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Research project on field data collection for honey bee colony model evaluation - datasets
<p><strong>Description of the datasets</strong></p> <p>The file 00_MUSTB_field_data_model.docx contains the data model according to which the data collected in the context of the MUSTB field data collection were reported to EFSA. The current data model description includes some modifications with respect to the specifications published before the beginning of the project (EFSA, 2017, https://doi.org/10.2903/sp.efsa.2017.EN-1234). All the tables included in the data model are published here in csv format. The underlying schemas are also published in xsd format.</p> <p>Sites: General information about the sites where the data collection took place;</p> <p>Polygons: General information about the polygons where the botanical survey took place.</p> <p>Table I: Pesticide application, reporting data on experimental spraying events;</p> <p>Table II: Resource providing unit and landscape fitness, reporting data on abundance of flowering plants in polygons mostly within 1.5 km, but in some cases up to 3 km of the experimental colony;</p> <p>Table III: Master list of all hives included in the study;</p> <p>Table IV: Colony management, reporting the log of the beekeeper regarding input (if material was added to the hive: e.g. empty frames, chemicals for varroa treatment, sugar), output (if material was removed from the hive, e.g. honey combs, supers), queen loss, swarming, or clinical signs observed in the experimental hives;</p> <p>Table V: Hive inspection, reporting data on in-hive measurements in the experimental colonies. This table contained several types of data, including:</p> <ul> <li>Data on brood development and food provision (“cell utilization”) obtained from image analysis of combs;</li> <li>Data on forager activity obtained from automatic video recordings and image analysis by a bee counter;</li> <li>Data on hive weight obtained from automatic logging by a hive scale;</li> <li>Data on adult bee strength, obtained by weight assessment of combs with and without adult bees (“bees per comb data”);</li> </ul> <p>Table VI: SSD2, reporting data on results of laboratory analyses of pollen, pesticide residues and parasites/pathogens. These four types of laboratory analyses involved different methods, and were reported according to different standards. Therefore, a number of the fields in the technical specifications for the SSD2 table (EFSA, 2017) were not applicable for records reporting results of some analyses, in particular palynological, parasite and pathogen analyses. These fields were left empty;</p> <p>Table VII: Colony observation, reporting observations of honey bee waggle dances from observation hives. Orientation denotes the angle of the waggling phase relative to the vertical axis on the comb. Direction denotes the actual direction in the landscape, as calculated from the orientation of the waggle dance.</p> <p>In all the csv files, columns with the suffix "_desc" have been included, where relevant, to include the name corresponding to the EFSA controlled terminology used in the previous column (e.g. resUnit contains EFSA term codes while resUnit_desc contains the term names).</p> <p><strong>Data storage</strong></p> <p>All data collected during the project was stored in a relational database. The database was developed in .NET Entity Framework Core, ran on a PostgreSQL, and was hosted by Amazon Web Service during the whole duration of the project development. Data could be imported or entered manually in the database through a web form. Administrators could create new users and administrators, new sites, and new colonies, i.e., administrators were allowed to enter or change data of all tables. Users were allowed to enter data, and could view, retrieve, and modify their own data of all tables, except for Table III (description of experimental colonies). Administrators could view and retrieve all data. Data was retrieved in CSV and XML formats, and were structured to secure a smooth transmission of data to the Data Collection Framework of EFSA. Furthermore, data flow from the field data collection to the development of ApisRAM was secured by direct communication between the field and modelling teams.</p> <p> </p> <p><strong>Version 2</strong> contains the UTM coordinates in tables Sites, Polygons and Resource providing unit.</p>
Data for: An invasive ant increases deformed wing virus loads in honey bees
<p>The majority of invasive species are best known for their effects as predators. However, many introduced predators may also be substantial reservoirs for pathogens. Honey bee-associated viruses are found in various arthropod species including invasive ants. We examined how the globally invasive Argentine ant (<em>Linepithema humile</em>), which can reach high densities and infest beehives, is associated with pathogen dynamics in honey bees. Viral loads of Deformed wing virus (DWV), which has been linked to millions of beehive deaths around the globe, and black queen cell virus significantly increased in bees when invasive ants were present. Microsporidian and trypanosomatid infections, which are more bee-specific, were not affected by ant invasion. The bee virome in autumn revealed that DWV was the predominant virus with the highest infection levels and that no ant-associated viruses were infecting bees. Viral spillback from ants could increase infections in bees. In addition, ant attacks could pose a significant stressor to bee colonies that may affect virus susceptibility. These viral dynamics are a hidden effects of ant pests, which could have a significant impact on disease emergence in an economically important pollinator. Our study contributes to unravel a perhaps overlooked effect of species invasions: changes in pathogen dynamics.</p>
BeeRoLaMa v1 Honey Bee Microbiota Database
<p>Genomic sequences of a variety of honey bee (<em>Apis mellifera</em>) microbes, curated from <a href="https://data.nal.usda.gov/dataset/holobee-database-v20161">HoloBee Database v2016.1</a> and <a href="https://zenodo.org/record/3747314">Bioinformatic pipeline: Vast differences in strain-level diversity in the gut microbiota of two closely related honey bee species</a>.</p> <p>Contains a multi-fasta file containing genomic sequences (<em>beerolama_v1.fna</em>) as well as a Kraken2 formatted version of the database (<em>hash.k2d, opts.k2d, taxo.k2d</em>) and a text file produced by the <em>kraken2-inspect </em>function.</p>
