Modelling Life Beneath Our Feet: A New Step Towards Realistic Soil Ecology At The Landscape Scale

New Formal Model in the open-access Agricultural and Environmental Modelling journal contributes to a more realistic soil ecology modelling at the landscape level.

Guest blog post by Liyan Xie

Why focus on soil organisms?

Agricultural landscape
Agricultural landscape. Image via Canva.

Soil health is a core priority of the EU Soil Strategy for 2030, and soil organisms like Collembola (springtails) play a fundamental role in sustaining it. With an estimated 100,000 individuals per square meter in healthy soils, these invertebrates drive essential processes like nutrient cycling, organic matter fragmentation, and microbial regulation, while also serving as crucial prey for predators like spiders and mites. Despite their ecological importance and their distinct chemical exposure pathways compared to earthworms, they remain underrepresented in landscape-level environmental risk assessments, which often rely on simplified laboratory studies.

Moving beyond simplified tests

Assessing multiple ecosystem stressors
A framework for assessing multiple ecosystem stressors. Image credit to Liyan Xie.

Traditional ecotoxicological testing, such as standard OECD laboratory tests, has provided valuable baseline data for over 60 years, but these tests are typically conducted under constant, highly controlled conditions. While informative, this approach overlooks the dynamic nature of environmental drivers like temperature and soil moisture, which jointly shape physiological performance.

For example, existing population models often ignore soil moisture entirely or rely on simplistic constant temperatures. Addressing this gap requires advanced modelling tools that can represent non-linear life-history processes, such as stage transitions and vital rates, under realistic, fluctuating conditions.

To achieve this, the researchers utilized the Animal, Landscape and Man Simulation System (ALMaSS), a spatially explicit modelling framework that integrates static landscape features like soil types with dynamic, daily components like hourly weather data, crop management practices, and vegetation growth to simulate realistic environments for species populations

A mechanistic model of a soil species

In a recently published Formal Model in the open-access Agricultural and Environmental Modelling journal, researchers developed a spatially explicit stage-structured population model for the springtail Folsomia candida within the ALMaSS framework. The model explicitly represents egg, juvenile, and adult life stages, linking development, reproduction, and survival to environmental conditions using empirically parameterized thermal performance curves and dose-response functions. 

A key highlight of the model is its advanced estimation of surface soil water potential, which integrates high-resolution ERA5 weather data, evapotranspiration, and physical soil properties. By grounding these processes in biological mechanisms and factoring in food quality, the model provides a highly realistic representation of how soil populations respond to their environment

Scaling up: from local processes to landscapes

Spatial and temporal populations modelling.
Spatial and temporal populations modelling. Image credit to Liyan Xie.

The model is spatially explicit, simulating populations across large agricultural landscapes, typically 10 km by 10 km, divided into detailed polygons and grid cells. 

Using daily time steps for simulations lasting up to five years, the model captures subpopulation dynamics at a high-resolution spatial scale of 100 square meters. It even incorporates realistic, density-dependent dispersal behaviors, triggering adult springtails to migrate to surrounding cells when population densities exceed 100,000 per square meter or when food availability is severely restricted

This allows local environmental conditions to shape subpopulations, which together determine broader population dynamics. Such an approach enables exploration of how small-scale processes propagate to landscape-level patterns, including population persistence and recovery.

A foundation for future risk assessment

Even though the current version of the model focuses purely on environmental stressors without chemical exposure, its flexible structure serves as a foundational framework that can be easily extended. By eventually integrating toxicity modules, the model will enable the investigation of population-level impacts driven by agrochemical usage, such as pesticides and fertilizers, across different European farming practices. This mechanistic framework improves the interpretation of standardised laboratory and higher-tier mesocosm tests, providing a crucial tool for assessing the impact of multiple stressors under environmentally realistic scenarios.

Why this matters

This work highlights the critical importance of developing robust, process-based ecological models before introducing the additional complexities of chemical stressors. By carefully balancing biological realism with empirical data availability, the model provides actionable outputs, such as population growth rates, spatial distributions, and population recovery times, which serve as essential indicators of relative environmental risk. Ultimately, models like this offer a pathway towards more scientifically grounded, realistic assessments of ecosystem health in a changing environment

Original source:

Xie L, Duan X, Norouzi S, de Jonge LW, Topping CJ (2026) Integrating spatial and environmental stressors in a population model of Folsomia candida (Collembola, Isotomidae): a Formal Model within ALMaSS framework. Agricultural and Environmental Modelling 8: e184962. https://doi.org/10.3897/aem.8.184962 

Agricultural and Environmental Modelling (AEM): A New Chapter for Modelling Science Publishing

Pensoft’s Agricultural & Environmental Modelling journal broadens its scope and strengthens its Open Science commitment across agri-food & environmental research.

