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. 

The program is open to students who want to apply for an MS or PhD in the Earth sciences or who have applied previously to a graduate program. Bridge programs like AGU’s are part of a raft of larger efforts to broaden participation in a field whose makeup does not reflect the U.S. population or other science professions.

The geosciences are the least diverse among all STEM fields, according to recent surveys of graduate degrees conferred, and faculty of color hold a mere 3.8% of tenured or tenure-track positions in the top 100 Earth science programs in the U.S. More troublingly still, these trends show little improvement over the last 40 years, so funders like NSF and professional societies like AGU are redoubling efforts to better connect to, recruit, and serve students from ethnic and racially diverse backgrounds.

“We in the biogeosciences have to do better when it comes to not just recruiting, but supporting scholars from marginalized communities throughout their careers,” said assistant research professor Mariah Carbone, one of the leads on the Ecoss AGU Bridge team. “The AGU Bridge Program will help our center better serve students from minoritized communities by sharing best practices and trainings, and by connecting us with these researchers who are a vital part of our field’s future.”

“We’re looking forward to working with students in this program at NAU,” said Ted Schuur, a Regents Professor in biology and Ecoss who led efforts to join the AGU Bridge Program. “Students accepted into the program will have the support of a nationwide peer network, and the program allows us to learn mentoring strategies from other institutions across the U.S.”

“A critical part of NAU’s mission is to make concerted, collaborative efforts to increase diversity, including recruiting students from historically underserved and underrepresented groups and diverse life experiences and backgrounds,” NAU president José Luis Cruz Rivera said. “Ecoss’ collaboration with the AGU Bridge Program is an important step in that process, and I’m excited to see this increased focus to increase participation in these fields so they are more representative of our communities.”

Learn more about the AGU Bridge Program and its partners here.

The team, which includes researchers from NAU, University of California-Berkeley, Lawrence Livermore National Laboratory, and University of Nebraska-Lincoln, will conduct experiments in rivers in Arizona and California. By manipulating nutrients and sunlight, they will look for the biological “switches” that get turned on and off by organisms living in the algal mat, a laminate composed of algae, bacteria, fungi, and tiny animals that grows on rocks and sediments of riverbeds.

“When does productive algae become toxic strains of Cyanobacteria, which can be really harmful to marine life, dogs, and humans, and what are the biological switches that flip?” said principal investigator Jane Marks, professor in biology in the Center for Ecosystem Science and Society at NAU. “Even in a relatively pristine river like the Eel, we get these very sudden shifts from productivity to toxicity, and we don’t really understand the tipping points.”

Because algal mats are long-studied and relatively accessible to observe, the team will use them as models to better learn how microbial communities beyond rivers behave. The team will combine field experiments with high-tech molecular tools and machine learning to unravel the complex interactions among bacteria and algae into a set of predictive rules. The experiments they conduct and computer models they develop will illumine which interactions among micro-organisms have the power to change the health of a river or a human gut.

“I’m excited to gather new kinds of measurements with this team, like species-specific carbon and nitrogen uptake rates,” said Toby Hocking, assistant professor in the School of Informatics, Computing and Cyber Systems at NAU and co-principal investigator on the project. “Most previous work has been limited to measurement of abundance data, which means counting the individuals of a species in a population. But having only abundance data makes it very difficult to infer more complex interactions such as mutualism and predation. Combining our metabolic data with abundance will reveal new details about interactions and relationships between species in these microbial communities.”

“Since we can’t walk through an algal forest to map out where nutrients are going, we need to use isotopic tools like qSIP (quantitative stable isotope probing) and NanoSIMS (nano secondary ion mass spectrometry), which allow us to follow carbon and nitrogen as it moves through the system,” said Marks.

“Pulling nitrogen into the river food web, as the diatom Epithemia does, is hugely important for fish like salmon and other riverine consumers,” said Mary Power, a professor at University of California-Berkeley and co-principal investigator on the project. “Using the sophisticated technology Ecoss developed, we can track how Epithemia—the Greek word for desire—and its amazing endosymbiont bring nitrogen into the river.”

The NSF award will support training 10 undergraduate students, two postdocs, and four graduate researchers at NAU. The team will collaborate with tribal community partners and citizen scientists to conduct field trips called “algal forays,” and plans to share what they learn about the algae microbiome through community art and science collaborations like Parched: the Art of Water in the Southwest.

