- Gabriel Popkin
A centuries-old concept in soil science has recently been thrown out. Yet
it remains a key ingredient in everything from climate models to advanced
carbon-capture projects.
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One teaspoon of healthy soil contains more bacteria, fungi and
other microbes than there are humans on Earth. Those hungry
organisms can make soil a difficult place to store carbon over long
periods of time. Catherine Ulitsky
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The hope was that the soil might save us. With civilization continuing to
pump ever-increasing amounts of carbon dioxide into the atmosphere, perhaps
plants — nature’s carbon scrubbers — might be able to package up some of that
excess carbon and bury it underground for centuries or longer.
That hope has fueled increasingly ambitious climate change–mitigation plans.
Researchers at the Salk Institute, for example,
hope
to bioengineer plants whose roots will churn out huge amounts of a carbon-rich,
cork-like substance called suberin. Even after the plant dies, the thinking
goes, the carbon in the suberin should stay buried for centuries.
This
Harnessing Plants Initiative
is perhaps the brightest star in a crowded firmament of climate change solutions
based on the brown stuff beneath our feet.
Such plans depend critically on the existence of large, stable, carbon-rich
molecules that can last hundreds or thousands of years underground. Such
molecules, collectively called humus, have long been a keystone of soil science;
major agricultural practices and sophisticated climate models are built on
them.
But over the past 10 years or so, soil science has undergone a quiet revolution,
akin to what would happen if, in physics, relativity or quantum mechanics were
overthrown. Except in this case, almost nobody has heard about it — including
many who hope soils can rescue the climate.
“There are a lot of
people who are interested in sequestration who haven’t caught up yet,” said
Margaret Torn, a soil scientist at Lawrence Berkeley National Laboratory.
A new generation of soil studies powered by modern microscopes and imaging
technologies has revealed that whatever humus is, it is not the long-lasting
substance scientists believed it to be.
Soil researchers have
concluded that even the largest, most complex molecules can be quickly devoured
by soil’s abundant and voracious microbes. The magic molecule you can just stick
in the soil and expect to stay there may not exist.
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Artificially colored scanning electron micrograph images of soils
from the island of Hawai’i. Thiago Inagaki, in collaboration with Lena Kourkoutis, Angela
Possinger and Johannes Lehmann
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“I have
The Nature and Properties of Soils in front of me — the
standard textbook,” said
Gregg Sanford, a soil researcher at the University of Wisconsin, Madison. “The theory of
soil organic carbon accumulation that’s in that textbook has been proven mostly
false … and we’re still teaching it.”
The consequences go far beyond carbon sequestration strategies. Major climate
models such as those produced by the Intergovernmental Panel on Climate Change
are based on this outdated understanding of soil.
Several
recent
studies
indicate that those models are underestimating the total amount of carbon that
will be released from soil in a warming climate.
In addition,
computer models that predict the greenhouse gas impacts of farming practices —
predictions that are being used in carbon markets — are probably overly
optimistic about soil’s ability to trap and hold on to carbon.
It may still be possible to store carbon underground long term. Indeed,
radioactive dating measurements suggest that some amount of carbon can stay in
the soil for centuries. But until soil scientists build a new paradigm to
replace the old — a process now underway — no one will fully understand why.
The Death of Humus
Soil doesn’t give up its secrets easily. Its
constituents
are tiny, varied and outrageously numerous. At a bare minimum, it consists of
minerals, decaying organic matter, air, water, and enormously complex ecosystems
of microorganisms.
One teaspoon of healthy soil
contains
more bacteria, fungi and other microbes than there are humans on Earth.
 The fine hairs surrounding roots are covered in hungry bacteria; soils slightly further away from the roots may have an order of magnitude fewer microbes. Courtesy of Jennifer Pett-Ridge and Erin Nuccio |
The German biologist Franz Karl Achard was an early pioneer in making
sense of the chaos. In a seminal 1786 study, he used alkalis to extract
molecules made of long carbon chains from peat soils.
Over the
centuries, scientists came to believe that such long chains, collectively called
humus, constituted a large pool of soil carbon that resists decomposition and
pretty much just sits there.
