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Pressures on honey bee health have substantially increased both colony mortality and beekeepers' costs for hive management across Europe. Although technological advances could offer cost-effective solutions to these challenges, there is little research into the incentives and barriers to technological adoption by beekeepers in Europe. Our study is the first to investigate beekeepers' willingness to adopt the Bee Health Card, a molecular diagnostic tool developed within the PoshBee EU project which can rapidly assess bee health by monitoring molecular changes in bees. The Bee Health Card, based on MALDI BeeTyping®, is currently on level six of the Technology Readiness Level scale, meaning that the technology has been demonstrated in relevant environments. Using an on-line survey from seven European countries, we show that beekeepers recognise the potential for the tool to improve colony health, and that targeted economic incentives, such as subsidises, may help reduce cost being a barrier to the adoption and frequent use of the tool. Based on the description of the tool, 43% of beekeepers appear to be moderately confident in the effectiveness of the Bee Health Card. This confidence could increase if the tool was easy to use and not time consuming, and a higher confidence could also contribute to raising the probability of accepting extra costs linked to it. We estimate that, in the worst-case scenario, the cost per single use of the Bee Health Card should be between €47-90 across a range of European countries, depending on the labour and postage costs. However, the monetary benefits in terms of honey production could exceed this. In order to successfully tackle colony health issues, it is recommended using the BHC five times per year, from the end to the beginning of winter. Finally, we discuss the knowledge needs for assessing beekeeper health tools in future research., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Cini et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Fiber is essential for rumen health, microbial fermentation, and the energy supply of herbivores. Even though the study of fecal fiber contents (neutral detergent fiber NDF, acid detergent fiber ADF, and acid detergent lignin ADL) using near-infrared reflectance spectroscopy (NIRS) has allowed investigating nutritional ecology of different herbivore species, NIRS calibrations are species-specific and require a large number of samples for predictions. A multispecies calibration would be an advantage since samples from different herbivores could be used to calibrate a model capable of predicting the fecal fiber content of other herbivores. To date, however, multispecies models have not been developed to predict fiber contents in the feces of herbivores. Here, we fill this gap by calibrating three fiber multispecies models (NDF, ADF and ADL) using fecal samples from domestic and wild herbivore species. We also evaluated the effect of incorporating sodium sulfite in fiber determination protocol. The initial dataset consisting of 445 samples of six herbivore species was used to calibrate (80% of the samples) and validate (20% of the samples) the models. Subsequently, 63 samples of five herbivores not included in the calibration set were used for the external validation of the model. Since sodium sulfite did not significantly improve fecal fiber prediction, our model was developed without this compound. The multispecies models obtained were highly accurate determining NDF, ADF and ADL (R2CAL, coefficient of determination in calibration, ≥ 0.93, R2VAL, coefficient of determination in validation, ≥ 0.91) and independent of external confounders. For external validation, the accuracy in predicting fecal samples in other herbivore species was also satisfactory, with consistently better values for NDF (R2VAL, 0.86-0.94) and ADF (R2VAL, 0.80-0.95) than for ADL (R2VAL, 0.66-0.89). We show that multispecies NIRS calibrations can be used with high accuracy to assess fecal fiber contents across diverse herbivore species. This finding represents a significant advance in the study of the nutritional ecology of herbivores with contrasting foraging patterns. In the future, widening the data range (e.g., species and locations) of the initial dataset could further improve the accuracy of these models., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2025 Rossa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Tropical Andes, one of the world's most biodiverse regions, is vital for ecological research and conservation. However, while researchers in Bolivia, Ecuador, and Peru contribute significantly to scientific knowledge, their publication rates in academic journals have historically lagged behind neighboring nations. A multifaceted strategy was employed to understand and address the publication divide in the Tropical Andes region. This approach focused on regional researchers and consisted of a three-day workshop to improve scientific writing skills, offer publication insights, and equip researchers with tools to overcome obstacles. A series of surveys were also conducted to explore the challenges faced by local researchers and their proposed solutions, covering topics such as participant demographics, factors contributing to lower publication rates, personal barriers, proposed strategies for improving publications, specific topics of interest, participant satisfaction, most valuable workshop topics, and future recommendations. The workshop had an overwhelming response, with over 500 interested participants registering in just a few days, mostly experienced professionals, highlighting the need for such initiatives in the region. About two-thirds had ready-to-publish materials, highlighting the potential impact of targeted interventions on unlocking untapped knowledge. The surveys revealed the challenges contributing to the publication divide, including insufficient training, cultural emphasis on economic development, language barriers, limited resource access, lack of institutional support, high publishing costs, and time and financial constraints. The most common personal barriers were insufficient knowledge and experience in the publication process, lack of self-confidence, and fears of rejection. Proposed solutions include conducting training workshops, fostering collaborative networks, improving resource accessibility, and an institutional and cultural shift that encourages publishing. Addressing challenges faced by experienced professionals in the Tropical Andes by understanding individual needs, fostering support, and demystifying the publication process offers a promising path to closing the publication divide and unlocking the region's valuable scientific contributions., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Valdez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Earthworms can stimulate microbial activity and hence greenhouse gas (GHG) emissions from soils. However, the extent of this effect in the presence of plants and soil moisture fluctuations, which are influenced by earthworm burrowing activity, remains uncertain. Here, we report the effects of earthworms (without, anecic, endogeic, both) and plants (with, without) on GHG (CO2, N2O) emissions in a 3-month greenhouse mesocosm experiment simulating a simplified agricultural context. The mesocosms allowed for water drainage at the bottom to account for the earthworm engineering effect on water flow during two drying-wetting cycles. N2O cumulative emissions were 34.6% and 44.8% lower when both earthworm species and only endogeic species were present, respectively, and 19.8% lower in the presence of plants. The presence of the endogeic species alone or in combination with the anecic species slightly reduced CO2 emissions by 5.9% and 11.4%, respectively, and the presence of plants increased emissions by 6%. Earthworms, plants and soil water content interactively affected weekly N2O emissions, an effect controlled by increased soil dryness due to drainage via earthworm burrows and mesocosm evapotranspiration. Soil macroporosity (measured by X-ray tomography) was affected by earthworm species-specific burrowing activity. Both GHG emissions decreased with topsoil macropore volume, presumably due to reduced moisture and microbial activity. N2O emissions decreased with macropore volume in the deepest layer, likely due to the presence of fewer anaerobic microsites. Our results indicate that, under experimental conditions allowing for plant and earthworm engineering effects on soil moisture, earthworms do not increase GHG emissions, and endogeic earthworms may even reduce N2O emissions., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Ganault et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The use of English as the common language of science represents a major impediment to maximising the contribution of non-native English speakers to science. Yet few studies have quantified the consequences of language barriers on the career development of researchers who are non-native English speakers. By surveying 908 researchers in environmental sciences, this study estimates and compares the amount of effort required to conduct scientific activities in English between researchers from different countries and, thus, different linguistic and economic backgrounds. Our survey demonstrates that non-native English speakers, especially early in their careers, spend more effort than native English speakers in conducting scientific activities, from reading and writing papers and preparing presentations in English, to disseminating research in multiple languages. Language barriers can also cause them not to attend, or give oral presentations at, international conferences conducted in English. We urge scientific communities to recognise and tackle these disadvantages to release the untapped potential of non-native English speakers in science. This study also proposes potential solutions that can be implemented today by individuals, institutions, journals, funders, and conferences. Please see the Supporting information files (S2-S6 Text) for Alternative Language Abstracts and Figs 5 and 6., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Amano et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Land-use intensification is one of the main drivers threatening biodiversity in managed grasslands. Despite multiple studies investigating the effect of different land-use components in driving changes in plant biodiversity, their effects are usually studied in isolation. Here, we establish a full factorial design crossing fertilization with a combined treatment of biomass removal, on 16 managed grasslands spanning a gradient in land-use intensity, across three regions in Germany. Specifically, we investigate the interactive effects of different land-use components on plant composition and diversity using structural equation modelling. We hypothesize that fertilization and biomass removal alter plant biodiversity, directly and indirectly, mediated through changes in light availability. We found that, direct and indirect effects of biomass removal on plant biodiversity were larger than effects of fertilization, yet significantly differed between season. Furthermore, we found that indirect effects of biomass removal on plant biodiversity were mediated through changes in light availability, but also by changes in soil moisture. Our analysis thus supports previous findings, that soil moisture may operate as an alternative indirect mechanism by which biomass removal may affect plant biodiversity. Most importantly, our findings highlight that in the short-term biomass removal can partly compensate the negative effects of fertilization on plant biodiversity in managed grasslands. By studying the interactive nature of different land-use drivers we advance our understanding of the complex mechanisms controlling plant biodiversity in managed grasslands, which ultimately may help to maintain higher levels of biodiversity in grassland ecosystems., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Andraczek et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The public perception of viruses has historically been negative. We are now at a stage where the development of tools to study viruses is at an all-time high, but society's perception of viruses is at an all-time low. The literature regarding viral interactions has been skewed towards negative (i.e., pathogenic) symbioses, whereas viral mutualisms remain relatively underexplored. Viral interactions with their hosts are complex and some non-pathogenic viruses could have potential benefits to society. However, viral research is seldom designed to identify viral mutualists, a gap that merits considering new experimental designs. Determining whether antagonisms, mutualisms, and commensalisms are equally common ecological strategies requires more balanced research efforts that characterize the full spectrum of viral interactions., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Jurburg et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