For Marks, who studies how freshwater food webs respond to environmental change, this project represents a return to her first scientific love: exploring life underwater.

“Jane first taught me to recognize Epithemia when she began her dissertation work in the Eel River three decades ago,” said Power. “Now we’re back on its trail, learning how changes in river temperatures, flows, and other factors can turn this algae from an excellent food source for salmon-bearing food chains into a victim of overgrowth by other toxic algae and Cyanobacteria.”

“I have loved algae for many, many years,” said Marks. “It’s green and slimy, but when you put it under the microscope, you enter this secret world. There are epiphytes of all colors and shapes, and structures that rival the planet’s densest forests. I love getting to go back there with new questions.”

**

Other co-principal investigators from NAU include Greg Caporaso of the School of Informatics, Computing and Cyber Systems and Bruce Hungate of the Center for Ecosystem Science and Society.

“Our fate is bound up with soil carbon, and its fate is bound up with these intricate microbial communities, whose individual capabilities and interactions we are only beginning to understand,” said Jennifer Pett-Ridge, the lead investigator and Environmental Isotope Systems Group Leader at LLNL. “Using new tools, some of which this team developed, we are asking: how can understanding the microbial lives unfolding in soil tell us about the future of carbon?”

These microscopic lives, the researchers say, are highly sensitive to soil moisture, and undergo significant changes as the weather patterns of our climate (rainfall, temperature) are changing. Pett-Ridge and others are mimicking shifts in California’s climate and tools linking metagenomics with stable isotope tracers to see how microbes respond to these changes. By observing who is actively growing, who is dying, and how the genes expressed in the microbiome change as a result, the research team will learn which functions of microorganisms are most relevant to keeping carbon in the soil, and what indicators predict when it will be released into the atmosphere.

“Some microbial communities seem to respond to drought like many plants and animals do: by waiting for a better year,” said Bruce Hungate, director of the Center for Ecosystem Science and Society at Northern Arizona University (NAU) and a collaborator on the project. “By studying wild microbes, outside of the lab and in their home soils, we’re beginning to understand how dynamic and nuanced these communities really are.”

The team, which includes researchers from LLNL, NAU, University of California-Berkeley, Lawrence Berkeley National Laboratory, University of Minnesota, Pacific Northwest National Laboratory, and University of California-Davis, has been asking questions about the way soil water patterns shape microbial communities, and this new “Microbes Persist” award allows it to ask new questions about how microbial capabilities change with soil depth and over time. A recent study published by the team, the first to apply quantitative stable isotope probing (qSIP) to all the different organisms in soil simultaneously, revealed that soil viruses that infect bacteria near plant roots were among the most active entities in the soil microbiome.

Alexa Nicolas, a graduate student on the project from UC Berkeley, says this project “opens a window into the life and death of soil microbes, to see their molecular afterlives. We can measure this by tracing molecules through microbial life and death along paths shaped by the DNA of the whole soil community.”

“We are now seeing the effects of climate change in our day to day lives, whether it’s wildfire smoke or a drought-depleted reservoir,” said Pett-Ridge. “Microbes are experiencing stresses from some of the same effects. We want to understand how that stress alters their living, growing, and dying, and what that means for the huge reservoirs of nutrients and carbon held in soils.”

The research is funded by the Department of Energy, Office of Science – Office of Biological and Environmental Research and the Genomic Science Program LLNL “Microbes Persist” Soil Microbiome Scientific Focus Area.

That’s why she created a user interface called “MIDA”—model-independent data assimilation—which allows a scientist to improve a model with data without extensive coding experience. The resulting study, “A model-independent data assimilation (MIDA) module and its applications in ecology,” was published in Geoscientific Model Development and is Huang’s first lead-author publication.

“A model is a powerful tool to approach the future with, which is why we wanted to expand access with this software,” said Huang. “In this data-rich era, we use data assimilation to integrate abundant observations into models. If an ecologist wants to train a model but doesn’t have extensive programming experience, they might run into technical issues. This software aims to remove that barrier.”

Huang is a member of Yiqi Luo’s EcoLab, where she and her colleagues work to make earth system models faster and more accurate through data assimilation and the matrix approach. “Even if a model is perfect, we need observations to constrain it. So data assimilation is a tool we use to bring the model and our observations together, to create a clearer picture of what the future looks like.”