Today marks the official relaunch of the Food and Ecological Systems Modelling Journal (FESMJ) under a new name – Agricultural and Environmental Modelling (AEM), an open-access journal dedicated to advancing the science and practice of computational and mathematical modelling across agriculture, food systems, natural resources, and environmental sciences.

The first editorial published under the AEM name sets out the journal’s expanded vision, its new article types, and its call to the modelling community.

What Has Changed and What Has Not

AEM retains the founding mission of its predecessors: to make ‘modelling research objects citable, discoverable, and reusable’ and transparent. The journal’s commitment to open access, rigorous peer review, and the recognition of modelling as a first-class scientific endeavour remains unchanged. Publication in AEM remains entirely free for all authors.

What has changed is the scope and structure. The journal’s disciplinary scope now spans the full breadth of modelling in the agricultural and environmental sciences, including management systems, production dynamics, agroecological modelling, as well as food safety, production, quality and supply-chain control, biotechnological research, socio-ecological systems, resource management and more.

Publishing the Full Modelling Lifecycle

A defining feature of AEM is its structured range of article types, designed to give formal, peer-reviewed recognition to each group of authors at every stage of a model’s development.

A complex model is not born in a single paper: it emerges through cycles of formal specification, software implementation, calibration, testing, and application, often carried out by different teams across different project phases. Each of those steps represents genuine scientific work; each deserves recognition.

reads the editorial

Among the most distinctive publication types is the Formal Model, which offers a citable recognition for foundational mathematical and conceptual design. Alongside the more standard article types, such as Review Article; Research Article; and Short Communication, AEM also welcomes contributions framed as Model Testing and Calibration; Model Implementation and Documentation; Software Description; and Data Paper. For each article, the journal’s team has provided an article template to assist authors.

Commitment to Open Science and Reproducibility

AEM is built around the FAIR principles – Findability, Accessibility, Interoperability, and Reusability – these are applied to data, code, and models as peer-reviewed outputs. As such, the journal mandates that all underlying data and source code are made openly available; while machine-learning methods must follow the DOME-ML reproducibility guidelines.

Published on Pensoft’s ARPHA Platform, the journal establishes transparency standards and requires author declarations for LLM use. AEM is archived in CLOCKSS, Zenodo, Portico, and Zendy, and indexed in more than 40 services, including AGRICOLA, Cabells, CABI, FAO AGRIS, and ResearchGate.

Recent research

Overview diagram of the conceptual population model for APODEMUS. The model simulates the wood mouse life cycle, growth and reproduction. Landscape composition is captured by habitat types (numbers) and influences the space use of the simulated wood mice. Exposures can be linked to the use of defined habitat patches and types. Credit to Singer et al., 2026

The most recent paper demonstrates how the Formal Model article type has been utilised to describe APODEMUS, a spatially-explicit simulation model designed to improve pesticide risk assessments for the wood mouse (Apodemus sylvaticus) in European agricultural landscapes. The model provides regulators with a rigorous, transparent blueprint for evaluating how agricultural pesticides affect wild animal populations at the landscape scale.

An Invitation: Submissions and Editorial Board Applications

AEM welcomes submissions from researchers across all disciplines within its scope – whether describing a formal mathematical framework, documenting the calibration of a long-standing model, sharing data, or presenting a new computational workflow. Authors are encouraged to contact the editors directly to discuss specific publication needs.

The journal also welcomes applications from editors worldwide who share AEM’s vision. Experts willing to actively contribute to this unique journal and its community are invited to get in touch via the journal website.

Agricultural and Environmental Modelling is the first journal designed around the full lifecycle of modelling research, from formal specification to calibration, implementation, and application. Every contribution is important; every contribution is citable; credit where credit is due.

commented the Editor-in-Chief, Prof. Christopher Topping

The renaming reflects a natural evolution of the journal’s mission. Agricultural and Environmental Modelling better represents the breadth of work it publishes – spanning the full spectrum of modelling across agricultural, food, and environmental sciences – and reaffirms the journal’s founding commitment to Open Science and to recognising every stage of model development as rigorous scientific work in its own right.

added Pensoft’s founder and CEO, Prof. Lyubomir Penev

You can follow the journal on social media – Bluesky, Facebook and LinkedIn, and sign up for the journal’s email newsletter through the journal’s homepage.

Original sources:

Topping CJ, Nogoy N, Boyadzhieva I, Stoev P, Penev L (2026) A journal by modellers, for modellers: Introducing Agricultural and Environmental Modelling. Agricultural and Environmental Modelling 8: e194160. https://doi.org/10.3897/aem.8.194160

Singer A, Schmolke A, Becher MA, von Blanckenhagen F, van den Brink N, Grimm T, Ibrahim L, Imholt C, Jacob J, Jakoby O, Laucht S, Løvik AN, Martin T, Muñoz CC, Preuss TG, Galic N (2026) Concept for APODEMUS – a wood mouse population model for pesticide risk assessment. Food and Ecological Systems Modelling Journal 7: e175714. https://doi.org/10.3897/fmj.7.175714