dehydration consistently responded to REW. Sub-daily, substantial growth occurred during daytime, with nighttime-to-daytime ratios ranging between 1.2 and 3.5 (Arbutus unedo ≈ Quercus faginea < Quercus ilex < Pinus halepensis in the mesic site, and Juniperus thurifera < P. halepensis in the xeric site). Overall, time windows favourable for growth were limited by soil (rather than atmospheric) drought, modulating annual and seasonal growth in Mediterranean species, and stems maintained non-negligible growth during daytime. These patterns contrast with observations from wetter or cooler biomes, demonstrating the growth plasticity of drought-prone species to more arid climate conditions.

Coexistence from a lion's perspective: Movements and habitat selection by African lions (Panthera leo) across a multi-use landscape

Diminishing wild space and population fragmentation are key drivers of large carnivore declines worldwide. The persistence of large carnivores in fragmented landscapes often depends on the ability of individuals to move between separated subpopulations for genetic exchange and recovery from stochastic events. Where separated by anthropogenic landscapes, subpopulations' connectivity hinges on the area's socio-ecological conditions for coexistence and dispersing individuals' behavioral choices. Using GPS-collars and resource- and step-selection functions, we explored African lion (Panthera leo) habitat selection and movement patterns to better understand lions' behavioral adjustments in a landscape shared with pastoralists. We conducted our study in the Ngorongoro Conservation Area (NCA), Tanzania, a multiuse rangeland, that connects the small, high density lion subpopulation of the Ngorongoro Crater with the extensive Serengeti lion population. Landscape use by pastoralists and their livestock in the NCA varies seasonally, driven by the availability of pasture, water, and disease avoidance. The most important factor for lion habitat selection was the amount of vegetation cover, but its importance varied with the distance to human settlements, season and time of day. Although we noted high levels of individual variation in tolerance for humans, in general lions avoided humans on the landscape and used more cover when closer to humans. Females showed more consistent avoidance of humans and stronger use of cover when near humans than did males. Connectivity of lion subpopulations does not appear to be blocked by sparse pastoralist settlements, and nomadic males, key to subpopulation connectivity, significantly avoided humans during the day, suggesting a behavioral strategy for conflict mitigation. These results are consistent with lions balancing risk from humans with exploitation of livestock by altering their behaviors to reduce potential conflict. Our study lends some optimism for the adaptive capacity of lions to promote coexistence with humans in shared landscapes.

Butterfly eggs prime anti-herbivore defense in an annual but not perennial Arabidopsis species

MAIN CONCLUSION

Unlike Arabidopsis thaliana, defenses of Arabidopsis lyrata against Pieris brassicae larval feeding are not primable by P. brassicae eggs. Thus, egg primability of plant anti-herbivore defenses is not phylogenetically conserved in the genus Arabidopsis. While plant anti-herbivore defenses of the annual species Arabidopsis thaliana were shown to be primable by Pieris brassicae eggs, the primability of the phylogenetically closely related perennial Arabidopsis lyrata has not yet been investigated. Previous studies revealed that closely related wild Brassicaceae plant species, the annual Brassica nigra and the perennial B. oleracea, exhibit an egg-primable defense trait, even though they have different life spans. Here, we tested whether P. brassicae eggs prime anti-herbivore defenses of the perennial A. lyrata. We exposed A. lyrata to P. brassicae eggs and larval feeding and assessed their primability by (i) determining the biomass of P. brassicae larvae after feeding on plants with and without prior P. brassicae egg deposition and (ii) investigating the plant transcriptomic response after egg deposition and/or larval feeding. For comparison, these studies were also conducted with A. thaliana. Consistent with previous findings, A. thaliana's response to prior P. brassicae egg deposition negatively affected conspecific larvae feeding upon A. thaliana. However, this was not observed in A. lyrata. Arabidopsis thaliana responded to P. brassicae eggs with strong transcriptional reprogramming, whereas A. lyrata responses to eggs were negligible. In response to larval feeding, A. lyrata exhibited a greater transcriptome change compared to A. thaliana. Among the strongly feeding-induced A. lyrata genes were those that are egg-primed in feeding-induced A. thaliana, i.e., CAX3, PR1, PR5, and PDF1.4. These results suggest that A. lyrata has evolved a robust feeding response that is independent from prior egg exposure.

