WorldFAIR (D10.3) Agricultural biodiversity FAIR data assessment rubrics

The WorldFAIR Case Study on Agricultural Biodiversity (WP10) addresses the challenges of advancing interoperability and mobilising plant-pollinator interactions data for reuse. Previous efforts, reported in WorldFAIR Deliverable 10.1, ‘Agriculture-related pollinator data standards use cases report’ (Trekels et al., 2023), provided an overview of projects, good practices, tools, and examples for creating, managing and sharing data related to plant-pollinator interactions. It also outlined a work plan for conducting pilot studies. Deliverable 10.2 (Drucker et al., 2024) presented Agricultural Biodiversity Standards, Best Practices and Guidelines Recommendations. This deliverable presented results from six pilot studies that adopted standards and recommendations from the earlier report. The current report complements the efforts with Agricultural Biodiversity FAIR data assessment rubrics.We introduce a set of FAIR assessment tools tailored to the plant-pollinator interactions domain. These tools are designed to help researchers and institutions evaluate adherence to the FAIR principles. In the discovery phase, we found that a significant amount of data on plant-pollinator interactions is available as supplementary files of research articles, in a diversity of formats such as PDFs, Excel spreadsheets, and text files. The diversity of approaches and the lack of appropriate data vocabularies lead to confusion, information loss, and the need for complex data interpretation and transformation. Our proposed framework primarily targets researchers in this domain who wish to assess the FAIRness of the data they produce and take action to improve it. However, we believe it can also benefit data reviewers, data stewards, data repository managers and librarians dealing with plant-pollinator data. Our approach focuses on being as familiar as possible with the researcher's practices, language, and jargon. Ultimately, we aim to promote data publishing and reuse in the plant-pollinator interactions domain.We present a ‘Rubric for the assessment of Plant-Pollinator Interactions Data’ with examples from the data from the pilots developed in Deliverable 10.2 and in relation to the FAIR Implementation Profile (FIP) created by Work Package 10. We conduct ‘dataset assessments’ of available data from research projects surveyed in the discovery phase. Additionally, we describe in detail the ‘Automated FAIR-enabled Data Reviews’ generated by the Global Biotic Interactions (GLoBI) infrastructure, with examples from the pilots. We believe the tools described in this report will encourage data publishing and reuse in the plant-pollinator interactions domain. Moving from diverse approaches and siloed initiatives to widely available FAIR plant-pollination interactions data for scientists and decision-makers will enable the development of integrative studies that enhance our understanding of species biology, behaviour, ecology, phenology, and evolution

WorldFAIR (D10.2) Agricultural Biodiversity Standards, Best Practices and Guidelines Recommendations

The WorldFAIR Case Study on Agricultural Biodiversity (WP10) addresses the challenges of advancing interoperability and mobilising plant-pollinator interactions data for reuse. Previous efforts, reported in Deliverable 10.1 - from our discovery phase - provided an overview of projects, best practices, tools, and examples for creating, managing and sharing data related to plant-pollinator interactions, along with a work plan for conducting pilot studies. The current report presents the results from the pilot phase of the Case Study, which involved six pilot studies adopting standards and recommendations from the discovery phase. The pilots enabled the handling  of concrete examples and the generation of reusable materials tailored to this domain, as well as providing better estimates for the overall costs of adoption for future projects. Our approach for plant-pollinator data standardisation is based on the widely-used standard for representing biodiversity data, Darwin Core, developed and maintained by the Biodiversity Information Standards (TDWG), in conjunction with a data model and vocabulary proposed by the Brazilian Network of Plant-Pollinator Interactions (REBIPP). The pilot studies also underwent a process of “FAIRification” (i.e., transforming data into a format that adheres to the FAIR data principles) using the Global Biotic Interactions (GloBI, Poelen et al. 2014) platform. Additionally, we present the publishing model for Biotic Interactions developed in collaboration with the Global Biodiversity Information Facility (GBIF), which leads the WorldFAIR Case Study on Biodiversity, as part of the proposed GBIF New Data Model, along with a concrete example of its use by one of the pilots. This effort led to the development of ‘FAIR best practices’ guidelines for sharing plant-pollinator interaction data. The primary focus of this work is to enhance the interoperability of data on plant-pollinator interactions, aligning with WorldFAIR efforts  to develop a Cross-Domain Interoperability Framework. We have successfully promoted the adoption of standards and increased the interoperability of plant-pollinator interactions data, resulting in a process that allows for tracing the provenance of the data, as well as facilitating the reuse of datasets crucial for understanding this essential ecosystem service and its changes due to human impact. Our effort demonstrates there are several possible paths for FAIRification, tailored to institutional needs, and we have shown that different approaches can contribute to promoting data interoperability and data availability for reuse, which is the ultimate goal of this initiative. Consequently, we have successfully ensured FAIR data for understanding plant-pollinator interactions at biologically-relevant scales for crops, with broad participation from initiatives in Europe, South America, Africa, North America, and elsewhere. We have also established concrete guidelines on FAIR data best practices customised for pollination data, metadata, and other digital objects, promoting the scalable adoption of these standards and FAIR data best practices by multiple initiatives. We believe this effort can assist similar initiatives in adopting interoperability standards for this domain and contribute to our understanding of how plant-pollinator interactions contribute to sustain life on Earth. Visit WorldFAIR online at http://worldfair-project.eu. WorldFAIR is funded by the EC HORIZON-WIDERA-2021-ERA-01-41 Coordination and Support Action under Grant Agreement No. 101058393. 