As the number of observations submitted to the citizen science platform iNaturalist continues to grow, it is increasingly important that these observations can be identified to the finest taxonomic level, maximizing their value for biodiversity research. Here, we explore the benefits of acting as an identifier on iNaturalist., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Altered climate, nutrient enrichment and changes in grazing patterns are important environmental and biotic changes in temperate grassland systems. Singly and in concert these factors can influence plant performance and traits, with consequences for species competitive ability, and thus for species coexistence, community composition and diversity. However, we lack experimental tests of the mechanisms, such as competition for light, driving plant performance and traits under nutrient enrichment, grazer exclusion and future climate. We used transplants of Silene latifolia, a widespread grassland forb in Europe, to study plant responses to interactions among climate, nutrients, grazing and light. We recorded transplant biomass, height, specific leaf area (SLA) and foliar carbon to nitrogen ratio (C:N) in full-factorial combinations of future climate treatment, fertilization, grazer exclusion and light addition via LED-lamps. Future climate and fertilization together increased transplant height but only in unlighted plots. Light addition increased SLA in ambient climate, and decreased C:N in unfertilized plots. Further, transplants had higher biomass in future climatic conditions when protected from grazers. In general, grazing had a strong negative effect on all measured variables regardless of added nutrients and light. Our results show that competition for light may lead to taller individuals and interacts with climate and nutrients to affect traits related to resource-use. Furthermore, our study suggests grazing may counteract the benefits of future climate on the biomass of species such as Silene latifolia. Consequently, grazers and light may be important modulators of individual plant performance and traits under nutrient enrichment and future climatic conditions., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Jessen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Hunting and its impacts on wildlife are typically studied regionally, with a particular focus on the Global South. Hunting can, however, also undermine rewilding efforts or threaten wildlife in the Global North. Little is known about how hunting manifests under varying socioeconomic and ecological contexts across the Global South and North. Herein, we examined differences and commonalities in hunting characteristics across an exemplary Global South-North gradient approximated by the Human Development Index (HDI) using face-to-face interviews with 114 protected area (PA) managers in 25 African and European countries. Generally, we observed that hunting ranges from the illegal, economically motivated, and unsustainable hunting of herbivores in the South to the legal, socially and ecologically motivated hunting of ungulates within parks and the illegal hunting of mainly predators outside parks in the North. Commonalities across this Africa-Europe South-North gradient included increased conflict-related killings in human-dominated landscapes and decreased illegal hunting with beneficial community conditions, such as mutual trust resulting from community involvement in PA management. Nevertheless, local conditions cannot outweigh the strong effect of the HDI on unsustainable hunting. Our findings highlight regional challenges that require collaborative, integrative efforts in wildlife conservation across actors, while identified commonalities may outline universal mechanisms for achieving this goal., Competing Interests: The authors have declared that no competing interests exist.

Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions., Competing Interests: The authors have declared that no competing interests exist.

Complex socio-economic, political and demographic factors have driven the increased conversion of Europe's semi-natural grasslands to intensive pastures. This trend is particularly strong in some of the most biodiverse regions of the continent, such as Central and Eastern Europe. Intensive grazing is known to decrease species diversity and alter the composition of plant and insect communities. Comparatively little is known, however, about how intensive grazing influences plant functional traits related to pollination and the structure of plant-pollinator interactions. In traditional hay meadows and intensive pastures in Central Europe, we contrasted the taxonomic and functional group diversity and composition, the structure of plant-pollinator interactions and the roles of individual species in networks. We found mostly lower taxonomic and functional diversity of plants and insects in intensive pastures, as well as strong compositional differences among the two grassland management types. Intensive pastures were dominated by a single plant with a specialized flower structure that is only accessible to a few pollinator groups. As a result, intensive pastures have lower diversity and specificity of interactions, higher amount of resource overlap, more uniform interaction strength and lower network modularity. These findings stand in contrast to studies in which plants with more generalized flower traits dominated pastures. Our results thus highlight the importance of the functional traits of dominant species in mediating the consequences of intensive pasture management on plant-pollinator networks. These findings could further contribute to strategies aimed at mitigating the impact of intensive grazing on plant and pollinator communities., Competing Interests: The authors have declared that no competing interests exist.

Sediment and nutrient retention are essential ecosystem functions that floodplains provide and that improve river water quality. During floods, the floodplain vegetation retains sediment, which settles on plant surfaces and the soil underneath plants. Both sedimentation processes require that flow velocity is reduced, which may be caused by the topographic features and the vegetation structure of the floodplain. However, the relative importance of these two drivers and their key components have rarely been both quantified. In addition to topographic factors, we expect vegetation height and density, mean leaf size and pubescence, as well as species diversity of the floodplain vegetation to increase the floodplain's capacity for sedimentation. To test this, we measured sediment and nutrients (carbon, nitrogen and phosphorus) both on the vegetation itself and on sediment traps underneath the vegetation after a flood at 24 sites along the River Mulde (Germany). Additionally, we measured biotic and topographic predictor variables. Sedimentation on the vegetation surface was positively driven by plant biomass and the height variation of the vegetation, and decreased with the hydrological distance (total R2 = 0.56). Sedimentation underneath the vegetation was not driven by any vegetation characteristics but decreased with hydrological distance (total R2 = 0.42). Carbon, nitrogen and phosphorus content in the sediment on the traps increased with the total amount of sediment (total R2 = 0.64, 0.62 and 0.84, respectively), while C, N and P on the vegetation additionally increased with hydrological distance (total R2 = 0.80, 0.79 and 0.92, respectively). This offers the potential to promote sediment and especially nutrient retention via vegetation management, such as adapted mowing. The pronounced signal of the hydrological distance to the river emphasises the importance of a laterally connected floodplain with abandoned meanders and morphological depressions. Our study improves our understanding of the locations where floodplain management has its most significant impact on sediment and nutrient retention to increase water purification processes., Competing Interests: The authors have declared that no competing interests exist.

