Press Coverage: 

The NAU Review • Date: Dec 26, 2024. (Coverage of Koch et al. 2024 in Communications Medicine.) NAU Review 

Publication: 

https://www.nature.com/articles/s43856-024-00693-7

Press Coverage: 

The NAU Review • Date: Feb 6, 2025. (Context for the Science special collection on the Arctic; quotes Regents’ Prof. Ted Schuur.) NAU Review

Publication: 

https://www.science.org/doi/abs/10.1126

“Here, we document the tractability of Epithemia spp. as an ecological model system for studies of how elemental fluxes scale through levels of biological and ecological organization in nature.”

Their results and those of others suggest that endosymbioses may help drive biogeochemical cycles and support productive food webs in many N-limited aquatic ecosystems. Deeper understanding of how Epithemia functions in nature should guide further discovery of its role in food webs and the conditions and selective pressures that influenced the evolution of its diazoplast from endosymbiont to proto-organelle.

Press Coverage in Earth.com: 

https://www.earth.com/news/salmon-have-their-own-secret-superfood-epithemia-diatoms-created-in-healthy-rivers-aids-survival/

PNAS paper: 

https://www.pnas.org/doi/10.1073/pnas.2503108122

A team of more than 40 scientists has been awarded $9.6 million by the National Science Foundation to investigate these and a web of connected questions in interior Alaska as part of the Bonanza Creek Long-Term Ecological Research Program (LTER). The project also is supported by the USDA Forest Service Pacific Northwest Research Station.  

Michelle Mack, principal investigator and Regents’ professor of biology at the Center for Ecosystem Science and Society at Northern Arizona University, said the next stage of research will happen over a potentially transformative period for the Arctic’s boreal forests.  

“We’ve seen how dramatic changes to fire and permafrost in the boreal forest caused by climate warming have already disrupted the way these ecosystems have stabilized themselves for millennia,” Mack said. “Over the next six years, we are going to observe how those legacies and disruptions are shaping the forest’s future and the future for communities who depend on the boreal forest.” 

Mack’s team will be asking how human activity has shaped the forests’ history, working with Alaska Native tribes to develop research questions that are relevant to their communities and roles managing fire today. The program also will convene an Alaska Native Advisory Council to better include Native communities’ perspectives and research priorities. 

Research over the next six years, which will be co-led by NAU investigators Ted Schuur, Xanthe Walker, Logan Berner, Scott Goetz and expert collaborators from nine academic institutions, the U.S. Forest Service and the U.S. Geological Survey, will build on decades of previous data collected through the Bonanza Creek LTER program since 1987. Bonanza Creek, based at the University of Alaska-Fairbanks Institute of Arctic Biology, is one of 28 LTER sites in the country. 

The team will work at a network of sites across interior Alaska investigating interlinked topics, including how fire affects successional trajectories, how permafrost thaw is changing hydrology in the region, how soil microbes are responding to warming and how the aspen leaf miner insect and plant pathogens like aspen running canker could determine the future ability of aspen to thrive and reproduce in the region.  

The team has found that increasingly frequent and intense fires in the boreal forest have resulted in faster-growing deciduous trees like paper birch and trembling aspen moving in where slower-growing but more flammable black spruce once dominated. Over the next six years, they will monitor a wider series of forest plots that have burned at different times, including some only reachable by helicopter, to construct a kind of time-lapse that illustrates how these forests are re-growing and changing, and what role fire plays. 

“Our work at Bonanza Creek LTER has shown us how uncertain the future of the Arctic boreal forest is,” Mack said. “The next stage is for this really talented team to map out what kinds of futures are possible and probable, and how humans will play a role in shaping them.” 

“What happens in the lab and what happens in wild soil are often worlds apart, and we need to be testing and challenging ideas about bacteria and microbes from the lab with what we see in the field,” said lead author Bram Stone, who conducted the research at NAU’s Center for Ecosystem Science and Society (Ecoss) and is now a Linus Pauling Postdoctoral Fellow at Pacific Northern National Laboratory. “Many of our society’s most urgent questions about carbon storage and how soils will respond to climate change rely on understanding better how microbes act in nature.” 

Suppose it is true that societal needs can sometimes accelerate the rate science is done through funding and policy prioritization. In that case, it’s also true that some fields are rapidly advancing yet still playing catchup to accelerating challenges like the climate crisis. Microbial ecology has grown by leaps and bounds in recent years as modern sequencing technology improves, becomes more widely available and gets applied in new ways. And yet, as global carbon budgets have tightened and human-caused emissions continue to fuel non-linear climate impacts, the need for knowing what the microbes will do in a warmer world has arguably accelerated even faster. Figuring out not only which microbes are where but who’s growing, who’s dying, what environmental factors affect their lives and how they interact is still a game of catchup. New data are needed to confirm or complicate some of the broad frameworks that scientists have used to make sense of this invisible world. Such conceptual frameworks and new data to test them are both necessary parts of the process to better understand microbial communities and their importance in supporting healthy soil and cycling carbon and other nutrients. 

Stone says the team’s findings echo the shift from hard categories toward statistically derived trait spectrums in other fields, including psychology. (Think the move away from the Myers-Briggs test toward the trait-based spectrum of “the Big Five” personality factors.)  

“Our goal is to identify the most salient microbial traits that determine actual behavior in the soil and that determine things like energy flow,” Stone said. “And we want to express those traits numerically. With a tool like that, we can make better predictions of how microbial communities react to climate change, or pollution, or a new crop rotation in an agricultural field.” 

 The study relies on data gathered via quantitative stable isotope probing, or qSIP, a technique that uses stable isotopes or atoms labeled with an extra neutron to track the fate of a water or sugar molecule through soil. Researchers analyze a sample of wild soil treated with this labeled water or sugar and look for where that molecular hashtag appears in DNA—meaning it has been incorporated by a microbe. By sequencing the DNA in that soil sample at different points in time, researchers at NAU, where the technique was developed, can see which microbes grew—and by how much—and how quickly the community changed.  

“It’s so exciting to me that we can get the data in nature, rather than speculate,” said Bruce Hungate, director of Ecoss and a co-author of the new study. “Being able to conduct microbiology in the field like this means we can reasonably scale up to predict fluxes for an entire ecosystem or region, all while retaining the high taxonomic resolution available from modern sequencing.” 

Other collaborators on the study include Paul Dijkstra, Raina Fitzpatrick, Megan Foley, Michaela Hayer, Ben Koch, Junhui Li, Ayla Martinez, Jane Marks, Rebecca Mau, Egbert Schwartz and Alicia Purcell of Ecoss, Lawrence Livermore National Laboratory, Pacific Northwest National Laboratory, University of California-Irvine, West Virginia University and the Institute for Environmental Genomics at the University of Oklahoma. This research was supported by grants from the U.S. Department of Energy’s Biological Systems Science Division Program in Genomic Science and the LLNL ‘Microbes Persist’ Soil Microbiome Scientific Focus Area and by the National Science Foundation. 

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.