28 Mar 2016: Report

Is Climate Change Putting
World's Microbiomes at Risk?

Researchers are only beginning to understand the complexities of the microbes in the earth’s soil and the role they play in fostering healthy ecosystems. Now, climate change is threatening to disrupt these microbes and the key functions they provide.

by jim robbins

The spores of an opportunistic soil fungus, Penicillium sp. View gallery.
Photo: PNNL
In 1994, scientists at the Pacific Northwest National Laboratory moved soil from moist, high-altitude sites to warmer and drier places lower in altitude, and vice versa. In 2011, they returned to the sites and looked again at the soil microbes and found that they had done little to adapt functionally to their new home. That's a bad sign, experts say, for a world convulsed by a changing climate.

"These microbes have somehow lost the capacity to adapt to the new conditions," said Vanessa Bailey, one of the authors of the study, published this month in PLOS One. That not what scientists anticipated, and it "calls into question the resilience of the overall environment to climate change," she said. "Soil is the major buffer for environmental changes, and the microbial community is the basis for that resilience."

As snow and ice melt, it's fairly straightforward to grasp what climate change means for the future of, say, polar bears in the Arctic or penguins in Antarctica. But it's far more difficult to understand what is happening to the planetary microbiome in the earth's crust and water, a quadrillion quadrillion microorganisms, according to Scientific American. Yet it is far more important, for microbes run the world. They are key players that perpetuate life on the planet, provide numerous ecosystem services, and serve as a major bulwark against environmental changes.
Researchers say that as the planet warms, essential diversity and function in the microbial world could be lost.
But they can also cause serious problems — as the world's permafrost melts, microbes are turning once-frozen vegetation into greenhouse gases at a clip that is alarming scientists.

As vital as they are, we are only beginning to understand microbes and the role they play in the world's ecosystems. The problem is that these fungi, archaea, and bacteria are so small that in a gram of soil (about a teaspoon), there are a billion or so, with many thousands of species. Perhaps 10 percent of the species are known. The Lilliputian communities that these microorganisms create are enormously complex, and their functions difficult to tease out. But in the last decade, new tools have been developed that have begun to change the research game.

"Soil was a black box," said Janet Jansson, chief scientist for Biology Earth and Biological Sciences at the Pacific Northwest National Laboratory and president of the International Society for Microbial Ecology. "I have been working in microbial ecology for decades, and it has been difficult, if not impossible, to study them. Now we have these new molecular processes, and suddenly the whole field is exploding."

There is a Manhattan Project-like urgency to sussing out these secrets. A paper in the journal Science last year called for a Unified Microbiome Initiative, and experts have held a series of meetings about it at the White House. The Earth Microbiome Project is a massive global effort to collect samples of microbial communities from thousands of ecosystems around the world. Meanwhile, the Global Soil Biodiversity Initiative got underway in 2011 — one-third of the world's biodiversity lives beneath our feet — and it’s focused on preserving the services that healthy soil ecosystems provide, such as a place for plants to grow, the breakdown of waste, and the natural filtration of water. The TerraGenome Project is sequencing the metagenome of soil microbes.

View gallery
Growth Lab

PNNL
Microbiologists at the Pacific Northwest National Laboratory are studying how soil microbes react to climate change.
And Jansson's project, Microbiomes In Transitions, is studying how "perturbations" — disruptions such as climate change and pollution — affect both the microbiomes around us and inside of us. "It's extraordinarily evident that bacteria, fungi, and viruses play a massive roll in the development of health and disease in humans, and in environmental settings and ecological systems," said Jack Gilbert, a microbial biologist at Argonne National Laboratory and a founding member of the Unified Microbiome Initiative.

The new tools came about because of keen interest in the human microbiome that new research shows is linked to everything from mood disorders to immune system dysfunction. Microbes play similarly essential and wide-ranging roles in the external world. They are a healthy foundation for the food web — plants and the critters that eat them are all dependent on soil microbes.

