UNIVERSITY PARK, Pa. — Maintaining connections between natural habitats may support beneficial microbes that help wildlife defend against disease. In a new study of tropical amphibians, a team led by Penn State biologists found that amphibians in connected natural forests and aquatic habitats were more likely to host beneficial skin microbes that inhibit a deadly fungal pathogen. But when these habitats become spatially separated due to planted crops, infrastructure development or other human land use, those microbial defenses weaken and pathogen infection levels can increase with potentially deadly results.
The findings, published this week in the journal Proceedings of the National Academy of Sciences, reveal a previously underappreciated link between landscape connectivity, beneficial microbes and disease resistance in wildlife, according to the researchers.
"Animals rely not only on their immune systems, but also on beneficial microbes that live on their bodies and help protect them from pathogens," said Gui Becker , associate professor of biology in the Eberly College of Science at Penn State and senior author of the study. "Our results show that when natural habitats become disconnected, these microbial defenses can be disrupted."
The researchers explained that habitat loss and fragmentation are widely recognized as major drivers of biodiversity decline, but scientists are increasingly realizing that environmental change can also alter the microbiome — the community of microbes that live in and on animals and often play key roles in health and immunity.
"Our study provides evidence that connectivity among habitats is essential for maintaining multiple levels of biodiversity, from host-associated bacteria with protective functions to their respective host species," said first author Daniel Medina, previously a postdoctoral scholar in Becker's lab at Penn State and currently a lecturer in tropical forest ecology and resource management at The School for Field Studies . "It highlights a critical link between environmental disturbance, microbial defenses and disease dynamics."
To investigate the connection between habitat fragmentation and animal microbiomes, the researchers studied amphibian populations in Brazil's Atlantic Forest, a biodiversity hotspot that has experienced extensive habitat alteration. Many amphibians depend on both forest habitats and aquatic breeding sites, requiring them to move between these environments during different stages of their life cycle.
The researchers focused on a phenomenon that Becker — a member of the Penn State One Health Microbiome Center — previously coined as "habitat split," where natural forests and aquatic habitats become separated by agriculture, development or other land uses. Across multiple frog species — collected from 40 sampling sites during the amphibian breeding season — the team found that animals living in landscapes with higher habitat split hosted fewer bacteria known to inhibit the deadly fungus, Batrachochytrium dendrobatidis, which has caused dramatic amphibian declines worldwide. In some species, infection levels of the fungus also increased as habitat split intensified.
"We showed such a link by indicating that spatial separation between critical habitats, such as natural forests and aquatic breeding sites, may impair amphibians' ability to recruit protective skin bacteria that defend against the fungus," Medina said.
The researchers propose that in intact landscapes, animals regularly encounter both environmental microbes and low levels of pathogens, which may help maintain microbial communities capable of suppressing disease. When natural habitats become disconnected, those ecological interactions can break down. Although the study focused on amphibians, the researchers said the findings could extend to many other animals that depend on multiple habitats throughout their life cycles.
"These results suggest that connected landscapes allow animals to maintain microbiomes that are better equipped to fight pathogens," Becker said. "Many species — from migratory birds to fish and large mammals — move among different habitats as they feed, breed or disperse. When those habitats become disconnected, it may not only affect movement but also alter how animals interact with beneficial microbes and pathogens."
Restoring and maintaining ecological connectivity between multiple classes of natural environments could serve as a critical strategy not only for fostering genetic diversity in wildlife populations but also for supporting the natural microbial defenses that help them resist disease. This could include habitat restoration strategies such as protecting riparian zones — vegetation rich areas at the edges of bodies of water — and reconnecting riparian habitats to larger areas of natural terrestrial vegetation, according to Becker.
"Protecting habitat connectivity may help preserve multiple layers of biodiversity, from the animals we see to the microbial communities that help keep them healthy," Becker said.
In addition to Becker and Medina, the research team included postdoctoral researcher Shannon Buttimer, graduate student Laura K. Schuck and Assistant Professor of Disease Ecology Molly Bletz at Penn State; Renato A. Martins and Célio F. B. Haddad at Universidade Estadual Paulista, in Rio Claro, Brazil; Paula Prist at the International Union for Conservation of Nature, in Washington D.C.; Wesley J. Neely at Texas State University; Sasha E. Greenspan at the Kennedy Krieger Institute in Baltimore, MD; Mariana L. Lyra at New York University Abu Dhabi in the UAE; Patrick J. Kearns and Douglas C. Woodhams at the University of Massachusetts Boston; and Vinicius A. São-Pedro at the Federal University of São Carlos in Brazil.
The U.S. National Science Foundation funded the research, with additional support provided by the São Paulo Research Foundation and the Brazilian National Council for Scientific and Technological Development.