Rhizosphere microbial community structure in high-producing, low-input switchgrass families

Switchgrass (Panicum virgatum L.) is a native, low-input North American perennial crop primarily grown for bioenergy, livestock forage, and industrial fiber. To achieve no-input switchgrass production that meets biomass needs, several switchgrass genotypes have been identified that have a low or negative response to nitrogen fertilizer, i.e., the biomass accumulation with added nitrogen is less than or equal to that when grown without nitrogen. In order to improve the viability of low-input switchgrass production, a more detailed understanding of the biogeochemical mechanisms active in these select genotypes is needed. 16S and ITS amplicon sequencing and qPCR of key functional genes were applied to switchgrass rhizospheres to elucidate microbial community structure in high-producing, no-input switchgrass families. Rhizosphere microbial community structure differed strongly between sites, and nitrogen responsiveness.

Elevated O3 has stronger effects than CO2 on soil nematode abundances but jointly inhibits their diversity in paddy soils

Anthropogenic activities have resulted in rising atmospheric concentrations of carbon dioxide (CO2) and ozone (O3), exerting substantial direct and indirect impacts on soil biodiversity within agroecosystems. Despite the considerable attention given to the individual impacts of elevated CO2 and O3 levels, the combined effects on soil nematode communities have not been extensively explored. In this study, we investigated the interactive effects of elevated CO2 (+200 ppm, eCO2) and O3 (+40 ppb, eO3) levels on the abundance, diversity, and trophic composition of soil nematode communities associated with two rice cultivars (Nanjing 5055, NJ5055 and Wuyujing 3, WYJ3). Our findings revealed that soil nematodes had greater abundances under eO3, whereas eCO2 had no significant impacts. Conversely, both eCO2 and eO3, and their combination led to significant reductions in nematode generic richness, accompanied by a decline in the diversity particularly associated with the WYJ3 cultivar. Moreover, eCO2 and eO3 influenced nematode community composition and environmental factors, particularly for the WYJ3 cultivar. Both eCO2 and eO3 significantly increased soil nitrate levels. The changes in nematode community composition were related to soil nitrate levels, as well as nitrogen and carbon concentrations in rice plant roots. Furthermore, interactions between eCO2 and eO3 significantly impacted soil nematode abundance and trophic composition, revealing intricate consequences for soil nematode communities that transcend predictions based on single-factor experiments. This study unveils the potential impacts posed by eCO2 and eO3 on soil biodiversity mediated by rice cultivars, plant functional characteristics and soil feedback mechanisms, thereby underscoring the complex and interactive outcomes arising from concurrent drivers of climate change within the soil food web.

Plant community responses to the individual and interactive effects of warming and herbivory across multiple years

Anthropogenic climate warming affects plant communities by changing community structure and function. Studies on climate warming have primarily focused on individual effects of warming, but the interactive effects of warming with biotic factors could be at least as important in community responses to climate change. In addition, climate change experiments spanning multiple years are necessary to capture interannual variability and detect the influence of these effects within ecological communities. Our study explores the individual and interactive effects of warming and insect herbivory on plant traits and community responses within a 7-year warming and herbivory manipulation experiment in two early successional plant communities in Michigan, USA. We find stronger support for the individual effects of both warming and herbivory on multiple plant morphological and phenological traits; only the timing of plant green-up and seed set demonstrated an interactive effect between warming and herbivory. With herbivory, warming advanced green-up, but with reduced herbivory, there was no significant effect of warming. In contrast, warming increased plant biomass, but the effect of warming on biomass did not depend upon the level of insect herbivores. We found that these treatments had stronger effects in some years than others, highlighting the need for multiyear experiments. This study demonstrates that warming and herbivory can have strong direct effects on plant communities, but that their interactive effects are limited in these early successional systems. Because the strength and direction of these effects can vary by ecological context, it is still advisable to include levels of biotic interactions, multiple traits and years, and community type when studying climate change effects on plants and their communities.

The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment

Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.

IMPORTANCE

This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.