Interest in microbiomes in the natural world is also exploding because many researchers realize that as the planet warms, essential diversity and function in the microbial world could be lost. Some areas may not be able to grow the same crops they are growing now — in the United States, for instance, no corn in Iowa or wheat in Kansas, because the microbes that currently fix nitrogen for the plants’ roots in the soil will no longer be able to do so. And, as we learn more about how microbes function, there may be ways to put them to work in the service of adaptation — enhancing plant growth, for example, in a warming climate.

Most urgent, though, is the fact that the earth has locked up a great deal of carbon and should it come unlocked as C02 it could dramatically speed up climate change. "The big question is whether soil will be a sink or source of greenhouse gases in the future," said Jansson.

One of the major areas of study is a feedback loop — the impact of climate change on microbes, and the role of microbes in climate change. Soil microbes are key players in how much greenhouse gas permafrost releases into the atmosphere, and it’s probably the most critical area of study. The frozen vegetation, rich in microorganisms, is thawing as the Arctic warms rapidly and microbes consume the newly available plant matter and release both C02 and methane, potent greenhouse gases.
There is concern that some key microbes could become extinct before we know what they do.
This could cause more warming and thawing, a positive feedback loop.

Understanding these dynamics is "really important because about 20 percent of the terrestrial surface of the earth is permafrost," said Jansson. "As much C02 is stored in permafrost as is stored in plants and the atmosphere. What happens when that carbon becomes accessible to newly activated microorganisms that are there? They can speed up climate warming, and it’s of concern."

It's not just permafrost. All soil contains large stores of CO2, and scientists are trying to understand how climate change will impact those stores, and how they could be released by land management practices. Much of this information will help create more accurate models of global climate change. And it will also provide insight into ways to alter land management practices to minimize the amount of CO2 released from soil. Tillage and desertification, for example, unlock greenhouse gases in the soil and allow them into the atmosphere. "There are certain soils that just dragging a plow through it displaces huge, huge quantities of carbon," said Bailey. No-till farming, which leaves residue from past crops on the soil and minimizes plowing, is far more beneficial because it gives the microbes food and shelter.

There are other functions that could be lost or diminished as climate conditions change. Microbes that have adapted to moist conditions in the old-growth forests of the Pacific Northwest, for example, may not be able to carry out their activities as the soil warms and dries. Consider the zone around tree roots, where a critically important relationship between microorganisms and trees exists. A densely packed community of microbes about the width of a finger live there, and in exchange for exudates — sugars — from the tree, they clean the water that the tree takes in, a critical filter system in the planet's hydrological cycle. It's such a robust phenomenon that some engineers use trees, especially willows and poplars, to clean up toxic waste, something called phyto-remediation. This ecosystem service could be diminished if these microbes cannot adapt to maintain this function as soil temperatures climb or if the microbes disappear. Fortunately, there is a lot of redundancy in these communities, so in some cases the function of microbes impacted by climate can be replaced by others.

A close-up image of a soil fungus surrounding a pine tree root. View gallery.
Photo: PNNL


The jury is out on how warming will impact the phyllosphere — the microbes that live on leaves that help trees to fix nitrogen and function as an immune system, allowing trees to ward off disease. "We are pretty ignorant about how those trees are going to respond and whether or not you make plants more susceptible to pathogens," when temperatures warm, said Mark Bradford, an expert in the role of microbes in forests and grasslands at the Yale School of Forestry and Environmental Studies.

Whether microbes can go extinct is not settled science. When it comes to microbes, “everything is everywhere” has been the adage among researchers who thought that all types lived everywhere, though abundance varied. Yet as more is learned about these tiniest of critters, some scientists believe that likely isn't true, and there is concern that some key microbes could be rendered extinct before we know what they do. In 2003, a study published in the journal Ecosystems estimated that the biodiversity of some 5 percent of U.S. soil was "in danger of substantial loss or complete extinction."