The widely held assumption that any important scientific information would be available in English underlies the underuse of non-English-language science across disciplines. However, non-English-language science is expected to bring unique and valuable scientific information, especially in disciplines where the evidence is patchy, and for emergent issues where synthesising available evidence is an urgent challenge. Yet such contribution of non-English-language science to scientific communities and the application of science is rarely quantified. Here, we show that non-English-language studies provide crucial evidence for informing global biodiversity conservation. By screening 419,679 peer-reviewed papers in 16 languages, we identified 1,234 non-English-language studies providing evidence on the effectiveness of biodiversity conservation interventions, compared to 4,412 English-language studies identified with the same criteria. Relevant non-English-language studies are being published at an increasing rate in 6 out of the 12 languages where there were a sufficient number of relevant studies. Incorporating non-English-language studies can expand the geographical coverage (i.e., the number of 2° × 2° grid cells with relevant studies) of English-language evidence by 12% to 25%, especially in biodiverse regions, and taxonomic coverage (i.e., the number of species covered by the relevant studies) by 5% to 32%, although they do tend to be based on less robust study designs. Our results show that synthesising non-English-language studies is key to overcoming the widespread lack of local, context-dependent evidence and facilitating evidence-based conservation globally. We urge wider disciplines to rigorously reassess the untapped potential of non-English-language science in informing decisions to address other global challenges. Please see the Supporting information files for Alternative Language Abstracts., Competing Interests: The authors have declared that no competing interests exist.

Since 1994, IUCN Red List assessments apply globally acknowledged standards to assess species distribution, abundance and trends. The extinction risk of a species has a major impact on conservation science and international funding mechanisms. Great ape species are listed as Endangered or Critically Endangered. Their populations are often assessed using their unique habit of constructing sleeping platforms, called nests. As nests rather than apes are counted, it is necessary to know the time it takes for nests to disappear to convert nest counts into ape numbers. However, nest decomposition is highly variable across sites and time and the factors involved are poorly understood. Here, we used 1,511 bonobo (Pan paniscus) nests and 15 years of climatic data (2003-2018) from the research site LuiKotale, Democratic Republic of the Congo, to investigate the effects of climate change and behavioural factors on nest decay time, using a Bayesian gamma survival model. We also tested the logistic regression method, a recommended time-efficient option for estimating nest decay time. Our climatic data showed a decreasing trend in precipitation across the 15 years of study. We found bonobo nests to have longer decay times in recent years. While the number of storms was the main factor driving nest decay time, nest construction type and tree species used were also important. We also found evidence for bonobo nesting behaviour being adapted to climatic conditions, namely strengthening the nest structure in response to unpredictable, harsh precipitation. By highlighting methodological caveats, we show that logistic regression is effective in estimating nest decay time under certain conditions. Our study reveals the impact of climate change on nest decay time in a tropical remote area. Failure to account for these changes would invalidate biomonitoring estimates of global significance, and subsequently jeopardize the conservation of great apes in the wild., Competing Interests: The authors have declared that no competing interests exist.

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines., Competing Interests: The authors declare no competing interests. The Siam Cement (Lampang) Co., Ltd. allowed access to the experimental sites and funded field work and lab analyses. However, the company played no role in experimental design, data collection, analysis, and interpretation, drafting the manuscript and decision to submit the work for publication. None of the authors were paid by the company. There are no patents, products in development or marketed products to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Building on the epidemiological SIR model, we present an economic model with heterogeneous individuals deriving utility from social contacts creating infection risks. Focusing on social distancing of individuals susceptible to an infection we theoretically characterize the gap between private and social cost of contacts. Our main contribution is to quantify this gap by calibrating the model with unique survey data from Germany on social distancing and impure altruism from the beginning of the COVID-19 pandemic. The optimal policy is to drastically reduce contacts at the beginning to almost eradicate the epidemic and keep them at levels that contain the pandemic at a low prevalence level. We find that also in laissez faire, private protection efforts by forward-looking, risk averse individuals would have stabilized the epidemic, but at a much higher prevalence of infection than optimal. Altruistic motives increase individual protection efforts, but a substantial gap to the social optimum remains., Competing Interests: The authors have declared that no competing interests exist.

Microinsurance is promoted as a valuable instrument for low-income households to buffer financial losses due to health or climate-related risks. However, apart from direct positive effects, such formal insurance schemes can have unintended side effects when insured households lower their contribution to traditional informal arrangements where risk is shared through private monetary support. Using a stylized agent-based model, we assess impacts of microinsurance on the resilience of those smallholders in a social network who cannot afford this financial instrument. We explicitly include the decision behavior regarding informal transfers. We find that the introduction of formal insurance can have negative side effects even if insured households are willing to contribute to informal risk arrangements. However, when many households are simultaneously affected by a shock, e.g. by droughts or floods, formal insurance is a valuable addition to informal risk-sharing. By explicitly taking into account long-term effects of short-term transfer decisions, our study allows to complement existing empirical research. The model results underline that new insurance programs have to be developed in close alignment with established risk-coping instruments. Only then can they be effective without weakening functioning aspects of informal risk management, which could lead to increased poverty., Competing Interests: The authors have declared that no competing interests exist.

Sediment retention is a key ecosystem function provided by floodplains to filter sediments and nutrients from the river water during floods. Floodplain vegetation is an important driver of fine sediment retention. We aim to understand which structural properties of the vegetation are most important for capturing sediments. In a hydraulic flume experiment, we investigated this by disentangling sedimentation on and underneath 96 vegetation patches (40 cm x 60 cm). We planted two grass and two herb species in each patch and conducted a full-factorial manipulation of 1) vegetation density, 2) vegetation height, 3) structural diversity (small-tall vs tall-tall species combinations) and 4) leaf pubescence (based on trait information). We inundated the vegetation patches for 21 h in a flume with silt- and clay-rich water and subsequently measured the amount of accumulated sediment on the vegetation and on a fleece as ground underneath it. We quantified the sediment by washing it off the biomass and off the fleece, drying the sediment and weighting it. Our results showed that all manipulated vegetation properties combined (vegetation density and height, and the interaction of structural diversity and leaf pubescence) explained sedimentation on the vegetation (total R2 = 0.34). The sedimentation underneath the vegetation was explained by the structural diversity and the leaf pubescence (total R2 = 0.11). We further found that vegetation biomass positively affected the sedimentation on and underneath the vegetation. These findings are crucial for floodplain management strategies with the aim to increase sediment retention. Based on our findings, we can identify management strategies and target plant communities that are able to maximize a floodplain's ability to capture sediments., Competing Interests: The authors have declared that no competing interests exist.

