Forest mysteries: using genetics to identify microbial patterns associated with hummingbirds and bats


Post author Jeremy Hsu is a graduate student in the Hadly lab.

Many animals that visit flowers are known to carry microfungal communities; these fungi are important ecologically because they have the potential to alter the attractiveness of nectar to these pollinators, thus influencing plant-animal interactions. The pollinators also act as vectors for the microfungi, helping distribute communities throughout the local ecosystem. In a recent paper in Fungal Ecology, Melinda Belisle, a then-graduate student in the Department of Biology in CEHG faculty member Tad Fukami’s lab, led a team of researchers at Stanford and in Costa Rica to investigate these relationships further and examine how the distribution of microfungi varies in space and time in a local ecosystem.

Hummingbirds, bats, and beyond: the Costa Rican landscape

To investigate this question, Melinda and colleagues focused on two specific pollinators: the hummingbird and bat. Both of these flying animals are known to carry microfungal communities in their mouths, and by dipping the animals’ bills or beaks in a sugar solution, the researchers were able to obtain samples of the microfungi communities that live there. The researchers caught hummingbirds and bats in a specific countryside landscape in southwestern Costa Rica over a span of two years. The location of the research, Coto Brus, was chosen for its diversity of different habitats, ranging from true forest areas to deforested areas now dominated by coffee plantations. The wide diversity of habitat types within this landscape allowed the team to test two of their predictions: first, that there would be differences in which microfungal species are present in various parts of the landscape, and second, that the presence and distribution of these microfungal communities would change over time.

Figure 1. Melinda and colleagues fed hummingbirds sugar water and then were able to test the sugar water solution for the presence of microfungal communities.

Figure 1. Melinda and colleagues fed hummingbirds sugar water and then were able to test the sugar water solution for the presence of microfungal communities.

Genetic identification of microbial communities

After catching the hummingbirds and bats, dipping their mouths in sugar water, and releasing the animals back into the wild unharmed, the researchers then spread the sugar water on a yeast-malt agar plate. This allowed any microfungal communities that were present on the beaks or bills of the hummingbirds and bats (and thus present in the sugar water) to grow into colonies. Following this growth, Melinda and the other researchers extracted DNA from these colonies and amplified and sequenced the large subunit nuclear ribosomal RNA gene. By examining the resulting unique DNA sequences, they could then identify specific species of microfungi present on each of the hummingbird and bat bills and beaks.

Microfungal communities vary in composition across time, but do not correlate with landscape

The researchers analyzed the composition of microfungal species across multiple sampling locations in the landscape over a period of two years. They discovered that microfungal community presence and composition differed substantially between the different sampling periods, including on both a micro- and macro- temporal scale (i.e., short and long amounts of time), confirming one of their hypotheses. However, they did not find any pattern or correlation between microfungal community composition and abundance with the landscape type, and no other spatial correlations were found, contrary to the researchers’ expectations. Thus, their results indicate that microfungal communities change significantly over time but are not directly influenced by the habitat type of hummingbirds and bats.

The authors were surprised that there was no spatial distribution pattern of microfungal communities and that the composition and abundance of these communities did not correlate with landscape type. These findings indicate that there may not be significant limitations on dispersal for microfungi, which would otherwise have resulted in geographic and spatial patterning as well as correlations between microfungal community composition and habitat type. However, the authors did find that this composition varied across both small and large amounts of time, and they speculate that this change could be triggered by differing environmental characteristics, such as variations in food supply and availability for the hummingbirds and bats in different seasons. Variation in diet for the animals could thus lead to differences in which microfungi are able to survive and proliferate in their mouths. To conclude, the researchers propose future work to determine the speed at which microfungal communities change over time and to determine whether these patterns are found in other types of pollinators, such as insects.


Belisle M., Mendenhall C. D., Brenes F. O., Fukami T. Fungal Ecology (2014). DOI: 10.1016/j.funeco.2014.02.007

Paper author Melinda Belisle was a graduate student in Tadeshi Fukami's lab. She is now a Senior Scientist at Exponent, Inc.

Paper author Melinda Belisle was a graduate student in the Fukami lab. She is now a Senior Scientist at Exponent, Inc.