Microbiomes carry out similar kinds of functions in oceans, where researchers forecast similar kinds of problems. There's a bacterium called trichodesmium, for example, that grows in nutrient-poor parts of the ocean and creates nitrogen gas that fertilizes everything, from plankton to whales. For a study published last year in the journal Nature Communications, these bacteria were placed in warmer conditions that simulate forecasts for a future climate, and they went into reproductive overdrive and began gobbling up iron and phosphorus, nutrients which are in limited supply and needed by other organisms. It's a scenario that could cause those other microorganisms to disappear, or, if the trichodesmium caused its own extinction, it would leave a gaping hole in the food web.

Microbes may also be able to be tapped for beneficial uses. Research shows microbes can be applied to seeds to activate natural plant defenses against pests to reduce pesticide use or make crops more resilient in the face of drought.

ALSO FROM YALE e360

Microbiomes at the Roots:
A New Look at Forest Ecology

Microbiomes at the Roots: A New Look at Forest Ecology
With advances in genetic sequencing technology, scientists are now able to readily identify the microbes living in and around the roots of trees. This information is proving to have important implications for everything from tropical forest restoration to climate change planning.
READ MORE
Certain kinds of vermicompost — fertilizer made from worm castings — have been shown to greatly enhance beneficial microbes in the soil, reducing disease in plants and boosting their natural defenses against insects.

And in Japan, fishermen learned about research that showed that decaying trees released humic acid into the ocean, a chemical that which allowed microorganisms called phytoplankton to fix iron, a fertilizer, and exponentially increase their growth. They formed a group called Forests are the Lovers of the Sea to plant trees around the country to bring fish and stocks back by stimulating the growth of the plankton, the bottom of the food web.

Knowledge of these tiniest of natural systems and their role in the world is key going into the future. "We need to understand clearly how microbes are going to behave in a changing climate," said Bailey. "By understanding what's going to happen, we can make better plans."

POSTED ON 28 Mar 2016 IN Biodiversity Biodiversity Business & Innovation Climate Forests Policy & Politics Science & Technology Africa Africa Antarctica and the Arctic Asia Australia Central & South America Europe Middle East North America 

COMMENTS


Climate will do what climate will do as it has for
hundreds of millions of years. Meanwhile, when
people make plans, it would be good to base them on
hard facts.

There are some crucial, verifiable facts - with
citations - about human-generated carbon dioxide
and its effect on global warming people should know
and understand at

hseneker.blogspot.com

The discussion is too long to post here but is a quick
and easy read. I recommend following the links in the
citations some of them are very educational.
Posted by hseneker on 28 Mar 2016


Nice land-sea connection Jim:

"...in Japan, fishermen learned about research that showed that decaying trees released humic acid into the ocean, a chemical that which allowed microorganisms called phytoplankton to fix iron, a fertilizer, and exponentially increase their growth. They formed a group called Forests are the Lovers of the Sea to plant trees around the country to bring fish and stocks back by stimulating the growth of the plankton, the bottom of the food web."

A Budding Model of a Truly Sustainable Community - http://www.triplepundit.com/2013/01/budding-model-sustainable-community/

"In 2006, the local non-profit Port Orford Ocean Resource Team (POORT) used Ecosystem-Based-Management (EBM) to guide them in forming the Port Orford Community Stewardship Area (POSCA). The Stewardship Area encompasses the traditional fishing grounds and the upland watersheds that feed into them. In total it covers 1,320 square miles – 385 miles of terrestrial and 935 square miles of ocean habitat... Non-profit Archangel Ancient Tree Archive and local SLDI partner Ocean Mountain Ranch planted champion redwood and sequoia tree clones in the POCSA in order to preserve the genetics of the largest and oldest livings organisms on Earth. This tree planting is in concert with an effort to assist with the migration of the species during coming climate change. In addition to preserving champion tree genetics for future research, the planned planting at the local high school will provide a focal point for ongoing model terrestrial sustainability initiatives within the local community stewardship area and surrounding Curry County, Oregon — a rare place on earth where beautiful wild and scenic rivers tumble down through steep canyons and the tallest and largest carbon-sequestering forests in the world on their way to the mighty Pacific Ocean."
Posted by Terry Mock on 28 Apr 2016