Stable isotope analysis is an increasingly used molecular tool to reconstruct the diet and ecology of elusive primates such as unhabituated chimpanzees. The consumption of C4 plant feeding termites by chimpanzees may partly explain the relatively high carbon isotope values reported for some chimpanzee communities. However, the modest availability of termite isotope data as well as the diversity and cryptic ecology of termites potentially consumed by chimpanzees obscures our ability to assess the plausibility of these termites as a C4 resource. Here we report the carbon and nitrogen isotope values from 79 Macrotermes termite samples from six savanna woodland chimpanzee research sites across equatorial Africa. Using mixing models, we estimated the proportion of Macrotermes C4 plant consumption across savanna woodland sites. Additionally, we tested for isotopic differences between termite colonies in different vegetation types and between the social castes within the same colony in a subset of 47 samples from 12 mounds. We found that Macrotermes carbon isotope values were indistinguishable from those of C3 plants. Only 5 to 15% of Macrotermes diets were comprised of C4 plants across sites, suggesting that they cannot be considered a C4 food resource substantially influencing the isotope signatures of consumers. In the Macrotermes subsample, vegetation type and caste were significantly correlated with termite carbon values, but not with nitrogen isotope values. Large Macrotermes soldiers, preferentially consumed by chimpanzees, had comparably low carbon isotope values relative to other termite castes. We conclude that Macrotermes consumption is unlikely to result in high carbon isotope values in either extant chimpanzees or fossil hominins., Competing Interests: The authors have declared that no competing interests exist.

Efficient biodiversity conservation requires that limited resources be allocated in accordance with national responsibilities and priorities. Without appropriate computational tools, the process of determining these national responsibilities and conservation priorities is time intensive when considering many species across geographic scales. Here, we have developed a computational tool as a module for the ArcGIS geographic information system. The ArcGIS National Responsibility Assessment Tool (NRA-Tool) can be used to create hierarchical lists of national responsibilities and priorities for global species conservation. Our tool will allow conservationists to prioritize conservation efforts and to focus limited resources on relevant species and regions. We showcase our tool with data on 258 bird species and various biophysical regions, including Environmental Zones in 58 Asian countries and regions. Our tool provides a decision support system for conservation policy with attractive and easily interpretable visual outputs illustrating national responsibilities and priorities for species conservation. The graphical output allows for smooth integration into assessment reports, such as the European Article 17 report, the Living Planet Index report, or similar regional and global reports., Competing Interests: The authors have declared that no competing interests exist.

Grasslands contribute to global biogeochemical cycles and can host a high number of plant species. Both-species dynamics and biogeochemical fluxes-are influenced by abiotic and biotic environmental factors, management and natural disturbances. In order to understand and project grassland dynamics under global change, vegetation models which explicitly capture all relevant processes and drivers are required. However, the parameterization of such models is often challenging. Here, we report on testing an individual- and process-based model for simulating the dynamics and structure of a grassland experiment in temperate Europe. We parameterized the model for three species and confront simulated grassland dynamics with empirical observations of their monocultures and one two-species mixture. The model reproduces general trends of vegetation patterns (vegetation cover and height, aboveground biomass and leaf area index) for the monocultures and two-species community. For example, the model simulates well an average annual grassland cover of 70% in the species mixture (observed cover of 77%), but also shows mismatches with specific observation values (e.g. for aboveground biomass). By a sensitivity analysis of the applied inverse model parameterization method, we demonstrate that multiple vegetation attributes are important for a successful parameterization while leaf area index revealed to be of highest relevance. Results of our study pinpoint to the need of improved grassland measurements (esp. of temporally higher resolution) in close combination with advanced modelling approaches., Competing Interests: The authors have declared that no competing interests exist.

A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more challenging. In this study, we manually curated 1235 SVs, which can ultimately be used to evaluate SV callers or train machine learning models. We developed a crowdsourcing app-SVCurator-to help GIAB curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy. SVCurator displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. 'Expert' curators were 93% concordant with each other, and 37 of the 61 curators had at least 78% concordance with a set of 'expert' curators. The curators were least concordant for complex SVs and SVs that had inaccurate breakpoints or size predictions. After filtering events with low concordance among curators, we produced high confidence labels for 935 events. The SVCurator crowdsourced labels were 94.5% concordant with the heuristic-based draft benchmark SV callset from GIAB. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies., Competing Interests: AC is an employee of Google Inc. AC is a former employee of DNAnexus Inc. NN is an employee of Illumina Inc.

The Arctic Ocean is an early warning system for indicators and effects of climate change. We use a novel combination of experimental and time-series data on effects of ocean warming and acidification on the commercially important Northeast Arctic cod (Gadus morhua) to incorporate these physiological processes into the recruitment model of the fish population. By running an ecological-economic optimization model, we investigate how the interaction of ocean warming, acidification and fishing pressure affects the sustainability of the fishery in terms of ecological, economic, social and consumer-related indicators, ranging from present day conditions up to future climate change scenarios. We find that near-term climate change will benefit the fishery, but under likely future warming and acidification this large fishery is at risk of collapse by the end of the century, even with the best adaptation effort in terms of reduced fishing pressure., Competing Interests: The authors have declared that no competing interests exist.

Research on canopy arthropods has progressed from species inventories to the study of their interactions and networks, enhancing our understanding of how hyper-diverse communities are maintained. Previous studies often focused on sampling individual tree species, individual trees or their parts. We argue that such selective sampling is not ideal when analyzing interaction network structure, and may lead to erroneous conclusions. We developed practical and reproducible sampling guidelines for the plot-based analysis of arthropod interaction networks in forest canopies. Our sampling protocol focused on insect herbivores (leaf-chewing insect larvae, miners and gallers) and non-flying invertebrate predators (spiders and ants). We quantitatively sampled the focal arthropods from felled trees, or from trees accessed by canopy cranes or cherry pickers in 53 0.1 ha forest plots in five biogeographic regions, comprising 6,280 trees in total. All three methods required a similar sampling effort and provided good foliage accessibility. Furthermore, we compared interaction networks derived from plot-based data to interaction networks derived from simulated non-plot-based data focusing either on common tree species or a representative selection of tree families. All types of non-plot-based data showed highly biased network structure towards higher connectance, higher web asymmetry, and higher nestedness temperature when compared with plot-based data. Furthermore, some types of non-plot-based data showed biased diversity of the associated herbivore species and specificity of their interactions. Plot-based sampling thus appears to be the most rigorous approach for reconstructing realistic, quantitative plant-arthropod interaction networks that are comparable across sites and regions. Studies of plant interactions have greatly benefited from a plot-based approach and we argue that studies of arthropod interactions would benefit in the same way. We conclude that plot-based studies on canopy arthropods would yield important insights into the processes of interaction network assembly and dynamics, which could be maximised via a coordinated network of plot-based study sites., Competing Interests: The authors have declared that no competing interests exist.

Spatially-explicit simulation models are commonly used to study complex ecological and socio-economic research questions. Often these models depend on detailed input data, such as initial land-cover maps to set up model simulations. Here we present the landscape generator EFFortS-LGraf that provides artificially-generated land-use maps of agricultural landscapes shaped by small-scale farms. EFForTS-LGraf is a process-based landscape generator that explicitly incorporates the human dimension of land-use change. The model generates roads and villages that consist of smallholder farming households. These smallholders use different establishment strategies to create fields in their close vicinity. Crop types are distributed to these fields based on crop fractions and specialization levels. EFForTS-LGraf model parameters such as household area or field size frequency distributions can be derived from household surveys or geospatial data. This can be an advantage over the abstract parameters of neutral landscape generators. We tested the model using oil palm and rubber farming in Indonesia as a case study and validated the artificially-generated maps against classified satellite images. Our results show that EFForTS-LGraf is able to generate realistic land-cover maps with properties that lie within the boundaries of landscapes from classified satellite images. An applied simulation experiment on landscape-level effects of increasing household area and crop specialization revealed that larger households with higher specialization levels led to spatially more homogeneous and less scattered crop type distributions and reduced edge area proportion. Thus, EFForTS-LGraf can be applied both to generate maps as inputs for simulation modelling and as a stand-alone tool for specific landscape-scale analyses in the context of ecological-economic studies of smallholder farming systems., Competing Interests: The authors have declared that no competing interests exist.

