Research

Revealing the ecological mechanisms linking environmental change, microbes, and wildlife health.

The Becker Lab studies how global environmental change reshapes interactions between wildlife and their symbiotic microbes, with a particular focus on amphibians in tropical ecosystems. Our work integrates field experiments, microbial ecology, and spatial data to test the mechanisms linking environmental change to biodiversity loss and disease emergence. Supported by multiple NSF grants led by the Becker Lab, our research combines observational and manipulative studies across tropical ecosystems to identify the ecological drivers of wildlife health and resilience, while pointing to interventions that may help safeguard biodiversity.

Habitat connectivity, disease dynamics, and amphibian declines

Many animals depend on multiple habitat types to complete their life cycles (e.g., terrestrial and aquatic habitats). When these habitats become spatially separated through land-use change, organisms experience a phenomenon known as habitat split. Our research has shown that habitat split is a major driver of amphibian declines by disrupting protective host-associated microbiomes (Fig 1A) and intensifying fungal pathogen infections (Fig 1B; Medina et al. 2026, PNAS). These effects are ultimately associated with elevated amphibian extinction risk in regions experiencing high levels of habitat split, as documented previously (Becker et al. 2007, Science). Recent synthesis work further demonstrates how disruption to spatial connectivity can reshape host–microbe interactions, host immunogenetics, stress physiology, and pathogen transmission (Becker et al. 2023, Biological Reviews).

Figure 1. Habitat split predicts a drop in microbiome function (A) and an increase in pathogen infection loads (B) in tropical amphibians.

Deforestation, drought, and wildlife disease

Environmental change often alters disease risk indirectly through its effects on climate and host behavior. Our work has revealed that large-scale deforestation can intensify drought conditions, which in turn disrupt the protective skin microbiomes of amphibians and alter disease transmission dynamics.

Through observational and manipulative field studies in the Atlantic Forest, we showed that drought conditions can destabilize host-associated microbial communities and promote host aggregation around moist refugia, increasing pathogen transmission even when the pathogen itself is sensitive to dry conditions (e.g., Buttimer et al. 2025, Global Change Biology). Complementary observational work detected a disease outbreak coinciding with a period of drought, further linking climate variability, microbiome dysbiosis and wildlife disease dynamics (Buttimer et al. 2024, Ecology Letters; Fig. 2). Together, these findings highlight how climate variability and land-use change interact to influence wildlife health.

Figure 2. Drought correlates with amphibian skin microbiome structure and may intensify disease transmission in tropical forests.

Global warming and microbiome disruption

Global warming can influence wildlife health not only through direct thermal stress but also through changes in ecological communities and host–microbiome interactions. Our manipulative field experiments demonstrated that warming can trigger microbiome dysbiosis and reduced growth in amphibian larvae, mediated by shifts in surrounding ecological communities rather than direct thermal stress alone (e.g., Greenspan et al. 2020, Nature Climate Change; Fig. 3). These results show that the ecological consequences of warming may be driven largely by indirect community-level interactions, emphasizing the need for ecosystem-level perspectives when predicting biological responses to climate change.

Figure 3. Experimental warming reshapes ecological communities, leading to microbiome dysbiosis and reduced vertebrate growth.

Microbiome diversity and species vulnerability

A central question emerging from our research is whether multiple scales of biodiversity contribute to the resilience of wildlife populations. Studies led by the Becker Lab have shown that formally endangered amphibian species tend to harbor lower skin-microbiome diversity than closely related non-threatened species in the same environments (Greenspan et al. 2022, Animal Microbiome; Fig. 4). Because microbiomes can play a critical role in pathogen defense and host health, these findings indicate that microbial diversity may represent an overlooked dimension of biodiversity loss. This emerging research direction seeks to determine whether microbiome structure can serve as an indicator of species vulnerability under global environmental change.

Figure 4. Threatened amphibians from two biodiversity hotspots harbor lower skin microbiome diversity than closely related non-threatened species.

By studying the ecological mechanisms linking environmental change, microbiomes, and wildlife health, our research seeks to identify the processes that promote resilience in natural systems and inform actions that safeguard biodiversity.

Background image: a specimen of Holoaden bradei, last seen in the wild in 1978 and likely extinct, sits in what was once its natural habitat: Itatiaia National Park, Rio de Janeiro / Minas Gerais, Brazil