POST A COMMENT

Comments are moderated and will be reviewed before they are posted to ensure they are on topic, relevant, and not abusive. They may be edited for length and clarity. By filling out this form, you give Yale Environment 360 permission to publish this comment.

Name 
Email address 
Comment 
 
Please type the text shown in the graphic.


jim robbinsABOUT THE AUTHOR
Jim Robbins is a veteran journalist based in Helena, Montana. He has written for the New York Times, Conde Nast Traveler, and numerous other publications. His latest book is The Man Who Planted Trees: Lost Groves, Champion Trees, and an Urgent Plan to Save the Planet. In a recent article for Yale Environment 360, he reported on how forest loss is leading to a rise in human disease.
MORE BY THIS AUTHOR

 
 

RELATED ARTICLES


Why CO2 'Air Capture' Could Be
Key to Slowing Global Warming

Physicist Klaus Lackner has long advocated deploying devices that extract carbon dioxide from the atmosphere to combat climate change. Now, as emissions keep soaring, Lackner says in a Yale Environment 360 interview that such “air capture” approaches may be our last best hope.
READ MORE

After Paris, A Move to Rein In
Emissions by Ships and Planes

As the world moves to slash CO2 emissions, the shipping and aviation sectors have managed to remain on the sidelines. But the pressure is now on these two major polluting industries to start controlling their emissions at last.
READ MORE

As Drought Grips South Africa,
A Conflict Over Water and Coal

Facing one of the worst droughts in memory, South Africa’s leaders have doubled down on their support of the water-intensive coal industry. But clean energy advocates say the smartest move would be to back the country’s burgeoning wind and solar power sectors.
READ MORE

Saving Amphibians: The Quest
To Protect Threatened Species

The decline of the world’s amphibians continues, with causes ranging from fungal diseases to warmer and drier climates. Now, researchers are looking at ways to intervene with triage measures that could help save the most vulnerable populations.
READ MORE

How Rising CO2 Levels May
Contribute to Die-Off of Bees

As they investigate the factors behind the decline of bee populations, scientists are now eyeing a new culprit — soaring levels of carbon dioxide, which alter plant physiology and significantly reduce protein in important sources of pollen.
READ MORE

 

MORE IN Reports


As Drought Grips South Africa,
A Conflict Over Water and Coal

by keith schneider
Facing one of the worst droughts in memory, South Africa’s leaders have doubled down on their support of the water-intensive coal industry. But clean energy advocates say the smartest move would be to back the country’s burgeoning wind and solar power sectors.
READ MORE

Saving Amphibians: The Quest
To Protect Threatened Species

by jim robbins
The decline of the world’s amphibians continues, with causes ranging from fungal diseases to warmer and drier climates. Now, researchers are looking at ways to intervene with triage measures that could help save the most vulnerable populations.
READ MORE

How Rising CO2 Levels May
Contribute to Die-Off of Bees

by lisa palmer
As they investigate the factors behind the decline of bee populations, scientists are now eyeing a new culprit — soaring levels of carbon dioxide, which alter plant physiology and significantly reduce protein in important sources of pollen.
READ MORE

Can Uber-Style Buses Help
Relieve India's Air Pollution?

by jason overdorf
India’s megacities have some the deadliest air and worst traffic congestion in the world. But Indian startups are now launching initiatives that link smart-phone apps and private shuttle buses and could help keep cars and other motorized vehicles off the roads.
READ MORE