As limited resources, soils are the largest terrestrial sinks of organic carbon. In this respect, 3D modelling of soil organic carbon (SOC) offers substantial improvements in the understanding and assessment of the spatial distribution of SOC stocks. Previous three-dimensional SOC modelling approaches usually averaged each depth increment for multi-layer two-dimensional predictions. Therefore, these models are limited in their vertical resolution and thus in the interpretability of the soil as a volume as well as in the accuracy of the SOC stock predictions. So far, only few approaches used spatially modelled depth functions for SOC predictions. This study implemented and evaluated an approach that compared polynomial, logarithmic and exponential depth functions using non-linear machine learning techniques, i.e. multivariate adaptive regression splines, random forests and support vector machines to quantify SOC stocks spatially and depth-related in the context of biodiversity and ecosystem functioning research. The legacy datasets used for modelling include profile data for SOC and bulk density (BD), sampled at five depth increments (0-5, 5-10, 10-20, 20-30, 30-50 cm). The samples were taken in an experimental forest in the Chinese subtropics as part of the biodiversity and ecosystem functioning (BEF) China experiment. Here we compared the depth functions by means of the results of the different machine learning approaches obtained based on multi-layer 2D models as well as 3D models. The main findings were (i) that 3rd degree polynomials provided the best results for SOC and BD (R2 = 0.99 and R2 = 0.98; RMSE = 0.36% and 0.07 g cm-3). However, they did not adequately describe the general asymptotic trend of SOC and BD. In this respect the exponential (SOC: R2 = 0.94; RMSE = 0.56%) and logarithmic (BD: R2 = 84; RMSE = 0.21 g cm-3) functions provided more reliable estimates. (ii) random forests with the exponential function for SOC correlated better with the corresponding 2.5D predictions (R2: 0.96 to 0.75), compared to the 3rd degree polynomials (R2: 0.89 to 0.15) which support vector machines fitted best. We recommend not to use polynomial functions with sparsely sampled profiles, as they have many turning points and tend to overfit the data on a given profile. This may limit the spatial prediction capacities. Instead, less adaptive functions with a higher degree of generalisation such as exponential and logarithmic functions should be used to spatially map sparse vertical soil profile datasets. We conclude that spatial prediction of SOC using exponential depth functions, in conjunction with random forests is well suited for 3D SOC stock modelling, and provides much finer vertical resolutions compared to 2.5D approaches., Competing Interests: The authors have declared that no competing interests exist.

While the area of plantation forest increased globally between 2010 and 2015, more than twice the area of natural forests was lost over the same period (6.5 million ha natural forest lost per year versus 3.2 million ha plantation gained per year). Consequently, there is an increasing need to understand how plantation land use affects biodiversity. The relative conservation value of plantation forests is context dependent, being influenced by previous land use, management regimes and landscape composition. What is less well understood, and of importance to conservation management, is the consistency of diversity patterns across regions, and the degree to which useful generalisations can be provided within and among bioregions. Here, we analyse forest birds in Ireland, France and Portugal, representing distinct regions across the Atlantic biogeographic area of Europe. We compared taxonomic, functional and phylogenetic diversity of bird communities among conifer plantations and semi-natural oak forests, and assessed correlations between species traits and forest type across these regions. Although bird composition (assessed with NMDS ordination) differed consistently between plantation and oak forests across all three regions, species richness and Shannon diversity did not show a consistent pattern. In Ireland and France, metrics of taxonomic diversity (richness and Shannon diversity), functional diversity, functional dispersion and phylogenetic diversity were greater in oak forests than plantations. However, in Portugal taxonomic and phylogenetic diversity did not differ significantly between forest types, while functional diversity and dispersion were statistically significantly greater in plantations. No single bird trait-forest type association correlated in a consistent direction across the three study regions. Trait associations for the French bird communities appeared intermediate between those in Ireland and Portugal, and when trait correlations were significant in both Ireland and Portugal, the direction of the correlation was always opposite. The variation in response of bird communities to conifer plantations indicates that care is needed when generalising patterns of community diversity and assembly mechanisms across regions., Competing Interests: The authors have declared that no competing interests exist.

The interplay of microbiota and the human host is physiologically crucial in health and diseases. The beneficial effects of lactic acid bacteria (LAB), permanently colonizing the human intestine or transiently obtained from food, have been extensively reported. However, the molecular understanding of how LAB modulate human physiology is still limited. G protein-coupled receptors for hydroxycarboxylic acids (HCAR) are regulators of immune functions and energy homeostasis under changing metabolic and dietary conditions. Most mammals have two HCAR (HCA1, HCA2) but humans and other hominids contain a third member (HCA3) in their genomes. A plausible hypothesis why HCA3 function was advantageous in hominid evolution was lacking. Here, we used a combination of evolutionary, analytical and functional methods to unravel the role of HCA3 in vitro and in vivo. The functional studies included different pharmacological assays, analyses of human monocytes and pharmacokinetic measurements in human. We report the discovery of the interaction of D-phenyllactic acid (D-PLA) and the human host through highly potent activation of HCA3. D-PLA is an anti-bacterial metabolite found in high concentrations in LAB-fermented food such as Sauerkraut. We demonstrate that D-PLA from such alimentary sources is well absorbed from the human gut leading to high plasma and urine levels and triggers pertussis toxin-sensitive migration of primary human monocytes in an HCA3-dependent manner. We provide evolutionary, analytical and functional evidence supporting the hypothesis that HCA3 was consolidated in hominids as a new signaling system for LAB-derived metabolites., Competing Interests: The authors have declared that no competing interests exist.

Recent years have seen an explosion in the availability of biodiversity data describing the distribution, function, and evolutionary history of life on earth. Integrating these heterogeneous data remains a challenge due to large variations in observational scales, collection purposes, and terminologies. Here, we conceptualize widely used biodiversity data types according to their domain (what aspect of biodiversity is described?) and informational resolution (how specific is the description?). Applying this framework to major data providers in biodiversity research reveals a strong focus on the disaggregated end of the data spectrum, whereas aggregated data types remain largely underutilized. We discuss the implications of this imbalance for the scope and representativeness of current macroecological research and highlight the synergies arising from a tighter integration of biodiversity data across domains and resolutions. We lay out effective strategies for data collection, mobilization, imputation, and sharing and summarize existing frameworks for scalable and integrative biodiversity research. Finally, we use two case studies to demonstrate how the explicit consideration of data domain and resolution helps to identify biases and gaps in global data sets and achieve unprecedented taxonomic and geographical data coverage in macroecological analyses., Competing Interests: The authors have declared that no competing interests exist.

Light driven primary production by plants is the main source of biomass in terrestrial ecosystems. But also in subsurface habitats like aquifers, life is fueled largely by this plant-derived biomass. Here, we investigate the degradation of plant-derived polysaccharides in a groundwater microbiome to identify the microbial key players involved, and compare them to those from soil of the groundwater recharge area. We quantified the activities of enzymes degrading the abundant plant polymers starch, cellulose and hemicellulose in oligotrophic groundwater samples, despite the low cell numbers present. Normalized to 16S rRNA gene copy numbers, these activities were only one order of magnitude lower than in soil. Stimulation of the groundwater microbiome with either starch or cellulose and hemicellulose led to changes of the enzymatic activity ratios, indicating autochthonous production of enzymes in response to the plant polymers. Furthermore, DNA stable isotope probing with 13C labelled plant polymers allowed us to identify microbes involved in the degradation of these compounds. In (hemi)cellulose microcosms, Bacteroidia and Candidatus Parcubacteria were active, while the active community in starch microcosms mostly comprised Candidatus Saccharibacteria, Cytophagia, and Actinobacteria. Not a single one of the active OTUs was also found to be labelled in soil microcosms. This indicates that the degradation of plant-derived polysaccharides in groundwater is driven by organisms completely distinct from those active in soil. The involvement of members of the candidate phyla Cand. Parcubacteria and Cand. Saccharibacteria, organisms known to be abundant in groundwater, in plant-derived organic matter degradation might strongly impact subsurface carbon cycling., Competing Interests: The authors have declared that no competing interests exist.