Huang, who received her masters from Tsinghua University in China, said publishing in Geoscientific Model Development means a great deal to her, since the journal is a gold standard in her field. The paper was co-authored by research associate Lifen Jiang, postdoctoral fellow Enqing Hou, and Regents’ professor Yiqi Luo of the Center for Ecosystem Science and Society, and assistant professor Igor Steinmacher and Regents’ professor Andrew Richardson of the School of Informatics, Computing, and Cyber Systems.

What’s next for Huang? She plans to use MIDA and data from the SPRUCE project in northern Minnesota to improve ecological forecasting.

“Climate forecasting, like weather forecasting, comes with uncertainty,” Huang said. “When we talk about modeling future aspects of the climate, this uncertainty is huge, especially around the nature of carbon sources and sinks and the processes that drive them. This is the work I want to dive into next.”

Permafrost, ground that stays frozen two or more years, contains nearly twice as much carbon as is in the atmosphere today. When permafrost thaws, soil microbes release CO2 and methane into the atmosphere, accelerating climate warming. Predicting what will happen to those vast stores of carbon being unlocked by warming temperatures in the North is a relatively new challenge for the modeling community, said Schädel, who coordinates the Permafrost Carbon Network with Schuur. “For many, many years the models showed that the carbon was there, but they assumed nothing happens to it,” she said.

But in the last two decades, those assumptions have changed, as both observational studies and warming experiments across the Arctic reveal how dynamic and vulnerable to change this pool of carbon is. Warming experiments, which use a variety of methods including open top chambers, snow fences, greenhouses, soil heating cables, have shown that rising air temperatures not only thaw permafrost, but change the moisture characteristics of the terrain, creating thermokarst features and wetter conditions in which some processes like microbial respiration slow. The experiments challenge another assumption baked into some earth system models: that warming stimulates plant photosynthesis (referred to as gross primary production) in permafrost regions. More plants taking up more CO2 could offset the release of carbon from microbes in thawing soil, but some experiments have found that the plant-stimulating effects of permafrost warming weren’t as significant as models predicted.

By analyzing and synthesizing warming experiments across the Arctic, Schädel’s team will create benchmarks that help the models refine their processes and make better predictions. Then they will test these data inputs with the help of modeling teams across the globe. Because climate and earth system modeling is such a computing- and time-intensive process, the project requires the cooperation from teams who run the enormous programs. Schädel said the modeling community was quick to get on board.

“I heard back from most of the modeling groups I wrote to within 24 hours,” Schädel said. “They are really excited about this project.” The team also plans to host virtual workshops that bring together modelers and experimentalists to share findings and new approaches.

Temperature records set in Siberia this June—air temperature topped 100 degrees Fahrenheit–demonstrate how urgent this research is, Schädel said. “It shows it’s not in the far future—things are changing now. Not too long ago, there was the assumption that not much is happening in the Arctic. And now it’s very obvious.”

Volunteers from the Institute for Tribal Environmental Professionals and the Center for Ecosystem Science and Society (Ecoss) at Northern Arizona University were visiting the class to talk about extremophiles — microbes that thrive in harsh conditions.

“Why are heat-loving bacteria important for compost piles?” Ecoss volunteer Pete Chuckran asked. “Feel free to annotate an answer.”

A few seconds passed. Then, in that miracle that has become commonplace since many of us moved our lives to Zoom, typing appeared on the slide: It’s beneficial to have different kinds of specialists in the compost, a student named Braiden Lynch suggested, rather than to have bacteria that all do their decomposing work under identical conditions.

“Great answer,” Chuckran said. Others chimed in in the chat. “Nice!” From her Zoom box, teacher Reny Mathew smiled.

The session was part of a STEM (Science Technology Engineering Math) summer enrichment program at Greyhills, where Mathew has been teaching and promoting STEM education for 13 years. This summer, her class is working virtually with the NAU engineers and scientists on a range of topics, including air quality monitoring, composting, soil analysis and coding.

This course is part of what Mathew calls her “homegrown STEM program,” which includes afterschool and summer programming, internships, and opportunities for students to present their research at science fairs on the Navajo Nation and in the wider region.

