before stray microbes from elsewhere could settle in. These
results suggest that a seedling in the shadow of more mature
trees will probably accumulate the same microbiome as its
To see if some of those transferred microbes protect the
cacao from disease-causing organisms, Christian rubbed a bit
of black pod rot on the leaves of plants in each group. Three
weeks later, she measured the size of the rotted spots.
Plants surrounded by cacao litter had the smallest lesions.
Those with litter from other trees had slightly more damage,
and plants with no litter had about double the damage of the
mixed litter plants.
“Getting exposed to the litter of their mother or their own
kind had a very strong beneficial effect on the resistance of
these young plants,” says plant biologist Keith Clay of Tulane
University in New Orleans, a coauthor of the study.
Scientists aren’t sure how the good fungi protect the plants
against the rot. It may be that the beneficial fungi simply take
up space in or on the leaves, leaving no room for the undesir-
ables, Christian says. Or a protective microbe like C. tropicale
might attack a pathogen via some kind of chemical warfare.
In the case of cacao, she thinks the most likely explanation
is that the good guys act as a sort of vaccine, priming the
plant’s immune system to fight off the rot. In support of this
idea, Mejía reported in 2014 in Frontiers in Microbiology that
C. tropicale causes cacao to turn on defensive genes.
Cacao farmers may need to rethink their practices. The farmers
normally clear leaf litter out of orchards to avoid transmitting
disease-causing microbes from decaying leaves to living trees,
says Christian, now a postdoc at the University of Illinois at
Urbana-Champaign. But her work suggests that farmers might
do well to at least hold on to litter from healthy trees.
Litter is a low-tech way to spread entire communities of
microbes — good and bad. But agricultural companies want
to grab only the good microbes and apply them to crops. The
hunt for the good guys starts with a stroll through a crop field,
says Barry Goldman, vice president and head of discovery at
Indigo Ag in Boston. Chances are, you’ll find bigger and hardier
plants among the crowd. Within those top performers, Indigo
has found endophytes that improve plant vigor and size, and
others that protect against drought.
The company, working with cotton, corn, rice, soybeans and
wheat, coats seeds with these microbes. Once the seeds germinate, the microbes cover the newborn leaves and can get inside
via cuts in the roots or through stomata, tiny breathing holes
in the leaves. The process is akin to what happens when a baby
travels through the birth canal, picking up beneficial microbial
partners from mom along the way.
For example, the first-generation Indigo Wheat, released in
2016, starts from seeds treated with a beneficial microbe. In
Kansas test fields, the treatment raised yields by 8 to 19 percent.
Farmers are also reporting improved drought tolerance.
Plant microbes can be good, bad or a
bit of both. Take the fungus living in
tall fescue (Lolium arundinaceum), a
grass that sways across 35 million
acres of lawns and pastures in the
eastern United States and beyond.
The fescue is wildly successful
because of the fungus. But the same
fungus also makes the grass a toxic
meal for livestock. It took scientists
decades to figure out why and come
up with a fix.
1800s Tall fescue finds its way to the United
States from Europe. The grass may have
come along with a shipment of meadow
fescue seed or, as one legend has it, as packing material for bone china.
1931 E.N. Fergus, an agronomist at the
University of Kentucky in Lexington, collects
a type of tall fescue from the local farm of
William Suiter. The grass grows well under
drought conditions and in poor soils. It
would become a popular ground cover and
feed crop known as Kentucky 31.
The fungus in the fescue 1940s Soon after the official release of
Kentucky 31, farmers report that animals
grazing on tall fescue exhibit bizarre
symptoms: They don’t gain weight as they
should. Their feet turn lame, swollen and
even gangrenous. Cows give less milk and
horses suffer miscarriages. The syndrome
is eventually called fescue toxicosis.
1977 Charles Bacon of the U.S. Department of Agriculture in Athens, Ga., and
colleagues report that a fungus living
inside the fescue is probably responsible
Defenses up After cacao plants were grown with or without leaf
litter around their roots, scientists exposed the plants to black pod fungus and measured rot damage. Microbes from cacao-based litter were
most beneficial to the plants, but even mixed litter offered protection
against the fungus. SOURCE: N. CHRIS TIAN E T AL /PROCEEDINGS OF THE ROYAL SOCIET Y B 2017
endophyte-free no litter mixed litter cacao litter
Cacao litter Mixed litter No litter