Data from: Quantifying the impact of crop coverings on honey bee orientation and foraging in sweet cherry orchards using RFID
<p>Advancements in agricultural production have seen the rapid adoption of protected cropping systems globally. Such systems have been optimised for plant growth and efficiency, with little understanding of the potential impacts on key insect pollinators. Here we investigate the effect of netting and polythene rain covers on the health and performance of honey bees (<em>Apis mellifera </em>L.) during the pollination of sweet cherry crops. Over two consecutive seasons, twelve full-strength colonies were equipped with tagged bees and radio frequency identification (RFID) systems. The colonies were equally divided between open control, netted, and polythene (semi-permanent VOEN in 2019 and retractable Cravo in 2020) groups. Over 1,300 individual bees were monitored for the duration of the commercial pollination period to determine behavioural parameters such as foraging commencement age, number and duration of trips, and overall survival. Bees began foraging within the optimum age range (mean 15.7-24.1 days) under all covering types, with little indication of prolonged stress or increased mortality during the short season. Polythene covers (VOEN & Cravo) were found to significantly increase the total time needed for bees to orientate successfully. Once orientated, bees placed under covers conducted up to 155% more foraging trips, with a longer cumulative duration. Covering type was found to significantly impact the amount and type of pollen collected, with the most restrictive system (VOEN) yielding the highest proportion of cherry pollen. Overall, we found little evidence to suggest that protective covers have a detrimental impact on honey bee foraging in cherry crops.</p>
Signatures of adaptive decreased virulence of deformed wing virus in an isolated population of wild honey bees (Apis mellifera)
<p>Understanding the ecological and evolutionary processes that drive host-pathogen interactions is critical for combating epidemics and conserving species. The <em>Varroa</em> <em>destructor</em> mite and deformed wing virus (DWV) are two synergistic threats to Western honey bee (<em>Apis</em> <em>mellifera</em>) populations across the globe. Distinct honey bee populations have been found to self-sustain despite <em>Varroa</em> infestations, including colonies within the Arnot Forest outside Ithaca, NY, USA. We hypothesized that in these bee populations, DWV has been selected to produce an avirulent infection phenotype, allowing for the persistence of both host and disease-causing agents. To investigate this, we assessed the titer of viruses in bees from the Arnot Forest and managed apiaries, and assessed genomic variation and virulence differences between DWV isolates. Across groups, we found viral abundance was similar, but DWV genotypes were distinct. We also found that infections with isolates from the Arnot Forest resulted in higher survival and lower rates of symptomatic deformed wings, compared to analogous isolates from managed colonies, providing preliminary evidence to support the hypothesis of adaptive decreased viral virulence. Overall, this multi-level investigation of virus genotype and phenotype across different contexts reveals critical insight into global bee health and the ecological and evolutionary processes driving host-pathogen interactions.</p>
Data from: Evaluating the foraging performance of individual honey bees in different environments with automated field RFID systems
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Signatures of adaptive decreased virulence of deformed wing virus in an isolated population of wild honey bees (Apis mellifera)
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Data from: Iridescence untwined - Honey bees can separate hue variations in space and time
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Synergistic negative effects between a fungicide and high temperatures on homing behaviours in honey bees
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The effect of Israeli acute paralysis infection on honey bee brood care behavior
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Ecological and evolutionary drivers of stingless bee honey variation at the global scale
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Pollen collection by the western honey bee and common eastern bumble bee foraging in a common landscape and applications for agri-environment schemes
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The more the better: Fatty acids are predictive markers of honey bee, Apis mellifera, worker longevity
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Data for: An invasive ant increases deformed wing virus loads in honey bees
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Data from: Quantifying the impact of crop coverings on honey bee orientation and foraging in sweet cherry orchards using RFID
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Supplemental data Effects of imidacloprid exposure on honey bee colony growth and activity
To better understand how exposure to a low (5 ppb) concentration of imidacloprid affects honey bee colonies we conducted five field experiments involving a total of 54 bee colonies. In each experiment, bee colonies in one treatment group were fed sugar syrup adulterated with 5ppb imidacloprid over six weeks, and colonies in the other group were fed unadulturated sugar syrup over the same time period. Treatments were intended to simulate nectar collection by the colonies. No commercial agriculture existed within 10 km of the sites. We collected data from hive assessments, including adult bee mass and mass of food resources, and the total surface area of capped brood; and we collected data from sensors, including continuous hive weight, internal temperature and, for two years of the study, internal CO2 concentration. We measured Varroa mite fall before and after treatment each year of the study, and for 3 years of the study we measured the dry weight of newly-emerged adult bees.