Trouble in Paradise: A Blight
Threatens Key Hawaiian Tree

by richard schiffman
The ʻohiʻa is Hawaii’s iconic tree, a keystone species that maintains healthy watersheds and provides habitat for numerous endangered birds. But a virulent fungal disease, possibly related to a warmer, drier climate, is now felling the island’s cherished 'ohi'a forests.
READ MORE

Climate Change Adds Urgency
To Push to Save World’s Seeds

by virginia gewin
In the face of rising temperatures and worsening drought, the world’s repositories of agricultural seeds may hold the key to growing food under increasingly harsh conditions. But keeping these gene banks safe and viable is a complicated and expensive challenge.
READ MORE

As World Warms, How Do We
Decide When a Plant is Native?

by janet marinelli
The fate of a tree planted at poet Emily Dickinson's home raises questions about whether gardeners can — or should — play a role in helping plant species migrate in the face of rising temperatures and swiftly changing botanical zones.
READ MORE

With New Tools, A Focus
On Urban Methane Leaks

by judith lewis mernit
Until recently, little was known about the extent of methane leaking from urban gas distribution pipes and its impact on global warming. But recent advances in detecting this potent greenhouse gas are pushing U.S. states to begin addressing this long-neglected problem.
READ MORE

As Electric Cars Stall, A Move
To Greener Trucks and Buses

by cheryl katz
Low gasoline prices and continuing performance issues have slowed the growth of electric car sales. But that has not stymied progress in electrifying larger vehicles, including garbage trucks, city buses, and medium-sized trucks used by freight giants like FedEx.
READ MORE

Food Insecurity: Arctic Heat
Is Threatening Indigenous Life

by ed struzik
Subsistence hunters in the Arctic have long taken to the sea ice to hunt seals, whales, and polar bears. But now, as the ice disappears and soaring temperatures alter the life cycles and abundance of their prey, a growing number of indigenous communities are facing food shortages.
READ MORE


e360 digest
Yale
Yale Environment 360 is
a publication of the
Yale School of Forestry
& Environmental Studies
.

SEARCH e360



Donate to Yale Environment 360
Yale Environment 360 Newsletter


CONNECT


ABOUT

About e360
Contact
Submission Guidelines
Reprints

E360 en Español

Universia partnership
Yale Environment 360 articles are now available in Spanish and Portuguese on Universia, the online educational network.
Visit the site.


DEPARTMENTS

Opinion
Reports
Analysis
Interviews
Forums
e360 Digest
Podcasts
Video Reports

TOPICS

Biodiversity
Business & Innovation
Climate
Energy
Forests
Oceans
Policy & Politics
Pollution & Health
Science & Technology
Sustainability
Urbanization
Water

REGIONS

Antarctica and the Arctic
Africa
Asia
Australia
Central & South America
Europe
Middle East
North America

e360 VIDEO

“video
Tribal people and ranchers join together to stop a project that would haul coal across their Montana land.
Watch the video.

e360 MOBILE

Mobile
The latest
from Yale
Environment 360
is now available for mobile devices at e360.yale.edu/mobile.

e360 PHOTO ESSAY

“Alaska
An aerial view of why Europe’s per capita carbon emissions are less than 50 percent of those in the U.S.
View the photos.

e360 VIDEO

“Battle
The 2015 Yale e360 Video Contest winner documents a Northeastern town's bitter battle over a wind farm.
Watch the video.

e360 VIDEO

Food waste
An e360 video series looks at the staggering amount of food wasted in the U.S. – a problem with major human and environmental costs.
Watch the video.

e360 VIDEO

Colorado wildfires
An e360 video goes onto the front lines with Colorado firefighters confronting deadly blazes fueled by a hotter, drier climate.
Watch the video.

e360 SPECIAL REPORT

“Tainted
A three-part series Tainted Harvest looks at the soil pollution crisis in China, the threat it poses to the food supply, and the complexity of any cleanup.
Read the series.

OF INTEREST



Yale