Environmental detection of the amphibian chytrid fungus in water bodies is associated with host infection along a deforestation gradient

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Abstract Many wildlife pathogens can persist in the environment independently of their hosts, with the habitat itself serving as a reservoir and potential source of transmission. However, reliably detecting and quantifying free‐living pathogen stages across heterogeneous landscapes using environmental DNA methods remains challenging. Understanding how landcover and habitat structure drive pathogen distribution at the environmental and host levels is critical for advancing disease surveillance and ecology. Amphibian chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis ( Bd ), provides a useful model system to address these broader challenges, yet most studies have focused on host–pathogen interactions, with less emphasis on Bd within environmental reservoirs. Using Bd as a model system, we investigated whether pathogen distribution in natural aquatic environments is associated with host infection patterns across gradients of habitat loss. We sampled four tropical amphibian species across eight rainforest landscapes and quantified Bd in paired water and host samples using a high‐capacity water filtration method coupled with digital and real‐time quantitative polymerase chain reaction detection assays. Our results revealed a strong positive correlation between Bd DNA concentrations in water and infection loads on amphibian skin, indicating that environmental Bd DNA is associated with host infection patterns. Forest cover and habitat split (i.e. spatial separation between forests and aquatic breeding sites) were the primary predictors of Bd occurrence, concentration and infection load across environmental and host‐associated forms, and both Bd ‐GPL and Bd ‐Asia‐2/Brazil lineages were detected across our study landscapes. Our study introduces and validates a robust protocol for detecting environmental Bd , providing a scalable approach to quantify pathogen–environment associations across multiple landscapes and environmental gradients. Synthesis and applications : Linking environmental pathogen detection with host infection patterns can improve surveillance of diseases involving environmental transmission, particularly where direct host sampling is logistically challenging. This approach enables the identification of areas of elevated transmission risk and supports targeted monitoring and management under habitat loss and degradation. It also provides a practical tool to guide conservation actions in landscapes undergoing rapid land‐use change.