How Shared Microbes Are Saving Chocolate


Stephen Luntz

Stephen has a science degree with a major in physics, an arts degree with majors in English Literature and History and Philosophy of Science and a Graduate Diploma in Science Communication.

Freelance Writer

cacao in hand

The product of these fruits make life worth living, so it is just as well the leaves host protections against disease, which can be passed on to seedlings. PixieMe/Shutterstock

Please try to remain calm, but the global chocolate supply is under threat. Along with climate change and failed cloning experiments, the future of the world's favorite treat is endangered by Phytopthora palmivora, a fungus thriving in warm, wet environments worldwide. Fortunately, adult Theobroma cacao plants, from which chocolate comes, have a defense mechanism, and now botanists have learned how this gets transferred to baby plants.

Over two decades of research at the Smithsonian Tropical Research Institute have shown that tropical plants have their own version of mammals' gut bacteria, or microbiome, which protects us against being colonized by pathogens. The fungus Colletotrichum tropicale, for example, usually forms a symbiotic relationship with plants, occupying their leaves and making them unappetizing to insects and hostile to pathogens.


"When human babies pass through the birth canal, their bodies pick up a suite of bacteria and fungi from their mother. These microbes strengthen their immune system and make the baby healthier," said University of Indiana PhD student Natalie Christian in a statement. "We showed that an analogous process happens in plants: adult cacao trees also pass along protective microbes to baby cacao plants."

Since seedlings spring from seeds, rather than being birthed through the mother's body, transmission of these protective bacteria and fungi is tricky. To see how it occurs, Christian and her colleagues had cacao seeds sprout in a sterile environment. They exposed a third to dead leaves from healthy cacao plants and a third to a random mixture of leaves from the forest floor, keeping the rest as controls that, like caeserian births, didn't get inoculated.

All three sets were then taken into a tropical forest to meet whatever might come, before being returned to the greenhouse and infected with P. palmicora, whose name means “plant destroyer” and is blamed for the loss of 10-20 percent of global cacao production.

In Proceedings of the Royal Society B, Christian reports that the seedlings exposed to adult cacao leaves suffered only half the damage of those that encountered the mixed-leaf litter. Unsurprisingly, they also did much better than the controls.


By culturing the microbial communities of the seedlings and sequencing the fungal DNA, Christian confirmed that the difference lay in the presence of C. tropicale. Having transferred from the leaves of adult cacao plants, the healthy fungus made it hard for pathogenic equivalents to gain space.

Cacao farmers can benefit from this work by inoculating their crops from healthy plants. The researchers hope to use the work as a launchpad for understanding how microbial communities develop in the wild. The findings demonstrate how plants can benefit from growing close to their relatives, counteracting the dangers experienced when high densities of a single species facilitate parasite spread.


  • tag
  • symbiosis,

  • microbiome,

  • chocolate,

  • cacao,

  • parasitic fungi,

  • Colletotrichum tropicale,

  • Phytopthora palmivora