Characterization of differences in seed endophytic microbiome in conventional and organic rice by amplicon-based sequencing and culturing methods

The seed serves as the primary source for establishing microbial populations in plants across subsequent generations, influencing plant growth and overall health. Cropping conditions, especially farming practices, can influence the composition and functionality of the seed microbiome. Very little is known about the differences in seed microbiome between organic and conventional production systems. In this study, we characterized the endophytic microbial populations in seeds of rice grown under organic and conventional management practices through culture-dependent and -independent analyses. The V4 region of 16S rRNA was used for bacterial taxa identification, and the ITS1 region was used for the identification of fungal taxa. Our results revealed significantly higher Shannon and Simpson indices for bacterial diversity in the conventional farming system, whereas the fungal diversity was higher for observed, Shannon, and Simpson indices in the organic farming system. The cultivable endophytic bacteria were isolated and identified using the full-length 16S rRNA gene. There was no difference in culturable endophytic bacterial isolates in rice seeds grown under both conventional and organic farming systems. Among 33 unique isolates tested in vitro, three bacteria-Bacillus sp. ST24, Burkholderia sp. OR5, and Pantoea sp. ST25-showed antagonistic activities against Marasmius graminum, Rhizoctonia solani AG4, and R. solani AG11, the fungal pathogens causing seedling blight in rice.

IMPORTANCE

In this paper, we studied the differences in the endophytic microbial composition of rice seeds grown in conventional and organic farming systems. Our results demonstrate a greater bacterial diversity in conventional farming, while organic farming showcases a higher fungal diversity. Additionally, our research reveals the ability of seed bacterial endophytes to inhibit the growth of three fungal pathogens responsible for causing seedling blight in rice. This study provides valuable insights into the potential use of beneficial seed microbial endophytes for developing a novel microbiome-based strategy in the management of rice diseases. Such an approach has the potential to enhance overall plant health and improve crop productivity.

Existing evidence on the effect of urban forest management in carbon solutions and avian conservation: a systematic literature map

BACKGROUND

Urgent solutions are needed in cities to mitigate twin crises of global climate change and biodiversity loss. Urban nature-based solutions (actions that protect, sustainably manage, and restore ecosystems while simultaneously providing human wellbeing and biodiversity benefits) are being advocated for as multi-functional tools capable of tackling these societal challenges. Urban forest management is a proposed nature-based solution with potential to address both climate change mitigation and biodiversity loss along with multiple other benefits. However, bodies of evidence measuring multiple outcomes (e.g., biodiversity conservation and nature-based climate solutions) remain siloed which limits conservation and management opportunities. In this article, we present a systematic map of the literature on urban forest management strategies that measure both biodiversity goals (through avian conservation) and climate change mitigation goals (through carbon storage and sequestration).

METHODS

Following a published protocol, we searched for evidence related to urban forest management strategies for (1) avian conservation and (2) carbon solutions within the global temperate region in academic and grey literature. In addition to Scopus, ProQuest and Web of Science Core Collection, we searched 21 specialist websites. We screened English language documents using predefined inclusion criteria on titles and abstracts, and then full texts. All qualifying literature items were coded, and metadata were extracted. No study validity appraisal was conducted. We identified knowledge clusters and gaps related to forest management strategies for both topics.

REVIEW FINDINGS

Our searches identified 19,073 articles published, of which 5445 were duplicates. The title and abstract screening removed a further 11,019 articles. After full-text screening (1762 and 1406), a total of 277 avian and 169 forest carbon literature items met the eligibility criteria and were included in the final database. We found a large knowledge base for broad-scale avian metrics: abundance, species richness. We similarly found that both avian and carbon solutions most often used broad-scale forest management components: land use type, composition, and forested area and least often considered fragmentation, connectivity, and diversity metrics (abundance, richness). The most understudied avian metrics were foraging, resources, and survival while the most understudied carbon solutions metrics were soil carbon, dead wood and organic matter and infrastructure. Avian literature most often used an experimental design (56% with comparator, 44% no comparator) while forest carbon solutions literature was dominated by observational studies (86%). In both topics, studies most often occurred over short timelines between 0 and 1 and 2-5 years. The body of evidence for both avian and carbon outcomes present a scale-mismatch between the scale of forest management strategy (e.g., land use type) and scale of application (e.g., patch). For example, the majority of studies considered forest strategies at broad scales, like land use type or composition, yet were conducted at a patch or multi-patch scale. Our systematic map also highlights that multi-city and regional urban scales are underrepresented in both carbon solutions and avian conservation and will require additional research efforts. Finally, we highlight gaps in the inclusion of recommendations in both bodies of literature. Roughly 30% of articles in each topic's database did not include recommendations for practitioners or researchers.

CONCLUSIONS

Our systematic map provides a database and identifies knowledge gaps and clusters of urban forest management strategies for (1) avian conservation and (2) carbon solutions. Overall, our map will allow researchers to fill existing gaps in literature through new research investigations, meta-analyses or systematic reviews while also pointing policymakers toward strong knowledge bases in addition to understudied or mismatched areas that require more funding.