Deadwood is an important structural component in forest ecosystems and plays a significant role in global carbon and nutrient cycling. Relatively little is known about the formation and decomposition of CWD by microbial communities in situ and about the factors controlling the associated processes. In this study, we intensively analyzed the molecular fungal community composition and species richness in relation to extracellular enzyme activity and differences in decomposing sapwood and heartwood of 13 temperate tree species (four coniferous and nine deciduous species, log diameter 30-40 cm and 4 m long) in an artificial experiment involving placing the logs on the forest soil for six years. We observed strong differences in the molecular fungal community composition and richness among the 13 tree species, and specifically between deciduous and coniferous wood, but unexpectedly no difference was found between sapwood and heartwood. Fungal species richness correlated positively with wood extractives and negatively with fungal biomass. A distinct fungal community secreting lignocellulolytic key enzymes seemed to dominate the decomposition of the logs in this specific phase. In particular, the relative sequence abundance of basidiomycetous species of the Meruliaceae (e.g. Bjerkandera adusta) correlated with ligninolytic manganese peroxidase activity. Moreover, this study reveals abundant white-rot causing Basidiomycota and soft-rot causing Ascomycota during this phase of wood decomposition., Competing Interests: The authors have declared that no competing interests exist.

Numerous experiments have shown positive diversity effects on plant productivity, but little is known about related processes of carbon gain and allocation. We investigated these processes in a controlled environment (Montpellier European Ecotron) applying a continuous 13CO2 label for three weeks to 12 soil-vegetation monoliths originating from a grassland biodiversity experiment (Jena Experiment) and representing two diversity levels (4 and 16 sown species). Plant species richness did not affect community- and species-level 13C abundances neither in total biomass nor in non-structural carbohydrates (NSC). Community-level 13C excess tended to be higher in the 16-species than in the 4-species mixtures. Community-level 13C excess was positively related to canopy leaf nitrogen (N), i.e. leaf N per unit soil surface. At the species level, shoot 13C abundances varied among plant functional groups and were larger in legumes and tall herbs than in grasses and small herbs, and correlated positively with traits as leaf N concentrations, stomatal conductance and shoot height. The 13C abundances in NSC were larger in transport sugars (sucrose, raffinose-family oligosaccharides) than in free glucose, fructose and compounds of the storage pool (starch) suggesting that newly assimilated carbon is to a small portion allocated to storage. Our results emphasize that the functional composition of communities is key in explaining carbon assimilation in grasslands., Competing Interests: The authors have declared that no competing interests exist.

Different ecosystem models often provide contrasting predictions (model uncertainty), which is perceived to be a major challenge impeding their use to support ecosystem-based fisheries management (EBFM). The focus of this manuscript is to examine the extent of model disagreements which could impact management advice for EBFM in the central Baltic Sea. We compare how much three models (EwE, Gadget and a multispecies stock production model) differ in 1) their estimates of fishing mortality rates (Fs) satisfying alternative hypothetical management scenario objectives and 2) the outcomes of those scenarios in terms of performance indicators (spawning stock biomasses, catches, profits). Uncertainty in future environmental conditions affecting fish was taken into account by considering two seal population growth scenarios and two nutrient load scenarios. Differences in the development of the stocks, yields and profits exist among the models but the general patterns are also sufficiently similar to appear promising in the context of strategic fishery advice. Thus, we suggest that disagreements among the ecosystem models will not impede their use for providing strategic advice on how to reach management objectives that go beyond the traditional maximum yield targets and for informing on the potential consequences of pursuing such objectives. This is especially true for scenarios aiming at exploiting forage fish sprat and herring, for which the agreement was the largest among our models. However, the quantitative response to altering fishing pressure differed among models. This was due to the diverse environmental covariates and the different number of trophic relationships and their functional forms considered in the models. This suggests that ecosystem models can be used to provide quantitative advice only after more targeted research is conducted to gain a deeper understanding into the relationship between trophic links and fish population dynamics in the Baltic Sea., Competing Interests: The authors have declared that no competing interests exist.

The presence of native grasses in communities can suppress native forbs through competition and indirectly benefit these forbs by suppressing the invasion of highly competitive exotic species. We conducted a greenhouse experiment to examine the potential of direct and indirect interactions to influence the aboveground biomass of four native forb species in the presence of the native perennial grass Schizachyrium scoparium and exotic invasive Lespedeza cuneata. We examined patterns of growth for the invasive legume, the perennial grass, and four native species in four scenarios: 1) native species grown with the grass, 2) native species grown with the legume, 3) native species grown with both the grass and legume together, and 4) native species grown alone. Schizachyrium scoparium significantly decreased biomass of all forb species (p<0.05). In contrast, L. cuneata alone only significantly affected biomass of Asclepias tuberosa; L. cuneata increased the biomass of A. tuberosa only when the grass was present. When S. scoparium and L. cuneata were grown together, L. cuneata had significantly lower biomass (p = 0.007) and S. scoparium had significantly greater biomass (p = 0.002) than when each grew alone. These reciprocal effects suggest a potential pathway by which L. cuneata could alter forb diversity in grassland communities In this scenario, L. cuneata facilitates grass growth and competition with other natives. Our results emphasize the importance of monitoring interactions between exotic invasive plant species and dominant native species in grassland communities to understand pathways of plant community change., Competing Interests: The authors have declared that no competing interests exist.

Persistent seed banks are predicted to have an important impact on population genetic processes by increasing effective population size and storing past genetic diversity. Accordingly, persistent seed banks may buffer genetic effects of disturbance, fragmentation and/or selection. However, empirical studies surveying the relationship between aboveground and seed bank genetics under changing environments are scarce. Here, we compared genetic variation of aboveground and seed bank cohorts in 15 populations of the partially cleistogamous Viola elatior in two contrasting early and late successional habitats characterized by strong differences in light-availability and declining population size. Using AFLP markers, we found significantly higher aboveground than seed bank genetic diversity in early successional meadow but not in late successional woodland habitats. Moreover, individually, three of eight woodland populations even showed higher seed bank than aboveground diversity. Genetic differentiation among populations was very strong (фST = 0.8), but overall no significant differentiation could be detected between above ground and seed bank cohorts. Small scale spatial genetic structure was generally pronounced but was much stronger in meadow (Sp-statistic: aboveground: 0.60, seed bank: 0.32) than in woodland habitats (aboveground: 0.11; seed bank: 0.03). Our findings indicate that relative seed bank diversity (i.e. compared to aboveground diversity) increases with ongoing succession and despite decreasing population size. As corroborated by markedly lower small-scale genetic structure in late successional habitats, we suggest that the observed changes in relative seed bank diversity are driven by an increase of outcrossing rates. Persistent seed banks in Viola elatior hence will counteract effects of drift and selection, and assure a higher chance for the species' long term persistence, particularly maintaining genetic variation in declining populations of late successional habitats and thus enhancing success rates of population recovery after disturbance events., Competing Interests: The authors have declared that no competing interests exist.