“The program is challenging,” Mathew said. “It takes a lot of their after-school time. But how much time do I have? Just these four years.”

The students’ commitment is evident: many of those enrolled in her STEM program work on the same research topic across multiple years, and are selected for competitive summer internships through the Native American Science and Engineering Program, the Indigenous Summer Enhancement Program at Dine College and elsewhere. Her students have received the Chief Manuelito Scholarship, a prestigious Navajo Nation award for undergraduate education, and prizes at the Arizona Science and Engineering Fair.

This year, four of Mrs. Mathew’s students presented at the state-level science fair: Sykora Chief (the antimicrobial properties of sage), Maria Bizahaloni (soil properties across an elevation gradient from Page to Flagstaff), and Marina and Beatriz Rodriguez, who demonstrated that low-cost, indoor air filters made of natural charcoal can be used to remove wood-stove associated pollution in homes. The Rodriguez team took second place in the environmental engineering division.

“I have developed countless skills during my time in Mrs. Mathew’s STEM program,” said Marina Rodriguez, who graduated as Greyhills salutatorian this year. “Besides learning about different science topics, I have been able to increase my communication skills, writing skills, and analytical-thinking skills. The STEM program has given me the opportunity to experience the professional scientific world while still in my high school years.”

Introducing the students to professional scientists and science skills has been a primary goal for Ayla Martinez, a graduate student at Ecoss who coordinated the team’s efforts. Martinez, who was born in Nogales, said coming from a border town influenced how she came to science, and the research questions she asks now: “I wanted to help students access the kinds of opportunities and tools that helped me choose a career in biology.”

When the pandemic forced remote instruction in 2020, Mrs. Mathew’s class faced extra challenges: reliable internet can be inconsistent or hard to access on the vast Navajo Nation. But Mathew said her students persisted and stayed engaged. Through the partnership with ITEP’s Environmental Education Outreach Program, coordinated by Julaire Scott, they received science kits to learn from home about composting and air quality.

“Since we typically hold outreach sessions in person with hands on activities, it was a learning curve for us to make the presentations as engaging as possible,” Scott said. She was impressed with the students’ final presentations and how they synthesized the online lessons.

The pandemic also provided a real-world opportunity to discuss the importance of reliable sources, Martinez said. “We were deep into the pandemic, and all this information was out there about COVID,” she said. “We wanted to give power to these students by making sure they knew how to identify reliable sources of information — in their research and in the news.”

Rodriguez said the reliable source seminars were helpful and provided her resources such as databases where she can verify information in the future. “They introduced me to the importance of finding the truth and using it in my scientific research.”

Jeff Propster, one of the team members, appreciates how Mathew invites her students to shape the after-school curriculum. “The group was close enough and we were flexible enough to tailor our help to what they wanted to learn,” he said.

This spring, the students asked the NAU team to act as an audience as they practiced their presentations for the Arizona Science and Engineering Fair in April.

Mathew is proud of how Greyhills students have become a fixture at the state science fair: “I see very few Navajo students there, but we are always there.”

Martinez agreed that representation is critical as students learn about potential career paths. As many in the sciences grapple with racism and other structural barriers that have led to a lack of diversity and equity in research, Martinez said her team’s collaboration with ITEP and Greyhills is a small step toward a more inclusive research community.

“It’s important that we help show that anyone can be part of STEM,” she said.

The team from Ecoss is also offering an introduction to coding in the programming language R this summer and plans to offer sessions again in the fall.

“The sophistication of their research questions is so impressive to me,” Propster said. “In a year where there were all these hurdles, it was really inspiring that these kids were willing to meet after school — on the internet again — to do science.”

Mansel Nelson, director of the ITEP Environmental Education Outreach Program, has worked with Mathew’s science classes for several years and helped connect her with NAU researchers, including the Ecoss team and professor Jani Ingram, who researches environmental contaminants and their health impacts.

“Reny provides opportunities for her students beyond the typical classroom,” Nelson said.

“It’s not just doing a little experiment,” Mathew said. “It’s about learning how to do extensive research and learning to communicate that. It’s challenging. But it will bring the best out of them. That is what I have seen.”