Genomic variation of European beech reveals signals of local adaptation despite high levels of phenotypic plasticity

Local adaptation is key for ecotypic differentiation and species evolution. Understanding underlying genomic patterns can allow the prediction of future maladaptation and ecosystem stability. Here, we report the whole-genome resequencing of 874 individuals from 100 range-wide populations of European beech (Fagus sylvatica L.), an important forest tree species in Europe. We show that genetic variation closely mirrors geography with a clear pattern of isolation-by-distance. Genome-wide analyses for genotype-environment associations (GEAs) identify relatively few potentially adaptive variants after correcting for an overwhelming signal of statistically significant but non-causal GEAs. We characterize the single high confidence genomic region and pinpoint a candidate gene possibly involved in winter temperature adaptation via modulation of spring phenology. Surprisingly, allelic variation at this locus does not result in any apparent fitness differences in a common garden. More generally, reciprocal transplant experiments across large climate distances suggest extensive phenotypic plasticity. Nevertheless, we find indications of polygenic adaptation which may be essential in natural ecosystems. This polygenic signal exhibits broad- and fine-scale variation across the landscape, highlighting the relevance of spatial resolution. In summary, our results emphasize the importance, but also exemplify the complexity, of employing natural genetic variation for forest conservation under climate change.

Rhizobiome diversity of field-collected hyperaccumulating Noccaea sp

Hyperaccumulating plants are able to (hyper)accumulate high concentrations of metal(loid)s in their above-ground tissues without any signs of toxicity. Studies on the root-associated microbiome have been previously conducted in relation to hyperaccumulators, yet much remains unknown about the interactions between hyperaccumulating hosts and their microbiomes, as well as the dynamics within these microbial communities. Here, we assess the impact of the plant host on shaping microbial communities of three naturally occurring populations of Noccaea species in Slovenia: Noccaea praecox and co-occurring N. caerulescens from the non-metalliferous site and N. praecox from the metalliferous site. We investigated the effect of metal enrichment on microbial communities and explored the interactions within microbial groups and their environment. The abundance of bacterial phyla was more homogeneous than fungal classes across all three Noccaea populations and across the three root-associated compartments (roots, rhizosphere, and bulk soil). While most fungal and bacterial Operational Taxonomic Units (OTUs) were found at both sites, the metalliferous site comprised more unique OTUs in the root and rhizosphere compartments than the non-metalliferous site. In contrast to fungi, bacteria exhibited differentially significant abundance between the metalliferous and non-metalliferous sites as well as statistically significant correlations with most of the soil parameters. Results revealed N. caerulescens had the highest number of negative correlations between the bacterial phyla, whereas the population from the metalliferous site had the fewest. This decrease was accompanied by a big perturbation in the bacterial community at the metalliferous site, indicating increased selection between the bacterial taxa and the formation of potentially less stable rhizobiomes. These findings provide fundamentals for future research on the dynamics between hyperaccumulators and their associated microbiome.

Combining citizen science data and literature to build a traits dataset of Taiwan's birds

Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.

Distinct biogeographic patterns for bacteria and fungi in association with Bursaphelenchus xylophilus nematodes and infested pinewood

Pinewood nematodes (PWN, Bursaphelenchus xylophilus) are destructive plant parasitic nematodes that cause pine wilt disease (PWD) by attacking the vascular systems of pine trees, resulting in widespread tree mortality. Research has shown that there are connections between nematode-associated microbes and PWD. Yet the variations in microbial communities across different geographic regions are not well-understood. In this study, we examined the bacterial and fungal communities associated with nematodes and infested wood collected from 34 sites across three vegetation zones in China, as well as samples from the United States, using 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing. The predominant genera Pseudomonas and Rhodococcus were found in nematodes, and Acinetobacter was present in the wood of PWD-infected pine trees across China. Network analysis revealed that core bacterial taxa belonged to the Pseudomonadota and Actinomycetota phyla for the nematodes, whereas the Pseudomonadota and Bacteroidota phyla were dominant in the infested wood. Identification of enriched key microbial taxa in nematodes and infested wood across vegetation zones indicates distinct biogeographic microbial community structures and key bacterial species. Although the nematode-associated bacterial community showed consistency across geographic distances, the similarity of the PWD pine trees' bacterial community decreased with distance, suggesting a spatial correlation with environmental variables. Our findings enhance our understanding of the microbiota associated with pinewood nematode (PWN) and offer valuable insights into PWD management.