Human use of the land (for agriculture and settlements) has a substantial negative effect on biodiversity globally. However, not all species are adversely affected by land use, and indeed, some benefit from the creation of novel habitat. Geographically rare species may be more negatively affected by land use than widespread species, but data limitations have so far prevented global multi-clade assessments of land-use effects on narrow-ranged and widespread species. We analyse a large, global database to show consistent differences in assemblage composition. Compared with natural habitat, assemblages in disturbed habitats have more widespread species on average, especially in urban areas and the tropics. All else being equal, this result means that human land use is homogenizing assemblage composition across space. Disturbed habitats show both reduced abundances of narrow-ranged species and increased abundances of widespread species. Our results are very important for biodiversity conservation because narrow-ranged species are typically at higher risk of extinction than widespread species. Furthermore, the shift to more widespread species may also affect ecosystem functioning by reducing both the contribution of rare species and the diversity of species' responses to environmental changes among local assemblages., Competing Interests: The authors have declared that no competing interests exist.

Competing Interests: The authors have declared that no competing interests exist.

Whiteflies are among the world's most significant agricultural pests and chemical insecticides are extensively used to reduce crop damage to acceptable levels. However, nearly all insecticides pose a threat to the environment and alternative control methods, such as breeding of crop varieties that are inherently insect-resistant, are needed. Previously, a strong source of plant-age dependent resistance to the cabbage whitefly (Aleyrodes proletella) has been identified in the modern white cabbage (Brassica oleracea var. capitata) variety Rivera. However, nothing is known about the molecular mechanisms or the genes involved in this resistance. In the present study, a multidisciplinary approach combining transcriptome and metabolome profiling with genetic mapping was used to identify the molecular players of whitefly resistance in cabbage. Transcriptome profiles of young (susceptible) and older (resistant) Rivera plants were analyzed using RNA sequencing. While many genes involved in general processes were differentially expressed between both ages, several defense-related processes were overrepresented in the transcriptome profile of older plants. Hormone measurements revealed that jasmonic acid (JA) levels decreased upon whitefly infestation at both plant ages. Interestingly, abscisic acid (ABA) levels showed contrasting effects in response to whitefly infestation: ABA levels were reduced in young plants but induced in older plants upon whitefly feeding. Auxin levels were significantly lower in older plants compared with young plants, independent of whitefly presence, while glucosinolate levels were higher. Additionally, whitefly performance was monitored in an F2 population derived from a cross between Rivera and the susceptible white cabbage variety Christmas Drumhead. Significant QTL intervals were mapped on chromosome 2 and 9 for oviposition rate and whitefly adult survival, respectively. Several genes that were higher expressed in older plants and located in the identified QTL intervals were orthologous to Arabidopsis genes that have been related to ABA signaling, suggesting a role for ABA in the regulation of resistance towards whiteflies. Our results show that combining different omics approaches is a useful strategy to identify candidate genes underlying insect resistance., Competing Interests: Two of the authors are employed by Keygene N.V., a commercial company. However, this does not alter our adherence to PLOS ONE policies on sharing data and materials.

Primary and secondary metabolites exuded by plant roots have mainly been studied under laboratory conditions, while knowledge of root exudate patterns of plants growing in natural communities is very limited. Focusing on ten common European grassland plant species, we asked to which degree exuded metabolite compositions are specific to species or growth forms (forbs and grasses), depend on environments and local neighbourhoods, and reflect traditional plant functional traits. Root exudates were collected under field conditions and analysed using a non-targeted gas chromatography coupled mass spectrometry (GC-MS) approach. In total, we annotated 153 compounds of which 36 were identified by structure and name as metabolites mainly derived from the primary metabolism. Here we show by using variance partitioning, that the composition of exuded polar metabolites was mostly explained by plot identity, followed by plant species identity while plant species composition of the local neighbourhood played no role. Total and root dry biomass explained the largest proportion of variance in exudate composition, with additional variance explained by traditional plant traits. Although the exudate composition was quite similar between the two growth forms, we found some metabolites that occurred only in one of the two growth forms. Our study demonstrated the feasibility of measuring polar exudates under non-sterile field conditions by mass spectrometry, which opens new avenues of research for functional plant ecology., Competing Interests: The authors have declared that no competing interests exist.

There is unequivocal evidence in the literature that epidemics adversely affect the livelihoods of individuals, households and communities. However, evidence in the literature is dominated by the socioeconomic impacts of HIV/AIDS and malaria, while evidence on the impact of the Ebola virus disease (EVD) on households' livelihoods remains fragmented and scant. Our study investigates the effect of the EVD epidemic on the livelihoods of Liberian households using the Sustainable Livelihood Framework (SLF). The study also explores the effect of the EVD epidemic on agricultural production and productive efficiency of farm households using Spatial Stochastic Frontier Analysis (SSFA). We collected data from 623 households across Liberia in 2015, using a systematic random sampling design. Our results indicated that the annual income of sample households from communities where EVD occurred did not differ from the annual income of households from communities where EVD did not occur. Nonetheless, the majority of sample households reported a decrease in their income, compared to their income in the year before the survey. This suggests that the impact of the EVD epidemic might not only have been limited to communities directly affected by the epidemic, but also it may have indirectly affected communities in areas where EVD was not reported. We also found that the community-level incidence of EVD negatively affected crop production of farm households, which may have exacerbated the problem of food insecurity throughout the country. Moreover, we found that the EVD epidemic weakened the society's trust in Liberian institutions. In a nutshell, our results highlight that epidemics, such as the recent EVD outbreak, may have long-lasting negative effects on the livelihoods of a society and their effect may extend beyond the communities directly affected by the epidemics. This means that the nation's recovery from the impact of the epidemic would be more challenging, and the social and economic impacts of the epidemic may extend well beyond the end of the health crisis., Competing Interests: The authors have declared that no competing interests exist.

In Mediterranean ecosystems, climate change is projected to increase fire danger and summer drought, thus reducing post-fire recruitment of obligate seeder species, and possibly affecting the population genetic structure. We performed a genome-wide genetic marker study, using AFLP markers, on individuals from one Central Spain population of the obligate post-fire seeder Cistus ladanifer L. that established after experimental fire and survived during four subsequent years under simulated drought implemented with a rainout shelter system. We explored the effects of the treatments on marker diversity, spatial genetic structure and presence of outlier loci suggestive of selection. We found no effect of fire or drought on any of the genetic diversity metrics. Analysis of Molecular Variance showed very low genetic differentiation among treatments. Neither fire nor drought altered the small-scale spatial genetic structure of the population. Only one locus was significantly associated with the fire treatment, but inconsistently across outlier detection methods. Neither fire nor drought are likely to affect the genetic makeup of emerging C. ladanifer, despite reduced recruitment caused by drought. The lack of genetic change suggests that reduced recruitment is a random, non-selective process with no genome-wide consequences on this keystone, drought- and fire tolerant Mediterranean species., Competing Interests: The authors have declared that no competing interests exist.

