Now, two decades later, a team of scientists at Northern Arizona University, Lawrence Livermore National Laboratory, Pacific Northwest National Laboratory and West Virginia University have received a new $3.4 million award from the U.S. Department of Energy to conduct a deeper dive into what these buckets of soil have to say about the future. Mapping and better understanding the interplay of soil microbes and how they control nutrients like carbon and nitrogen will help researchers predict and potentially manage soil microbial communities to keep more carbon out of the air and in the soil—a critical piece of the climate puzzle. 

The experiment, located along an elevation gradient in the San Francisco Peaks in northern Arizona, is arrayed across four life zones found in temperate climates: mixed conifer forest at the highest elevation, then ponderosa pine forest, pinyon-juniper woodland and desert grassland. By moving the intact community of plants and soil microbes in a carefully preserved pail of soil down the mountain to a new home in the next life zone, scientists can simulate climate warming and drying and compare what happens to soil communities left at higher elevations. 

This low-tech design has been one key to the success of the experiment, said Bruce Hungate, Regents’ professor of biology, director of the Center for Ecosystem Science and Society (Ecoss) and designer of the initial experiment in 2002. Compared to other warming experiments that rely on manipulating temperatures through mechanical means, Hungate said part of the elegance was the simplicity: “You could just pick up an ecosystem and move it downslope.” This meant that the treatment was sustainable to maintain over a long period of time, allowing Hungate’s team to accrue longitudinal insights into what was happening belowground.  

And such long-term data are vital to answering one of the big questions that has guided Hungate’s research since coming to NAU. “Will different ecosystems respond to change in qualitatively similar ways,” he said, “or will we have to tell just-so stories about every ecosystem we care about to learn what is going to happen to it as the climate changes?”  

The new project builds on what Hungate and collaborators have learned from 15 years of warming, and the signals are complex, he said. Significant amounts of carbon were lost to the atmosphere in most ecosystems. In the pinyon-juniper plots, some carbon was gained. As nutrients grew scarcer over time, the team saw dynamics familiar from aboveground food webs: diversity fell, microbial interactions became more antagonistic and a few predators became more relevant in what happened to nutrients. They wondered: what if these microbial relationships hold keys to the fate of soil nutrients in a warmer world?  

Ember Morrissey, assistant professor of environmental microbiology at West Virginia University and a lead investigator on the new award, said this project could expand a frontier of soil microbiology. “Soil contains a wealth of microbial species that interact with each other. And while we understand a few of these interactions, most of them remain entirely undescribed by science.” 

“My team is asking how climate change influences cooperative and competitive interactions during decomposition,” Morrissey said. “By studying simple and complex root carbon inputs, we hope to see how mutualism and competition influence the decomposition and stabilization of these important carbon inputs to soil.” 

“We are taking a holistic approach in which we consider all microbial groups, from bacteria and archaea to fungi and protists, and associations among them, such as prey-predator interactions,” said Javier Ceja-Navarro, an associate professor of biology at Ecoss. “This work has the potential to improve current and future ecological models that aim to understand the influence of microbes on biogeochemical cycling and climate change.” 

The established warming experiment and the development of high-precision sequencing tools in the two decades since it began are adding up to a unique opportunity to ask these new questions of familiar soil. Using ‘omics tools and a state-of-the-art technique called quantitative Stable Isotope Probing, or qSIP, the team of researchers can assemble not just a picture of who lives in the soil at a given point, but a kind of molecular time-lapse that reveals who is growing, who is interacting and who disappears over time. 

The award was made as part of a $178 million investment by the Department of Energy into bioenergy and microbiome and climate-related research. “These projects will continue to advance the boundaries of biotechnology and support the emergence of a thriving U.S. bioeconomy that creates good-paying jobs and helps us meet our climate goals,” said U.S. Secretary of Energy Jennifer Granholm.  

Hungate, Morrissey and Ceja-Navarro are joined by NAU investigators professor Egbert Schwartz, senior research scientist Ben Koch, Regents’ professor Michelle Mack, assistant professor Toby Hocking, Jennifer Pett-Ridge and Steve Blazewicz at Lawrence Livermore National Laboratory and Kirsten Hofmockel and Bram Stone at Pacific Northwest National Laboratory. 

But that’s only one possible future for the vast stores of carbon locked in the formerly perennially frozen but now-thawing ground in the Arctic. Using more than a decade of synthesis science and region-based models, a new study led by Northern Arizona University and the international Permafrost Carbon Network and published in Annual Review of Environment and Resources forecasts cumulative emissions from this “country of permafrost” through 2100 under low, medium and high warming scenarios.  

“We hope that these forecasts of future Arctic carbon emissions not only update the scientific picture but act as new guide rails for policymakers who are working to stabilize the climate and avoid exceeding temperature targets,” said Ted Schuur, Regents’ professor in the Department of Biological Sciences and Center for Ecosystem Science and Society at NAU and lead author of the study.  

The team estimates that under a low warming scenario—one that could be achieved if the global community limited warming to 2 degrees Celsius or below by reducing fossil fuel emissions—permafrost would release 55 petagrams (Pg) of carbon by the end of the century in the form of greenhouse gases carbon dioxide (CO2) and methane (CH4). If nothing is done to mitigate climate warming, the study estimates the Arctic could release 232 Pg of carbon by the end of the century. 

The team’s projections go beyond previous international forecasts by accounting for hydrological and biogeochemical dynamics and tipping points unique to the permafrost zone.  

For instance, scientists are witnessing abrupt thaw in many permafrost regions, where rapid melting of ground ice in permafrost causes the land surface to collapse, forming lakes or other changes to surface hydrology. Once formerly frozen ground erodes or subsides, the carbon stored there can enter the atmosphere via microbial respiration or methane. Such rapid, non-linear shifts quickly and permanently change permafrost’s ability to store carbon and could toggle large swaths of the Arctic region from carbon sinks to carbon sources. Recent estimates suggest that one-fifth of current permafrost terrain is vulnerable to abrupt thaw.  

“Once permafrost carbon emissions increase in response to climate warming as some models predict, there won’t be a way for us to stop that process,” said Roisin Commane, assistant professor of Earth and environmental sciences at Columbia University and co-author of the new study. “We may need to reduce our fossil fuel emissions much sooner than currently planned by many governments to avoid triggering possible tipping points in Earth’s climate.” 

The potential to cross both regional and systemwide tipping points is one reason the story of Arctic carbon and its future security remains only partially written. The new study describes nine different futures based on how climate warming progresses and what actions global leaders take to reduce fossil fuel emissions. 

“Permafrost emissions will be a large and substantial contributing factor to atmospheric greenhouse gases, no matter which of the possible scenarios becomes reality,” said Guido Grosse, head of the permafrost research section at the Alfred Wegener Institute in Potsdam, Germany, and co-author of the study. “But there will be huge differences between mitigation scenarios that matter to the overall global carbon budget.”  

Curbing human-caused emissions, Grosse said, will help ensure permafrost makes a smaller contribution to global climate warming, while “doing business as usual” will guarantee that the “nation” of permafrost will have a sizable role in warming and represent a higher hurdle for mitigation efforts to clear.  

Because the Arctic is not regulated by any one state and its remoteness makes terrain hard to monitor comprehensively, the authors emphasize that international emission reduction efforts must account for this “country of permafrost” in climate targets and actions going forward. The study also underscores the importance of monitoring this quickly changing region using collaborative networks like the Permafrost Carbon Network and scientific tools like remote sensing technology.  

“Remote sensing products can really help us see and track what is happening to permafrost in a physical way,” Commane said. “High-resolution sensors can see evidence of thermokarst soil collapse, how water bodies are changing and even how wet or frozen the soils are. But satellites that tell us how much carbon from permafrost ends up in the atmosphere are limited, and there needs to be investment from space agencies in these capabilities as soon as possible.”  

Schuur said his research team is seeing evidence of rapid change on the ground, as well.  