IMPORTANCE

Our research uncovered specific bacteria and fungi linked to pinewood nematode (PWN) and infested wood in three different vegetation zones in China, as well as samples from the United States. This sheds light on the critical roles of certain microbial groups, such as Pseudomonas, Acinetobacter, and Stenotrophomonas, in influencing PWN fitness. Understanding these patterns provides valuable insights into the dynamics of PWN-associated microbiomes, offering potential strategies for managing pine wilt disease (PWD). We found significant correlations between geographic distance and similarity in bacterial communities in the infested wood, indicating a spatial influence on wood-associated microbial communities due to limited dispersal and localized environmental conditions. Further investigations of these spatial patterns and driving forces are crucial for understanding the ecological processes that shape microbial communities in complex ecosystems and, ultimately, for mitigating the transmission of PWN in forests.

Floristic changes following the chestnut blight may be delayed for decades

A survey conducted in the 1920s, prior to the chestnut blight, indicated that chestnuts and oaks were codominant canopy species in White Oak Canyon, Shenandoah National Park, Virginia. A second survey in 1977 suggested that chestnuts were being replaced by tree species present before the blight, particularly oaks. In 2021, we resurveyed the 10 sites included in our 1977 survey and also recorded canopy and understory trees that grew above remnant chestnut sprouts. The canopy changed more substantially during the second interval (since 1977). Birch and maples were now more abundant. Hemlock declined, and oaks were less common in the canopy. In general, the trees considered as early to mid-successional have replaced oaks and hemlock. Chestnut sprouts have become much less common since 1977, presumably as repeated cycles of diebacks have weakened rootstocks. Those sites where chestnut sprouts have persisted until 2021 differed from neighboring sites without them. Chestnut sprouts were rare in sites with birch and hemlock; chestnut has persisted in locations with red oaks in the canopy and with few other understory competitors. This survey has been conducted over a longer time interval than previous studies that asked similar questions and our results suggest that changes to the forest composition following the loss of the American chestnut may be greater than previously recognized although the relative contribution of losing this codominant species is unclear.

Unraveling the multiple facilitative effects of consumers on marine primary producers

The loss of consumers threatens the integrity of ecological systems, but the mechanisms underlying the effects on communities and ecosystems remain difficult to predict. This is, in part, due to the complex roles that consumers play in those systems. Here, we highlight this complexity by quantifying two mechanisms by which molluscan grazers-typically thought of as consumers of their algal resources-facilitate algae on rocky shores. Initial observations in high-zone tide pools revealed that both water-column ammonium concentrations and photosynthetic biomass were higher in pools containing higher densities of grazers, suggesting that local-scale nutrient recycling by the grazers could be enhancing algal biomass. We assessed this possibility by experimentally manipulating grazer abundances at the level of whole tide pools but controlling access of those grazers to experimental plots within each pool. Contrary to predictions that algal biomass inside grazer exclusions would increase as grazer abundances in the pools increased, we found that algal biomass inside grazer-exclusion fences was unaffected by grazer abundances. Instead, the consumptive effects of grazers that were evident at low grazer abundances transitioned to facilitative effects as experimentally manipulated grazer abundances increased. This finding suggested that these positive interactions were associated with the physical presence of grazers and not just grazers' effects on nutrient availability. Subsequent experiments highlighted the potential role of "slime"-the pedal mucous trails left behind as the mollusks crawl on the substratum-in promoting the recruitment of algae and thereby mediating a spatial subsidy of new organic matter into the system. Furthermore, different grazer groups contributed disproportionately to ammonium excretion (i.e., turban snails) versus slime production (i.e., littorine snails), suggesting a potential role for grazer diversity. Our work highlights the complex ways in which consumers affect their resources, including multiple, complementary mechanisms by which these grazers facilitate the algae they consume.