Plant genetic diversity structures animal communities and affects plant population productivity. However, few studies have investigated which traits are involved and the mechanisms mediating these effects. We studied the consequences of varying the expression of a single biosynthetic gene in jasmonate (JA) defense hormones, which are essential for defense against herbivores but constrain plant growth, in experimental mesocosm populations of wild tobacco (Nicotiana attenuata) plants under attack from three native herbivores. Empoasca leafhoppers preferentially attack JA-deficient N. attenuata plants in nature, and the specialist Tupiocoris notatus mirids avoid Empoasca-damaged plants. However, in experimental mesocosm populations having equal numbers of wild-type (WT) and JA-deficient plants that are silenced in the expression of the biosynthetic gene lipoxygenase 3 (LOX3), Empoasca sp. attacked both genotypes. Empoasca sp. damage, rather than JA, determined T. notatus damage, which was reduced in mixed populations. The growth of specialist Manduca sexta larvae was reduced on WT vs. asLOX3 monocultures, but differed in mixtures depending on caterpillar density. However, seed capsule number remained similar for WT and asLOX3 plants in mixtures, not in monocultures, in two experimental scenarios reflecting high and low caterpillar attack. At high caterpillar density, WT plants growing in mixtures produced more seed capsules than those growing in monocultures while seed production of asLOX3 plants did not differ by population type. However, at low caterpillar density, asLOX3 plants growing in mixed populations produced more seed capsules than those growing in monoculture, while seed capsule production did not differ for WT by population type. Thus, mixed populations had a more stable output of seed capsules under the two scenarios. This may result from a balance between JA-mediated herbivore defense and plant competitive ability in mixed populations., Competing Interests: The authors have declared that no competing interests exist.

The concentration of atmospheric carbon dioxide (CO2) and polycyclic aromatic hydrocarbons (PAHs) contents in the environment have been rising due to human activities. Elevated CO2 (eCO2) levels have been shown to affect plant physiology and soil microbes, which may alter the degradation of organic pollutants. Here, we study the effect of eCO2 on PAH accumulation in a paddy soil grown with rice. We collected soil and plant samples after rice harvest from a free-air CO2 enrichment (FACE) system, which had already run for more than 15 years. Our results show that eCO2 increased PAH concentrations in the soil, and we link this effect to a shift in soil microbial community structure and function. Elevated CO2 changed the composition of soil microbial communities, especially by reducing the abundance of some microbial groups driving PAH degradation. Our study indicates that elevated CO2 levels may weaken the self-cleaning ability of soils related to organic pollutants. Such changes in the function of soil microbial communities may threaten the quality of crops, with unknown implications for food safety and human health in future climate scenarios.

Climate change is predicted to impact species' genetic diversity and distribution. We used Senegalia senegal (L.) Britton, an economically important species distributed in the Sudano-Sahelian savannah belt of West Africa, to investigate the impact of climate change on intraspecific genetic diversity and distribution. We used ten nuclear and two plastid microsatellite markers to assess genetic variation, population structure and differentiation across thirteen sites in West Africa. We projected suitable range, and potential impact of climate change on genetic diversity using a maximum entropy approach, under four different climate change scenarios. We found higher genetic and haplotype diversity at both nuclear and plastid markers than previously reported. Genetic differentiation was strong for chloroplast and moderate for the nuclear genome. Both genomes indicated three spatially structured genetic groups. The distribution of Senegalia senegal is strongly correlated with extractable nitrogen, coarse fragments, soil organic carbon stock, precipitation of warmest and coldest quarter and mean temperature of driest quarter. We predicted 40.96 to 6.34 per cent of the current distribution to favourably support the species' ecological requirements under future climate scenarios. Our results suggest that climate change is going to affect the population genetic structure of Senegalia senegal, and that patterns of genetic diversity are going to influence the species' adaptive response to climate change. Our study contributes to the growing evidence predicting the loss of economically relevant plants in West Africa in the next decades due to climate change.

Aim: A database based on distributional records of Eurasian Zephyrus hairstreaks (Lepidoptera: Lycaenidae: Theclini) was compiled to analyse their areas of endemism (AoEs), species richness and distribution patterns, to explore their locations of past glacial refugia and dispersal routes., Methods: Over 2000 Zephyrus hairstreaks occurrences are analysed using the NDM/VNDM algorithm, for the recognition of AoEs. Species richness was calculated by using the option 'Number of different classes' to count the different classes of a variable presented in each 3.0°×3.0° grid cell, and GIS software was used to visualize distribution patterns of endemic species., Results: Centres of species richness of Zephyrus hairstreaks are situated in the eastern Qinghai-Tibet Plateau (EQTP), Hengduan Mountain Region (HDMR) and the Qinling Mountain Region (QLMR). Latitudinal gradients in species richness show normal distribution with the peak between 25° N and 35° N in the temperate zone, gradually decreasing towards the poles. Moreover, most parts of central and southern China, especially the area of QLMR-EQTP-HDMR, were identified as AoEs that may have played a significant role as refugia during Quaternary global cooling. There are four major distributional patterns of Zephyrus hairstreaks in Eurasia: Sino-Japanese, Sino-Himalayan, high-mountain and a combined distribution covering all three patterns., Conclusions: Zephyrus hairstreaks probably originated at least 23-24 Myr ago in E. Asia between 25° N to 35° N in the temperate zone. Cenozoic orogenies caused rapid speciation of this tribe and extrusion of the Indochina block resulted in vicariance between the Sino-Japanese and the Sino-Himalayan patterns. The four distribution patterns provided two possible dispersal directions: Sino-Japanese dispersal and Sino-Himalayan dispersal.

The spread of invasive plants along elevational gradients is considered a threat to fragile mountain ecosystems, but it can also provide the opportunity to better understand some of the basic processes driving the success of invasive species. Ageratina adenophora (Asteraceae) is an invasive plant of global importance and has a broad distribution along elevational gradients in the Western Himalayas. Our study aimed at understanding the role of evolutionary processes (e.g. local adaptation and clinal differentiation) and different life history stages in shaping the distribution pattern of the invasive plant along an elevational gradient in the Western Himalaya. We carried out extensive distributional surveys, established a reciprocal transplant experiment with common gardens at three elevational levels, and measured a suite of traits related to germination, growth, reproduction and phenology. Our results showed a lack of local adaptation, and we did not find any evidence for clinal differentiation in any measured trait except a rather weak signal for plant height. We found that seed germination was the crucial life-cycle transition in determining the lower range limit while winter mortality of plants shaped the upper range limit in our study area, thus explaining the hump shaped distribution pattern. Differences in trait values between gardens for most traits indicated a high degree of phenotypic plasticity. Possible causes such as apomixis, seed dispersal among sites, and pre-adaptation might have confounded evolutionary processes to act upon. Our results suggest that the success and spread of Ageratina adenophora are dependent on different life history stages at different elevations that are controlled by abiotic conditions.

Ecology has become a data intensive science over the last decades which often relies on the reuse of data in cross-experimental analyses. However, finding data which qualifies for the reuse in a specific context can be challenging. It requires good quality metadata and annotations as well as efficient search strategies. To date, full text search (often on the metadata only) is the most widely used search strategy although it is known to be inaccurate. Faceted navigation is providing a filter mechanism which is based on fine granular metadata, categorizing search objects along numeric and categorical parameters relevant for their discovery. Selecting from these parameters during a full text search creates a system of filters which allows to refine and improve the results towards more relevance. We developed a framework for the efficient annotation and faceted navigation in ecology. It consists of an XML schema for storing the annotation of search objects and is accompanied by a vocabulary focused on ecology to support the annotation process. The framework consolidates ideas which originate from widely accepted metadata standards, textbooks, scientific literature, and vocabularies as well as from expert knowledge contributed by researchers from ecology and adjacent disciplines.

Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS). However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus) using cotton swabs, thermal desorption (TD) tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113), with half of those compounds being volatile (N = 52). The mobile GC-MS captured the fewest compounds (N = 35), of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55), but very few volatiles (N = 10). Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%). Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor.