When you look at dirt, you might not know you're looking at a complex, living community.
But the dirt from these rice roots contains millions of microbes — and they just might
hold the key to stopping a significant source of greenhouse gas emissions.
Rice is a staple crop for more than half the world’s population. But the way we grow rice is
responsible for 12% of food-related greenhouse gas emissions globally, second only to beef.
And rice emissions are mainly methane – a greenhouse gas that can trap 25 times more heat
than carbon dioxide. But the microbes in the soil below just may hold the key to changing this.
Rice is typically grown in paddies that are flooded to keep weeds from growing.
This pesticide-free weed control has a lot of benefits — but it also affects soil microbes.
When the paddies are flooded,
it creates an anaerobic environment, which means there’s no oxygen or very low oxygen
in the soils, and that allows certain microbes to grow that produce methane.
Just like our diet or hygiene habits can change our microbiome,
when paddies are flooded, the soil microbiome changes.
But which microbes are these exactly? Bethany Kolody, a postdoc working with
IGI’s microbiology director Jill Banfield, is taking the lead on a new project to find out.
The big question that we’re trying to answer is “What is the genetics behind the methane emissions
that come out of rice paddies?” So we’re going to look at all of the microbes and their genomes
that are associated with rice paddies over the course of a full season.
To get to know these microbes - and the helpful microbes that can eat methane - the Banfield
lab team is taking soil samples here at the Rice Experiment Station in Biggs, California.
They’ll take samples over the course of a growing season,
seeing how the community of microbes changes through the rice life cycle.
The team is taking soil cores at different depths to see how the types of microbes change as you go
deeper. they're especially interested in the microbes around the roots of the rice plants.
We really wanted to know which microbes are directly interacting with the plants.
And so the microbes that are on the root of the plant–they’re called the rhizosphere microbes.
So we would pull a single plant, and we would section off
the root, cut the root, and wash off all of the soil that’s directly associated with the root.
The team is also looking at how soil methane escapes into the
atmosphere – either from the soil itself, or through the plant, which acts as a pipe.
In the field, they measure methane escape from plants with an instrument called a Picarro.
We’re basically having chambers that have the plants in them and also control chambers that
don’t have plants in them. And we are comparing the two to show how important
the role of a plant is in acting as a path for methane to escape.
When the team gets back to the lab, they’ll use a special technique pioneered by the Banfield lab.
In the Banfield lab, we’re really experts on metagenomics. So metagnomics–you probably know
about your genome or the human genome, or maybe you’ve done 23andMe. Your genome is the set of all
of your DNA in your body for a single cell, it’s the same for every cell. And a metagenome is when
you take a sample, so for example a soil sample, and you just sequence everybody’s DNA–so all of
the microbes in that piece of soil. And then you have to take it back to the computer and piece
all of the little pieces together like a puzzle and figure out who’s who. But once you do that,
it’s a really good tool to see what microbes are doing and what microbes are capable of doing.
The team is using an additional technique to capture a snapshot of
which genes are turned on right when they collect the plants.
Knowing who's there and what they’re doing helps paint the picture of how the microbes
work together to form a soil ecosystem. Once we know more about these microbial communities,
it might be possible to manipulate them to reduce methane output.
Because we’re working with rice, which is a major food staple across the globe, anything that
we learn from this small scale could really be scaled up to make big changes all over the world.
Rice cultivation is a remarkable achievement that has fed generations around the globe -
and with new tools, we can keep feeding a growing population without contributing to climate change.