“Changes we are witnessing in the field show the urgent need to curb emissions and keep permafrost carbon in the ground. This summer, at my study site in Eight Mile Lake, Alaska, we saw widespread permafrost thaw after a winter with record snowfall, and carbon losses four times larger than the average over the past several decades,” he said. “These observations match predicted tipping points in permafrost and carbon that we expect to see as human-caused emissions from elsewhere on Earth rapidly warm the Arctic.” 

The study was authored by an international team of scientists from NAU, Alfred Wegener Institute, Columbia University, Brigham Young University, University of New Hampshire, University of Alaska-Fairbanks, Stockholm University, U.S. Geological Survey, Lawrence Berkeley National Laboratory, National Center for Atmospheric Research, Colgate University, University of Texas-El Paso, University of Alberta, Woodwell Climate Research Center, Oak Ridge National Laboratory and University of Colorado-Boulder. The Permafrost Carbon Network synthesis work is supported by a grant from the National Science Foundation. 

Illustration by Victor Leshyk

Antibiotic-resistant bacteria are widespread and are increasingly associated with human infections.  Inappropriate antibiotic use – both in people and in animals raised for food – drives the evolution of multi-drug-resistant pathogens and threatens a post-antibiotic era – one in which minor infections can kill.

The majority of antibiotics are actually sold for use in food animals, rather than in people, and as a result, farms are major sources of many new types of antibiotic-resistant bacteria.

“We clearly need to use antibiotics more responsibly,” says Ecoss researcher Ben Koch.  “However, limiting the spread of antibiotic resistance also requires knowing the extent to which antibiotic-resistant microbes move among farms, the environment, and people.”

Koch, along with Ecoss colleagues Bruce Hungate and Lance Price, published a study in the journal Frontiers in Ecology and the Environment that examined the potential for merging ecology and genomics to better understand those microbial movements.

They found that combining ecological principles with newly available genomic data on antibiotic-resistant bacteria provides a highly detailed view into the transmission patterns and lifestyles of antibiotic-resistant bacteria.

By merging ecology and genomics in this way, Koch aims to find new ways of combating antibiotic resistance beyond just developing more and stronger antibiotics.

Permafrost, the “always-frozen” deep soil layers of the Arctic, naturally undergoes freeze-thaw cycles with the passage of the brief Arctic spring and summer, which thaws the uppermost layers and fosters a burst of tundra plant growth and pooling meltwater from thawed soil. For millennia, this cycle has re-frozen the soil in winter, with a net gain in permafrost as new plant matter adds to the depth of soil.  However, new Ecoss research via field warming experiments reveals that recent climate warming can disturb that trend, as warmer seasons allow deeper thaws, with the result that soil microbes can remain active through the winter months in deep layers of soil that do not re-freeze.  Alarmingly, this new effect can allow microbes a new schedule of digesting ancient permafrost soil carbon year-round, with the net result that greenhouse gas emissions from active microbes can become consistent enough to exceed the seasonal carbon “drawdown” by tundra plant growth, converting Arctic landscapes into carbon Sources rather than terrestrial carbon Sinks.  Increased emissions from tundra can then feed back into increased climate warming, further deepening the microbial mobilization of deeper and deeper layers of ancient stored permafrost carbon.

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Biochar illustration by Victor O. Leshyk

Biochar, a fine-grained carbon residue of charred plant material, has recently been promoted as a universal amendment to soil to improve moisture and nutrient content with the expectation of higher agricultural yields, fostering the rise of a large global biochar industry.  In the original context of “terra preta,” the rich organic soil left over from many seasons of burn-based ancient agriculture in Mesoamerica, the increased fertility of these deposits compared to normally-poor tropical soil is very obvious, but until now, the hope of higher yields from biochar had never been investigated for other growing zones.  In a landmark meta-analysis, Ecoss research revealed that there is NO INCREASED YIELD from biochar addition for anything grown outside of 30 degrees from the equator, although biochar caused greatly increased yields within that tropical zone.  A likely explanation is that biochar works by improving tropical soils so that they approach the fertility of naturally nutrient-rich temperate soils, but temperate soils already perform near maximum fertility, especially with use of modern fertilizers and practices.

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