A smaller fraction consisting of
shorter molecules was thought to feed microbes, which respired carbon dioxide to
the atmosphere.
This view was occasionally challenged, but by the mid-20th century, the humus
paradigm was “the only game in town,” said
Johannes Lehmann, a soil scientist at Cornell University.
Farmers were instructed
to adopt practices that were supposed to build humus. Indeed, the existence of
humus is probably one of the few soil science facts that many non-scientists
could recite.
What helped break humus’s hold on soil science was physics. In the second half
of the 20th century, powerful new microscopes and techniques such as nuclear
magnetic resonance and X-ray spectroscopy allowed soil scientists for the first
time to peer directly into soil and see what was there, rather than pull things
out and then look at them.
What they found — or, more specifically, what they didn’t find — was shocking:
there were few or no long “recalcitrant” carbon molecules — the kind that don’t
break down. Almost everything seemed to be small and, in principle,
digestible.
“We don’t see any molecules in soil that are so recalcitrant that they can’t be
broken down,” said
Jennifer Pett-Ridge, a soil scientist at Lawrence Livermore National Laboratory. “Microbes will
learn to break anything down — even really nasty chemicals.”
Lehmann, whose studies using advanced microscopy and spectroscopy were among the
first to reveal the absence of humus, has become the concept’s
debunker-in-chief.
A 2015 Nature paper he co-authored
states that “the available evidence does not support the formation of
large-molecular-size and persistent ‘humic substances’ in soils.”
In
2019, he gave a talk with a slide containing a mock death announcement for “our
friend, the concept of Humus.”
Over the past decade or so, most soil scientists have come to accept this view.
Yes, soil is enormously varied. And it contains a lot of carbon. But there’s no
carbon in soil that can’t, in principle, be broken down by microorganisms and
released into the atmosphere.
The latest edition of
The Nature and Properties of Soils, published in 2016, cites Lehmann’s 2015 paper and acknowledges that “our
understanding of the nature and genesis of soil humus has advanced greatly since
the turn of the century, requiring that some long-accepted concepts be revised
or abandoned.”
Old ideas, however, can be very recalcitrant. Few outside the field of soil
science have heard of humus’s demise.
Buried Promises
At the same time that soil scientists were
rediscovering what exactly soil is, climate researchers were revealing that
increasing amounts of carbon dioxide in the atmosphere were rapidly warming the
climate, with potentially catastrophic consequences.
Thoughts soon turned to using soil as a giant carbon sink. Soils contain
enormous amounts of carbon — more carbon than in Earth’s atmosphere and all its
vegetation combined.
And while certain practices such as plowing can
stir up that carbon — farming, over human history, has released an estimated
133 billion metric tons of carbon
into the atmosphere — soils can also take up carbon, as plants die and their
roots decompose.
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Farming practices such as plowing can reduce the amount of carbon
stored in soil. Helena
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Scientists began to suggest that we might be able to coax large volumes of
atmospheric carbon back into the soil to dampen or even reverse the damage of
climate change.
In practice, this has proved difficult. An early idea to increase carbon stores
— planting crops without tilling the soil — has mostly fallen flat. When farmers
skipped the tilling and instead drilled seeds into the ground, carbon stores
grew in upper soil layers, but they disappeared from lower layers.
Most experts now believe that the practice redistributes carbon
within the soil rather than increases it, though it can improve other factors
such as water quality and soil health.
Efforts like the Harnessing Plants Initiative represent something like soil
carbon sequestration 2.0: a more direct intervention to essentially jam a bunch
of carbon into the ground.
The initiative emerged when two plant geneticists at the Salk Institute,
Joanne Chory
and
Wolfgang Busch, came up with an idea: Create plants whose roots produce an excess of
carbon-rich molecules. By their calculations, if grown widely, such plants might
sequester up to 20% of the excess carbon dioxide that humans add to the
atmosphere every year.
The researchers zeroed in on a complex, cork-like molecule called suberin, which
is produced by many plant roots. Studies from the 1990s and 2000s had hinted
that suberin and similar molecules could resist decomposition in soil.