Slower but deeper community change: Intrinsic dynamics regulate anthropogenic impacts on species temporal turnover

Understanding the mechanisms behind biodiversity dynamics is central to assessing and forecasting anthropogenic impacts on ecological communities. However, the manner in which external environmental drivers act in concert with intrinsic ecological processes to influence local temporal turnover is currently largely unexplored. Here, we determine how human impacts affect multiple metrics of bird community turnover to establish the ecological mechanisms behind compositional change. We used US Breeding Bird Survey data to calculate transect-level rates of three measures of temporal species turnover: (1) "short-term" (initial rate of decline of Sørensen similarity), (2) "long-term" (asymptotic Sørensen similarity), and (3) "throughput" (overall species accumulation rate from species-time relationship exponents) over 2692 transects across 27 regional habitat types. We then hierarchically fit linear models to estimate the effect of anthropogenic impact on these turnover metrics, using the Human Modification Index proxy, while accounting for observed species richness, the size of the species pool, and annual environmental variability. We found broadly consistent impacts of increased anthropogenic pressures across diverse habitat types. The Human Modification Index was associated with greater turnover at long timescales, but marginally slower short-term turnover. The species "throughput" (accumulation rate) was not notably influenced. Examining anthropogenic impacts on different aspects of species turnover in combination allows greater ecological insight. Observed human impacts on short-term turnover were the opposite of existing expectations and suggest humans are disrupting the background turnover of these systems, rather than simply driving rapid directed turnover. The increased long-term turnover without concurrent increases in species accumulation implies human impacts lead to shifts in species occurrence frequency rather than simply greater arrival of "new" species. These results highlight the role of intrinsic dynamics and caution against simple interpretations of increased species turnover as reflections of environmental change.

Population structure analysis of Phlebotomus papatasi populations using transcriptome microsatellites: possible implications for leishmaniasis control and vaccine development

BACKGROUND

Phlebotomus papatasi is considered the primary vector of Leishmania major parasites that cause zoonotic cutaneous leishmaniasis (ZCL) in the Middle East and North Africa. Phlebotomus papatasi populations have been studied extensively, revealing the existence of different genetic populations and subpopulations over its large distribution range. Genetic diversity and population structure analysis using transcriptome microsatellite markers is important to uncover the vector distribution dynamics, essential for controlling ZCL in endemic areas.

METHODS

In this study, we investigated the level of genetic variation using expressed sequence tag-derived simple sequence repeats (EST-SSRs) among field and colony P. papatasi samples collected from 25 different locations in 11 countries. A total of 302 P. papatasi sand fly individuals were analyzed, including at least 10 flies from each region.

RESULTS

The analysis revealed a high-level population structure expressed by five distinct populations A through E, with moderate genetic differentiation among all populations. These genetic differences in expressed genes may enable P. papatasi to adapt to different environmental conditions along its distribution range and likely affect dispersal.

CONCLUSIONS

Elucidating the population structuring of P. papatasi is essential to L. major containment efforts in endemic countries. Moreover, the level of genetic variation among these populations may improve our understanding of Leishmania-sand fly interactions and contribute to the efforts of vaccine development based on P. papatasi salivary proteins.

Exploring the phylogeny and depth evolution of cusk eels and their relatives (Ophidiiformes: Ophidioidei)

With 289 known species in 51 genera, the ophidiiform family Ophidiidae together with their relatives from the Carapidae (36 species in eight genera) of the same suborder Ophidioidei dominate the deep sea, but some occur also in shallow water habitats. Despite their high species diversity in the deep sea and wide bathymetric distributions, their phylogenetic relationships and evolution remain unexplored due in part to sampling difficulties. Thanks to the biodiversity exploratory program entitled "Tropical Deep-Sea Benthos" and joint efforts between Taiwan and French teams for sampling from different localities across the Indo-West Pacific over the last two decades, we are able to compile comprehensive datasets for investigations. In this study, 59 samples representing 36 of 59 known ophidioid genera are selected and used to construct a multi-gene dataset to infer the phylogenetic relationships of ophidioid fishes and their relatives. Our results reveal that the Ophidiidae forms a paraphyletic group with respect to the Carapidae. The four main clades of Ophidioidei resolved are the (1) clade comprising species from the subfamily Brotulinae; (2) clade that includes species in the genera Acanthonus and Xyelacyba; (3) clade grouping Hypopleuron caninum with species from the family Carapidae; and (4) clade containing the species in the subfamily Brotulotaenilinae, Neobythitinae (in part), and Ophidiinae. Accordingly, we suggest the following new revisions based on our results and proposed morphological diagnoses. The subfamily Brotulinae should be elevated to the family level. The genera Xyelacyba and probably Tauredophidium (unsampled in this study) should be included in the newly established family Acanthonidae with Acanthonus. The families Carapidae and Ophidiidae are re-defined. Our time-calibrated phylogenetic and ancestral depth reconstructions enable us to clarify the evolutionary history of ophidiiform fishes and infer past patterns of species distributions at different depths. While Ophidiiformes is inferred to have originated in shallow waters around 96.25 million years ago (Mya), the common ancestor to the Ophidioidei is inferred to have invaded the deep sea around 90.22 Mya, the dates coinciding with the global anoxic event of the OAE2. The observed bathymetric distribution patterns in Ophidioidei most likely point to the mesopelagic zone as the center of origin and diversification. This was followed by multiple events of depth transitions or range expansions towards either shallower waters or greater depth zones, which were likely triggered by past climate changes during the Paleogene-Neogene.