The findings, led by research specialist Melissa Boyd and Regents’ professor Michelle Mack of the Center for Ecosystem Science and Society and published in Ecosphere, offer more clues to the scientific mystery of what causes trees to die, and a possible preview of these forests’ future as the climate warms. NAU assistant research professors Xanthe Walker and Logan Berner, Regents’ professor Scott Goetz, and postdoctoral researcher Adrianna Foster also contributed to the study.

“Climate warming in the boreal forest has brought with it more frequent drought and insect outbreaks,” Boyd said. “It’s important we understand how these increasingly common events might alter the fate of aspen in northern forests.”

Boyd and her team used tree rings, long-term ecological data, and satellite imagery to reconstruct the story of eight sites in interior Alaska that experienced aspen mortality during the leaf miner outbreak between 1997-2013. They found that a 1957 drought hampered the growth of some trees.  Decades later, those trees, light-starved in the sub-canopy, were predisposed to die during the insect outbreak.

The researchers also found that the “normalized difference vegetation index,” a satellite-based measurement of vegetation productivity, did a better job at capturing the growth of living trees than it did the insect-wrought fate of dying trees that were in the lower canopy. To accurately detect insect-driven growth declines and mortality of aspen, and thus create a fuller picture of what’s happening to these forests, the researchers suggest that we cannot solely rely on NDVI.

“As the northern latitudes grow warmer, forests that were historically dominated by conifers are shifting to deciduous-dominated ones,” said Mack, the study’s senior author. “As they do, threats to these deciduous trees become a matter of global concern. It’s imperative we learn more about how and why these trees die.”

Boyd enjoys working with aspen in part because their histories can be challenging to read, given their indistinct ring boundaries. She said her findings about what caused certain trees to die raises more questions about the trees that survive. “Can the growth of surviving aspen recover after a leaf miner outbreak?” Boyd asked. “How resilient are these trees, and how much damage can they sustain?”

Like every other life form on earth, bacteria belong to intricate food webs in which organisms are connected to one another by whom they consume and how. In macro webs, ecologists have long understood that when resources like grass and shrubs are added to lower levels of the web, predators at the top, such as wolves, often benefit. The research team, led by Bruce Hungate and researchers from Northern Arizona University and Lawrence Livermore Laboratory, wanted to test whether the same was true in the microbial food webs found in wild soil.

“We’ve known predation plays a role in maintaining soil health, but we didn’t appreciate how significant predator bacteria are to these ecosystems before now,” said Hungate, who directs the Center for Ecosystem Science and Society at Northern Arizona University.

To understand who and how much predator bacteria were consuming, the research team assembled a big picture using dozens of smaller data “snapshots”: 82 sets of data from 15 sites in a range of ecosystems. The team used information about how bacteria behave in culture to categorize bacteria as obligate or facultative predators. About seven percent of all bacteria in the meta-analysis were identified as predators, and the majority of those were facultative, or omnivorous.

Obligate predatory bacteria like Bdellovibrionales and Vampirovibrionales grew 36 percent faster and took up carbon 211 percent faster than non-predators did. When the soil received a boost of carbon, predator bacteria used it to grow faster than other types. Researchers saw these effects in the omnivorous bacteria, as well, though the differences were less profound.

All the experiments were conducted using a state-of-the-art technique called quantitative Stable Isotope Probing, or qSIP. Researchers used labeled isotopes, which act a little like molecular hashtags, to track who is active and taking up nutrients in the soil. By sequencing the DNA in a soil sample and looking for these labels, the team could see who was growing and eating whom at the level of bacterial taxa.

“While analyzing my data, I noticed that Vampirovibrio was super enriched. Since we know Vampirovibrio is a predator, I became interested in looking for other potential predators in my other data,” said Brianna Finley, a postdoctoral research at University of California-Irvine and co-author on the study. “That we could pick up on these signals really validates qSIP as a tool.”

Soil ecosystems contain more carbon than is stored in all the plants on Earth, so understanding how carbon and other elements move among soil organisms is crucial to predicting future climate change. And because bacteria are so abundant in soil, they have an enormous role in how nutrients are stored there or lost. And learning more about how predator bacteria act as ‘antibiotics’ could have therapeutic implications, down the road.

“Until now, predatory bacteria have not been a part of that soil story,” said Hungate. “But this study suggests that they are important characters who have a significant role determining the fate of carbon and other elements. These findings motivate us to take a deeper look at predation as a process.”