A scanning electron micrograph of suberized cork cells. José Graça
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With flashy marketing, the Harnessing Plants Initiative gained attention. An
initial round of fundraising in 2019
brought in
over $35 million.
Last year, the multibillionaire Jeff Bezos
contributed $30 million from his “Earth Fund.”
But as the project gained momentum, it attracted doubters. One group of
researchers noted in 2016 that no one had actually observed the suberin
decomposition process.
When those authors did the relevant
experiment, they found that much of the suberin decayed quickly.
In 2019, Chory described the project at a TED conference.
Asmeret Asefaw Berhe, a soil
scientist at the University of California, Merced, who spoke at the same
conference, pointed out to Chory that according to modern soil science, suberin,
like any carbon-containing compound, should break down in soil. (Berhe, who has
been nominated to lead the U.S. Department of Energy’s Office of Science,
declined an interview request.)
Around the same time,
Hanna Poffenbarger, a soil researcher at the University of Kentucky, made a similar comment after
hearing Busch speak at a workshop. “You should really get some soil scientists
on board, because the assumption that we can breed for more recalcitrant roots —
that may not be valid,” Poffenbarger recalls telling Busch.
Questions about the project surfaced publicly earlier this year, when
Jonathan Sanderman, a soil scientist at the Woodwell Climate Research Center in Woods Hole,
Massachusetts,
tweeted, “I thought the soil biogeochem community had moved on from the idea that
there is a magical recalcitrant plant compound. Am I missing some important new
literature on suberin?”
Another soil scientist
responded, “Nope, the literature suggests that suberin will be broken down just like
every other organic plant component. I’ve never understood why the
@salkinstitute has based their Harnessing Plant Initiative on this premise.”
Busch, in an interview, acknowledged that “there is no unbreakable biomolecule.”
But, citing
published
papers
on suberin’s resistance to decomposition, he said, “We are still very optimistic
when it comes to suberin.”
“The theory of soil organic carbon accumulation that’s in that textbook
has been proven mostly false … and we’re still teaching it.”
Gregg Sanford
He also noted a second initiative Salk researchers are pursuing in parallel to
enhancing suberin. They are trying to design plants with longer roots that could
deposit carbon deeper in soil. Independent experts such as Sanderman agree that
carbon tends to stick around longer in deeper soil layers, putting that solution
on potentially firmer conceptual ground.
Chory and Busch have also launched collaborations with Berhe and Poffenbarger,
respectively. Poffenbarger, for example, will analyze how soil samples
containing suberin-rich plant roots change under different environmental
conditions.
But even those studies won’t answer questions about how long suberin sticks
around, Poffenbarger said — important if the goal is to keep carbon out of the
atmosphere long enough to make a dent in global warming.
Beyond the Salk project, momentum and money are flowing toward other climate
projects that would rely on long-term carbon sequestration and storage in soils.
In an April speech to Congress, for example, President Biden
suggested
paying farmers to plant cover crops, which are grown not for harvest but to
nurture the soil in between plantings of cash crops.
Evidence
suggests that when cover crop roots break down, some of their carbon stays in
the soil — although as with suberin, how long it lasts is an open question.
Not Enough Bugs in the Code
Recalcitrant carbon may also be warping climate prediction.
In the 1960s, scientists began writing large, complex computer programs to
predict the global climate’s future. Because soil both takes up and releases
carbon dioxide, climate models attempted to take into account soil’s
interactions with the atmosphere. But the global climate is fantastically
complex, and to enable the programs to run on the machines of the time,
simplifications were necessary.
For soil, scientists made a big one:
They ignored microbes in the soil entirely. Instead, they basically divided soil
carbon into short-term and long-term pools, in accordance with the humus
paradigm.
More recent generations of models, including ones that the Intergovernmental
Panel on Climate Change uses for its widely read reports, are essentially
palimpsests built on earlier ones, said Torn. They still assume soil carbon
exists in long-term and short-term pools.