Mesophotic zone as buffer for biodiversity protection: A promising opportunity to enhance MPA effectiveness

Coastal areas conservation strategies often left deeper habitats, such as mesophotic ones, unprotected and exposed to anthropogenic activities. In this context, an approach for including the mesophotic zone inside protection plans is proposed, considering 27 Italian Marine Protected Areas (MPAs) as a model. MPAs were classified considering their bathymetries, exposure to marine heat waves (MHWs), mass mortality events (MMEs) and, using a local ecological knowledge (LEK) approach, the estimated resilience of certain sessile species after MMEs. Only 8 MPAs contained considerable mesophotic areas, with stronger MHWs mainly occurring in shallower MPAs, and MMEs mostly affecting coralligenous assemblages. Even with only a 10% response rate, the LEK approach provided useful information on the resilience of certain species, allowing us to suggest that the presence of nearby mesophotic areas can help shallower habitats facing climate change, thus making the "deep refugia" hypothesis, usually related to tropical habitats, applicable also for the Mediterranean Sea.

Unveiling the overlooked: Current and future distribution dynamics of kissing bugs and palm species linked to oral Chagas disease transmission

Chagas disease, a neglected global health concern primarily transmitted through the bite and feces of kissing bugs, has garnered increasing attention due to recent outbreaks in northern Brazil, highlighting the role of oral transmission facilitated by the kissing bugs species Rhodnius robustus and Rhodnius pictipes. These vectors are associated with palm trees with large crowns, such as the maripa palm (Attalea maripa) and moriche palm (Mauritia flexuosa). In this study, we employ maximum entropy (MaxEnt) ecological niche models to analyze the spatial distribution of these vectors and palm species, predicting current and future climate suitability. Our models indicate broader potential habitats than documented occurrences, with high suitability in northern South America, southern Central America, central Africa, and southeast Asia. Projections suggest increased climate suitability by 2040, followed by a reduction by 2080. This study identifies present and future areas suitable for kissing bugs and palm tree species due to climate change, aiding in the design of prevention and management strategies.

Differential responses of soil phosphorus fractions to varied nitrogen compound additions in a meadow steppe

Nitrogen (N) addition can greatly influence soil inorganic phosphorus (Pi) and organic phosphorus (Po) transformations. However, whether and how the N compound forms may differentially affect the soil P fractions remain unclear. Here, we investigated the responses of soil Pi (labile Pi, moderately-occluded Pi, and recalcitrant Pi) and Po fractions (labile Po and stable Po) to varying addition rates of three N compounds ((NH4)2SO4, NH4NO3, and urea) in a meadow steppe in northern China. Our studies revealed that with increasing N addition rate, soil labile and moderately-occluded Pi increased, accompanied by decreases in soil recalcitrant Pi. This shift was attributed to N-induced soil acidification, which accelerated the conversion of recalcitrant Pi into labile and moderately-occluded Pi. Soil labile Po decreased with increasing rate of N addition, whilst soil stable Po was not affected. Regardless of the compound forms, N addition increased soil Olsen-P, suggesting a potential alleviation of P limitation in this grassland ecosystem. The effect of N addition on soil labile Pi was significantly greater with addition of urea than with addition of either (NH4)2SO4 or NH4NO3, indicating that urea was more efficient in enhancing soil P availability. Addition of (NH4)2SO4 imposed a more pronounced positive effect on soil moderately-occluded Pi than the addition of either NH4NO3 or urea, mainly due to the greater mobilization of recalcitrant Pi as a result of higher soil acidification strength of (NH4)2SO4. These findings underscore the importance of considering the distinct effects of different N compounds when studying grassland soil P dynamics and availability in response to N addition.

Macroevolution of the plant-hummingbird pollination system

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.