Research Ideas and Outcomes :
Forum Paper
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Corresponding author: Jürgen Groeneveld (juergen.groeneveld@ufz.de)
Academic editor: Dmitry Schigel
Received: 11 Apr 2024 | Accepted: 15 May 2024 | Published: 11 Jun 2024
© 2024 Jürgen Groeneveld, Tomas Martinovic, Tuomas Rossi, Ondrej Salamon, Kata Sara-aho, Volker Grimm
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Groeneveld J, Martinovic T, Rossi T, Salamon O, Sara-aho K, Grimm V (2024) Prototype Biodiversity Digital Twin: honey bees in agricultural landscapes. Research Ideas and Outcomes 10: e125167. https://doi.org/10.3897/rio.10.e125167
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Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate-change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land-cover maps and daily weather data. We have developed the pDT for simulating large areas and have tested it for the whole of Germany. We have also developed a web-based GUI that users can use to run the pDT for specific sites. Hive weight data from hundreds of hives will be used for calibration and validation.
pollination, biodiversity, honey bees, multiple stressors, agricultural landscapes, resilience
Pollinators are ubiquitous in ecosystems and play a critical role in our food supply, although the risks of their decline, including to biodiversity, are not fully understood (
While single stressors, such as modern pesticides, may play an important role, the current general consensus is that the combination of multiple stressors impairs the resilience of honey bee colonies. Even if each stressor has no detectable effect at the colony level, their combination can lead to colony mortality (
Numerous simulation models have, therefore, been developed to support and extrapolate empirical research (
BEEHAVE is a typical high-resolution ecological model: it has a relatively small spatial extent. It represents only the landscape around a single hive, i.e. 5 x 5 km². As such, it cannot be used to assess the status of honey bees and their habitat across regions, countries or beyond. Existing workflows for BEEHAVE rely on maps of fields and crops in the surrounding landscape, which are rarely available, as are data to test model predictions of colony performance. BEEHAVE has been used in more than 25 studies (Suppl. material
As a first step, a prototype DT, HONEYBEE-pDT, was developed to enable the automated application of the BEEHAVE model for the whole of Germany. This includes two types of applications. First, to produce maps of Germany that visualise, for example, the number of adult bees before winter or the amount of honey that has been produced during a year. For such maps, we have run the HONEYBEE-pDT on a raster with a resolution of 5 km on the EuroHPC supercomputer LUMI (see Performance section). Second, to run BEEHAVE for specific hive locations. Users only need to specify the coordinates of the hive, but they can also modify the model parameters and the parameters of the floral resources. This user execution of HONEYBEE-pDT is possible via a web interface on a cloud environment (https://app.biodt.eu, see Interface and Outputs section). The pDT can also be used for education and training in sustainable practices.
Fig.
The pDT requires land-cover data, weather data and the specification of model parameters and flower resource parameters. In the pDT, the land-cover data are based on a map by Preidl and colleagues (
So far, HONEYBEE-pDT is limited to Germany, but the workflows can be applied to other countries if the relevant data, such as land-cover maps, are available.
BEEHAVE (
The foraging module is agent-based, with one agent representing 100 bees. It simulates the foraging behaviour of bees, including scouting for new rewarding floral resources in the landscape and recruiting foragers via a waggle dance that communicates the foraging efficiency of particular flower fields. Foragers collect nectar and pollen in the given landscape, but only when the weather permits. The temporal resolution of the foraging module is implicit and takes into account flight and handling time in seconds.
The mite model represents the dynamics of the Varroa mite population in the hive. Mites can be either inside the brood cells or phoretic, i.e. attached to an adult bee. Mites transmit viruses that increase the mortality of infected larvae or adult bees. The mite module includes optional control measures, such as treatment with acaricides. Other optional beekeeping practices include honey harvesting and swarm control.
BEEHAVE can be run with stylised settings for theoretical studies, i.e. all floral resources in the landscape are represented by two resource patches not representing a real landscape. Resource patches are the model entities describing areas with floral resources (e.g. fields or meadows) that are characterised by their size, distance to the honey bee colony and amount of nectar and pollen. However, it is also possible to import land-cover and weather data for specific locations and years. The landscape is represented as a list of fields, or patches, that provide nectar and/or pollen sooner or later in the year. Each patch is characterised by its distance from the hive, the likelihood of detection by foragers, the flowering period, the nectar and pollen supply and the handling time for the bees. The latter increases with increasing use of the patch, i.e. the foraging efficiency, for example, the resources of a patch can change over the course of a day. Weather data on temperature and rainfall are converted into the number of foraging hours per day, as bees do not forage in rain and low temperatures. BEEHAVE comes with example datasets for a landscape in England. The input file for BEEHAVE is a text file that can be created manually or by using the software tool BEESCOUT (
BEEHAVE was implemented in NetLogo (
Fig.