As a consequence, these models may be overestimating how much carbon
will stick around in soils and underestimating how much carbon dioxide they will
emit.
Last summer, a
study published in Nature
examined how much carbon dioxide was released when researchers artificially
warmed the soil in a Panamanian rainforest to mimic the long-term effects of
climate change.
They found that the warmed soil released 55% more
carbon than nearby unwarmed areas — a much larger release than predicted by most
climate models. The researchers think that microbes in the soil grow more active
at the warmer temperatures, leading to the increase.
The study was especially disheartening because most of the world’s soil carbon
is in the tropics and the northern boreal zone.
Despite this,
leading soil models are calibrated to results of soil studies in temperate
countries such as the U.S. and Europe, where most studies have historically been
done.
“We’re doing pretty bad in high latitudes and the tropics,”
said Lehmann.
Even temperate climate models need improvement. Torn and colleagues
reported earlier this year
that, contrary to predictions, deep soil layers in a California forest released
roughly a third of their carbon when warmed for five years.
Ultimately, Torn said, models need to represent soil as something closer to what
it actually is: a complex, three-dimensional environment governed by a
hyper-diverse community of carbon-gobbling bacteria, fungi and other microscopic
beings. But even smaller steps would be welcome. Just adding microbes as a
single class would be major progress for most models, she said.
Fertile Ground
If the humus paradigm is coming to an end, the question becomes: What will
replace it?
One important and long-overlooked factor appears to be the three-dimensional
structure of the soil environment. Scientists describe soil as a world unto
itself, with the equivalent of continents, oceans and mountain ranges.
This complex microgeography determines where microbes such as
bacteria and fungi can go and where they can’t; what food they can gain access
to and what is off limits.
A soil bacterium “may be only 10 microns away from a big chunk of organic matter
that I’m sure they would love to degrade, but it’s on the other side of a
cluster of minerals,” said Pett-Ridge. “It’s literally as if it’s on the other
side of the planet.”
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A microfluidics experiment shows organic matter, in green,
attaching itself to clay. Halfway through the experiment, an enzyme
is injected. The enzyme allows bacteria to consume the
carbon. Judy Q. Yang
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Another related, and poorly understood, ingredient in a new soil paradigm is the
fate of carbon within the soil. Researchers now believe that almost all organic
material that enters soil will get digested by microbes.
“Now it’s really clear that soil organic matter is just this loose
assemblage of plant matter in varying degrees of degradation,” said Sanderman.
Some will then be respired into the atmosphere as carbon dioxide.
What remains could be eaten by another microbe — and a third, and so on. Or it
could bind to a bit of clay or get trapped inside a soil aggregate: a porous
clump of particles that, from a microbe’s point of view, could be as large as a
city and as impenetrable as a fortress.
Studies of carbon isotopes
have shown that a lot of carbon can stick around in soil for centuries or even
longer. If humus isn’t doing the stabilizing, perhaps minerals and aggregates
are.
Before soil science settles on a new theory, there will doubtless be more
surprises. One may have been
delivered
recently by a group of researchers at Princeton University who constructed a
simplified artificial soil using microfluidic devices — essentially, tiny
plastic channels for moving around bits of fluid and cells.
The
researchers found that carbon they put inside an aggregate made of bits of clay
was protected from bacteria. But when they added a digestive enzyme, the carbon
was freed from the aggregate and quickly gobbled up.
“To our
surprise, no one had drawn this connection between enzymes, bacteria and trapped
carbon,” said
Howard Stone, an engineer who led the study.
Lehmann is pushing to replace the old dichotomy of stable and unstable carbon
with a “soil continuum model” of carbon in progressive stages of decomposition.
But this model and others like it are far from complete, and at this point, more
conceptual than mathematically predictive.
Researchers agree that soil science is in the midst of a classic paradigm shift.
What nobody knows is exactly where the field will land — what will be written in
the next edition of the textbook.
“We’re going through a conceptual revolution,” said
Mark Bradford, a soil scientist at Yale University. “We haven’t really got a new cathedral
yet. We have a whole bunch of churches that have popped up.”
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