Ensuring access to high-quality resources reduces the impacts of heat stress on bees

International audiencePollinators are experiencing declines globally, negatively affecting the reproduction of wild plants and crop production. Well-known drivers of these declines include climatic and nutritional stresses, such as a change of dietary resources due to the degradation of habitat quality. Understanding potential synergies between these two important drivers is needed to improve predictive models of the future effects of climate change on pollinator declines. Here, bumblebee colony bioassays were used to evaluate the interactive effects of heat stress, a reduction of dietary resource quality, and colony size. Using a total of 117 colonies, we applied a fully crossed experiment to test the effect of three dietary quality levels under three levels of heat stress with two colony sizes. Both nutritional and heat stress reduced colony development resulting in a lower investment in offspring production. Small colonies were much more sensitive to heat and nutritional stresses than large ones, possibly because a higher percentage of workers helps maintain social homeostasis. Strikingly, the effects of heat stress were far less pronounced for small colonies fed with suitable diets. Overall, our study suggests that landscape management actions that ensure access to high-quality resources could reduce the impacts of heat stress on bee decline

A metabarcoding tool to detect predation of the honeybee Apis mellifera and other wild insects by the invasive Vespa velutina

The invasive Vespa velutina has been widely referred as an effective predator of honeybees. Despite the potential risk to pollination services provision and honey production, there is no accurate quantification and assessment of its real consequences for honeybees. To date, the identification of the honeybee and other insects in the diet of V. velutina has been investigated by direct observation of adult foraging or examination of food pellets. To overcome these limitations, in this study we used a DNA metabarcoding approach to evaluate the usefulness of different types of sample (jaws and stomachs collected from workers and larval faecal pellets taken from the hornet comb) to investigate the predation of V. velutina upon honeybees, and potentially on other insects. Honeybee DNA was identified in all types of samples, but larval faecal pellets retrieved the higher number of reads of honeybee DNA and the largest diversity at all taxonomic levels. Over all samples we could identify 4 orders, 9 families, 6 genera and 1 species of prey. We estimate that collecting 6 workers is sufficient to identify honeybee predation by a colony using worker’s jaws. Stomachs were the least useful sample type to detect honeybee DNA. The presence of honeybee DNA in all analysed colonies irrespective of collection site, and the variety of insect orders detected in the diet support current concerns over the acknowledged negative impact of V. velutina on managed honeybees and its potential threat to pollination services provision.info:eu-repo/semantics/publishedVersio

Understanding and addressing shortfalls in European wild bee data

Understanding and reversing biodiversity decline in the Anthropocene requires robust data on species taxonomic identity, distribution, ecology, and population trends. Data deficits hinder biodiversity assessments and conservation, and despite major advances over the past few decades, our understanding of bee diversity, decline and distribution in Europe is still hampered by such data shortfalls. Using a unique digital dataset of wild bee occurrence and ecology, we identify seven critical shortfalls which are an absence of knowledge on geographic distributions, (functional) trait variation, population dynamics, evolutionary relationships, biotic interactions, species identity, and tolerance to abiotic conditions. We describe “BeeFall,” an interactive online Shiny app tool, which visualizes these shortfalls and highlights missing data. We also define a new impediment, the Keartonian Impediment, which addresses an absence of high-quality in situ photos and illustrations with diagnostic characteristics and directly affects the outlined shortfalls. Shortfalls are highly correlated at both the provincial and national scales, identifying key areas in Europe where knowledge gaps can be filled. This work provides an important first step towards the long-term goal to mobilize and aggregate European wild bee data into a multi-scale, easy access, shareable, and updatable database which can inform research, practice, and policy actions for the conservation of wild bees.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Evidence of time-lag in the provision of ecosystem services by tropical regenerating forests to coffee yields