Gleditsia triacanthos (honey locust) field experiments in Southern Appalachian Mountains region
Gleditsia triacanthos seeds were planted at field sites in the Southern Appalachian Mountains region to examine whether recruitment was habitat limited. Sites contain mixed open (fields) and closed (early to mid-successional forest) habitats, and the riverine geomorphology includes riparian terraces and wet floodplain depressions. Three habitat types - forest edge, floodplain and riparian; were chosen to expose seeds to soil moisture, temperature and light gradients. Measurements of germination success, seedling height, soil moisture, soil temperature, diffuse light, and vegetation cover were taken.
Gleditsia triacanthos (honey locust) greenhouse experiment
Gleditsia seeds were tested for germination success with moisture and light treatments. Seeds were extracted from the fruit pulp, scarified, and placed in a peat medium and exposed to varying degrees of sunlight and soil moisture.
Experimental infection of bumble bees with honey bee associated viruses: no direct fitness costs but potential future threats to novel wild bee hosts
<p>Pathogen spill-over represents an important cause of biodiversity decline. For wild bee species such as bumble bees, many of which are in decline, correlational data point toward viral spill-over from naged honey bees as a potential cause. Yet impacts of honey bee viruses on wild bees are rarely evaluated. Here, in a series of highly controlled laboratory infection assays with well characterised viral inocula, we show that three viral types isolated from honey bees (<i>Deformed wing virus</i> genotype A, <i>Deformed wing virus</i> genotype B and <i>Black queen cell virus</i>) readily replicate within hosts of the bumble bee <i>Bombus terrestris</i>. Impacts of these honey bee-derived viruses – either injected or fed – on the mortality of <i>B. terrestris </i>workers were, however, negligible and likely dependent on host condition. Our results highlight the potential threat of viral spill-over from honey bees to novel wild bee species, though they also underscore the importance of additional studies on this and other non- bee species under field-realistic conditions to evaluate whether pathogen spill-over has a negative impact on wild bee individuals and population fitness.</p>
Floral tea polyphenols can improve honey bee memory retention and olfactory sensitivity
<p>Animal-pollinated plants face a common problem, how their defensive anti-herbivore compounds may impair or alter pollinator behavior. Evolution has tailored multiple solutions, which largely involve pollinator tolerance or manipulation, to the benefit of the plant, not the removal of these compounds from pollen or nectar. The tea plant, <em>Camilla sinensis</em>, is famous for the caffeine and tea polyphenols (TP) that it produces in its leaves. However, these compounds are also produced in its nectar, which honey bees readily collect. We examined the effects of these compounds on bee foraging choices, learning, memory, and olfactory sensitivity. Foragers preferred a sucrose feeder with 100 µg or 10 µg TP/ml over a control feeder. Caffeine, but not TP, weakly increased honey bee learning. Both caffeine and TP significantly increased memory retention, even when tested 7 d after the last learning trial. In addition, TP generally elevated EAG responsiveness to alarm pheromone odors. These results demonstrate that not only caffeine, but other secondary plant compounds, can attract pollinators and influence their learning and memory.</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.