Overview of the BEEHAVE model from the model description (ODD protocol available at https://beehave-model.net).
The BEEHAVE model is well documented and freely accessible. The BEEHAVE version used and all developed scripts are published as open source on the BioDT GitHub repository (https://github.com/BioDT). All input data are freely available (see Data for details). Currently, the model outcomes of the HONEYBEE-pDT produced in the web GUI will not be stored long term and the GUI user is responsible for the data.
The simulation experiments can be specified and executed by R scripts using the nlrx package (
The communication between the user and the pDT is done by a R shiny web application hosted at https://app.biodt.eu. The user can vary parameters of the model and the floral resources. In addition, a location within Germany can be chosen. As outputs, the number of adult bees, honey production and flight time are visualised. A screenshot of the GUI for the site specific application is shown in Fig.
During the project lifetime, we already have run the pDT on different HPCs (LUMI and Karolina). Thus, in principle, the pDT can be easily migrated between computational infrastructure. One option after the end of the project is to host the HONEYBEE-pDT using resources from the Helmholtz Association to which the lead authors of this paper belong.
The HONEYBEE-pDT would benefit from links with other DT initiatives such as DestineE and EOSC, as information on extreme events, droughts and other environmental information is crucial for reliable prediction of honey bee flight and foraging behaviour. It would also be beneficial to attempt to link the HONEYBEE-pDT with DTs of vegetation DTs such as the GRASSMIND-pDT.
The prototype presented here, HONEYBEE-pDT, demonstrates the concept of a digital twin for supporting two important aspects of biodiversity conservation, pollination and agricultural land use. DTs are intended to support decisions in a more robust and relevant way than traditional models. Two characteristics of DTs are that
Turning a simulation model, such as BEEHAVE, into a DT requires infrastructure and expertise far beyond what is normally available for modellers. Expertise is required to create data structures and workflows for key relevant input data, to create workflows for running BEEHAVE in parallel on a supercomputer, to containerise these workflows and the many complex software tools required and to create a professional GUI. The infrastructure required to run BEEHAVE at all relevant spatial scales was a supercomputer such as LUMI. The pDT development has been a team effort; while the modellers involved would not have had the time and expertise to create HONEYBEE-pDT on their own, the data and computer scientists involved would not have been able to take a model like BEEHAVE off the shelf and plug it into the workflows and infrastructure, as this would have required expertise in modelling and honey bee ecology. Certainly, frequent meetings and updates were needed to develop a mutual understanding of all the elements of the pDT, but the effort was well worth it, as the results and the prospect of the final, fully implemented DT far exceeded our expectations. Biodiversity modellers have always struggled with the choice between large-scale models that are too unrealistic at the local scale and small-scale models that are realistic, but too small in scale to be useful for supporting management and policy development. HONEYBEE-pDT was an important milestone in the adoption of the concept of DTs for biodiversity research, management and conservation (
HONEYBEE-pDT is aimed at different end-users. Firstly, we encourage beekeepers to simulate a virtual honey bee colony at a location of interest to them and compare the simulation results with their own experience and give us feedback. As it is difficult for academic researchers to reach the practitioners, we work closely with the German bee institutes and present at their annual meetings. We have also organised workshops and training on the BEEHAVE model to disseminate our tools. As a second target group, we have identified other researchers. At our user workshop in Leipzig in November, we realised that we need to allow them to upload customised versions of the BEEHAVE simulation model so that they can use the pDT for their work. The same goes for the third target group, industry. Companies, such as Bayer, also use BEEHAVE and may be interested in using a service such as the HONEYBEE-pDT, but they would want to use their own version of BEEHAVE, which includes a pesticide exposure and effects module (
We thank all the participants of the Honeybee-pDT team and Taimur Khan for very useful comments on an earlier version of this manuscript. This study has received funding from the European Union's Horizon Europe Research and Innovation Programme under grant agreement No. 101057437 (BioDT project, https://doi.org/10.3030/101057437). Views and opinions expressed are those of the author(s) only and do not necessarily reflect those of the European Union or the European Commission. Neither the European Union nor the European Commission can be held responsible for them. We acknowledge the EuroHPC Joint Undertaking and CSC – IT Center for Science, Finland for awarding this project access to the EuroHPC supercomputer LUMI, hosted by CSC – IT Center for Science and the LUMI consortium, through Development Access calls. We also acknowledge CSC – IT Center for Science, Finland, for computational resources in Pouta and Rahti services. This work was supported by the Ministry of Education, Youth and Sports of the Czech Republic through the e-INFRA CZ (ID:90254). We acknowledge IT4Innovations National Supercomputing Center and the use of Karolina.
List of peer reviewed publications in which the honeybee colony simulation model BEEHAVE (Becher et al. 2014) has been used (chronological order).