Restoration of native tropical forests is crucial for protecting biodiversity and ecosystem functions, such as carbon stock capacity. However, little is known about the contribution of early stages of forest regeneration to crop productivity through the enhancement of ecosystem services, such as crop pollination and pest control. Using data from 610 municipalities along the Brazilian Atlantic Forest (30 m spatial resolution), we evaluated if young regenerating forests (YRFs) (less than 20 years old) are positively associated with coffee yield and whether such a relationship depends on the amount of preserved forest in the surroundings of the coffee fields. We found that regenerating forest alone was not associated with variations in coffee yields. However, the presence of YRF (within a 500 m buffer) was positively related to higher coffee yields when the amount of preserved forest in a 2 km buffer is above a 20% threshold cover. These results further reinforce that regional coffee yields are influenced by changes in biodiversity-mediated ecosystem services, which are explained by the amount of mature forest in the surrounding of coffee fields. We argue that while regenerating fragments may contribute to increased connectivity between remnants of forest fragments and crop fields in landscapes with a minimum amount of forest (20%), older preserved forests (more than 20 years) are essential for sustaining pollinator and pest enemy’s populations. These results highlight the potential time lag of at least 20 years of regenerating forests’ in contributing to the provision of ecosystem services that affect coffee yields (e.g. pollination and pest control). We emphasize the need to implement public policies that promote ecosystem restoration and ensure the permanence of these new forests over time

Data from: Anthropogenic disturbance of tropical forests threatens pollination services to açaí palm in the Amazon river delta

The açaí palm Euterpe oleracea Mart. in the Amazon river delta has seen rapid expansion to meet increased demand for its fruit. This has been achieved by transforming lowland forest habitats (floodplains) into simplified agroforests and intensive plantation in upland areas. As açaí palm makes an important contribution to the economy and food security of local communities, identifying management approaches that support biodiversity and ecosystem processes that underpin fruit production on açaí farms is essential. We compared flower-visitor communities and açaí fruit production in floodplain forests and upland plantations, across gradients of local management intensity (i.e. açaí density per ha) and surrounding forest cover. The relative contribution of biotic pollination and degree of pollen limitation were assessed using insect exclusion and hand-pollination experiments. We found that açaí flower visitors are highly diverse (c. 200 distinct taxa) and had variable responses to disturbance. Bee visitation was higher in floodplains and positively related to surrounding forest cover, but other flower visitors, including specialised curculionid beetles, were unresponsive to changes in surrounding forest cover. However, intensive management practices (i.e. high açaí palm densities) in floodplains and uplands had contrasting effects on flower-visitor communities, with flower-visitor richness being lower on intensively managed floodplain farms and ant densities being higher on intensive upland farms. Pollination experiments revealed açaí palm to be highly dependent on biotic pollination. Fruit set in open-pollinated inflorescences was positively related to flower-visitor richness and specialised curculionid beetle visitation, whereas the presence of ants on inflorescences had a negative effect. Synthesis and applications. Our study shows that pollinators are essential for açaí fruit production, but that intensive farming practices have eroded the relationship between surrounding forest cover and ecosystem function in floodplains (i.e. conversion of native forest into simplified agroforests) and increased the frequency of antagonistic interactions in uplands (e.g. high ant densities). These findings underline the value of extensive management practices, such as the maintenance of other tree species within farms and adjacent unmanaged forest patches, to ensure the long-term sustainability of açaí fruit production in the Amazon river delta

Acai flower-visitor richness (sum data)

Dataset used to test effects of anthropogenic disturbance on pollinator richness and similarity (Jaccard's index). Data calculated from sum data (all surveys per site, n = 18) and presented in table 2 and figure 3 in main text (see README.txt for more details)

Acai flower-visitor surveys

Dataset for repeat observations of flower-visiting insect activity on acai palm (Euterpe oleracea) in the Amazon river delta. A total of 322 observations (10 minutes visual survey + 10 minutes for species collection. Data from observations and collections were combined - thus, where an insect was collected but not observed a value of 0.1 was attributed. Data was analysed using generalised mixed effects models and presented in Table 1, Table 2, and Figure 3 in the main manuscript (see README.txt for more details)