Limited ecosystems research as a persistent gap in One Health frameworks for emerging infectious diseases

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Decades ago, the One Health framework emerged as an interdisciplinary public health approach addressing the interconnected health of humans, other animals, and the wider environment (FAO et al. 2008, OHHLEP et al. 2022). The One Health framework is frequently used to describe emergence of new pathogens, particularly in humans. Technological advances fueling pathogen discovery including unbiased sequencing approaches, AI-supported analytical methods, and expanding global surveillance efforts have accelerated the discovery of previously unrecognized pathogens in wildlife and other animal hosts (Carlson et al. 2025). However, pathogen discovery alone provides limited insight into the ecological, ecosystem related mechanisms governing pathogen maintenance, amplification in reservoirs, and zoonotic spillover. In this Viewpoint, we use the term ecosystem to refer to the dynamic interactions among organisms, including pathogenic microorganisms such as viruses and bacteria, their hosts’ habitats, predator-prey relationships, landuse and landcover changes with anthropogenic impacts across spatial and temporal scales and climatic conditions. Although environmental variables are increasingly incorporated into One Health research, efforts to investigate ecosystem-related ecological processes remain comparatively underrepresented within emerging infectious disease research (Zinsstag et al. 2011). Existing studies often focus on specific components of ecosystem change, such as antimicrobial resistance (Essack 2018), vector ecology (Arisco et al. 2024), or wildlife-associated virus prevalence (Eby et al. 2023). We argue that there is a need to move beyond documenting pathogen occurrence in a siloed setting toward understanding how ecosystem processes, structure, and function and also human social and behavioral processes shape pathogen transmission dynamics and zoonotic risk in an integrated approach, ideally within long-term studies and ecologically validated replicates. We suspect, however, that financial, methodological, and structural barriers continue to limit ecosystem-oriented research relative to pathogen discovery efforts that are methodologically less demanding and often lack broader ecological context. In this Viewpoint, we describe below several challenges as illustrated in figure 1 and summarized in box 1 to comprehensive studies based on our own and other researchers’ experience and suggest means to overcome these challenges. Species-specific sampling complexity Sampling designs need to fit the animal species under study, including vertebrate and invertebrate organisms with differing home ranges and responses to anthropogenic landcover change. Capturing ecosystem-level dynamics across multiple taxa with sufficient ecological replicates and sampling plots requires exhaustive assessments that are methodologically cumbersome (Brouard et al. 2015), potentially dangerous particularly in tropical settings, and resource-intensive. At the same time, minimum methodological standards allowing comparisons across studies remain insufficiently harmonized (Schwantes et al. 2025). Lack of ecologically validated replicate data Longitudinal studies across ecologically validated replicates are needed to account for seasonal and climatic variation affecting both environmental conditions and pathogen circulation in reservoir hosts (Eby et al. 2023). However, such datasets remain limited, constraining efforts to understand pathogen emergence across space and time. Historical ecosystem-level data are frequently unavailable at local scales, including information on past pollution affecting biodiversity and trophic interactions. Limitations in resolution and availability of historical spatial data Remote sensing has substantially improved ecosystem monitoring capacities, and research linking landuse and landcover change with infectious disease emergence has expanded substantially in recent years. Although availability of high-resolution data from commercial sensor systems has increased, spatial resolution of publicly available sensor data is often not sufficient to assess plot-level dynamics (e.g., with Landsat data available since the late 1970s with a resolution of only 100 m and later 30 m), and long-term coverage is scarce (Zeng et al. 2022). Remote sensing can therefore complement but not replace ground-level in-situ ecological assessments. Complexity of ecosystem-scale interactions Ecosystems overlap entailing interactions between wildlife, domestic animals, and livestock along rural-to-urban gradients. Such interactions can lead to pathogen exchange and amplifications. Ecosystem-based interactions, but also alterations do not affect all hosts, vectors, or pathogens uniformly. Species differ in ecological specialization, mobility, trophic interactions, and tolerance to anthropogenic disturbance such as landuse changes and climate change, producing highly context-dependent pathogen dynamics across disturbance gradients (Ecke et al. 2025). Ecosystem restoration as a transient anthropogenic disturbance (ibid) could be framed as a nature-based solution to reducing risks of infectious diseases when also benefiting biodiversity and providing ecosystem services but evaluating these effects and outcomes is challenging. In addition, certain host taxa and associated pathogens may only occur at the extremes of disturbance gradients, limiting robust assessments of the extent of ecosystem alteration on pathogen abundance and genomic diversity (Hermanns et al. 2023). Microbial interaction complexity Understanding ecosystem interactions among micro-organisms remains particularly challenging because interactions within and between pathogen taxa are still poorly resolved. For example, insect-specific viruses may differentially affect arbovirus infectivity (Jansen et al. 2025), but many additional interactions likely remain undiscovered. Experimental validation of such interactions is technically difficult and resource-intensive. Similarly, pathogens vary widely in environmental stability, replication intensity, and shedding routes, leading to different concentrations in given analyzed biological specimens. Arguably, pathogens with different levels of host specificity, environmental stability, and shedding patterns will respond differently to ecosystem alterations in a context-specific manner and in parallel show stark differences in laboratory detectability that need to be accounted for. Constraints of serological and molecular surveillance Serological approaches can complement molecular detection by assessing lifetime exposure to pathogens across host populations and environmental gradients. However, antibody assays for emerging pathogens often lack validation across wildlife species and remain difficult to standardize, many being developed and validated for one host species only. Similarly, antibody tests can yield positive results with antigens derived from different pathogens, and those cross-reactive immune responses must not be interpreted as direct evidence for a specific pathogen having infected the vertebrate under study (Fischer et al. 2021). At the same time, direct pathogen detection commonly done by molecular tools can vary with seasonality, infection dynamics, host immune status and other traits and again, sampling in few locations and time points may bias test results substantially (Chen, 2023). Complexity of climate change-driven ecological alterations Climate-driven ecosystem changes can alter habitat suitability and vector abundance exemplified by increasing suitability of previously temperate regions in Europe for tropical vectors such as Aedes albopictus and related pathogen emergence including dengue and chikungunya viruses (Farooq et al. 2025). Understanding these ecosystem changes and related processes requires integrating observational studies on vector ecology with long-term and short-term meteorological, landuse, and landcover variables. Generating such high