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. 

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.”

The terrestrial biosphere—the activity of land plants and soil microbes—does much of Earth’s ‘breathing,’ exchanging carbon dioxide and oxygen. Ecosystems across the globe pull in carbon dioxide through photosynthesis and release it back to the atmosphere via the respiration of microbes and plants. Over the past few decades, the biosphere has generally taken in more carbon than it has released, mitigating climate change.

But as record-breaking temperatures continue to spread across the globe, this may not continue; the NAU and Waikato researchers have detected a temperature threshold beyond which plant carbon uptake slows and carbon release accelerates.

Lead author Katharyn Duffy, a postdoctoral researcher at NAU, noticed sharp declines in photosynthesis above this temperature threshold in nearly every biome across the globe, even after removing other effects such as water and sunlight.

“The Earth has a steadily growing fever,” said Duffy, “and much like the human body, we know every biological process has a range of temperatures at which it performs optimally, and ones above which function deteriorates. So we wanted to ask, how much can plants withstand?”

This study is the first to detect a temperature threshold for photosynthesis from observational data at a global scale. While temperature thresholds for photosynthesis and respiration have been studied in the lab, the Fluxnet data provide a window into what ecosystems across Earth are actually experiencing and how they are responding.

“We know that the temperature optima for humans lie around 37^oC (98^oF),” Duffy said, “but we in the scientific community didn’t know what those optima were for the terrestrial biosphere.” She teamed up with two researchers at the University of Waikato in New Zealand who recently developed a new approach to answer that question: MacroMolecular Rate Theory (MMRT). With its basis in the principles of thermodynamics, MMRT allowed the researchers to generate temperature curves for every major biome and the globe.

The results were alarming.

The researchers found that temperature “peaks” for carbon uptake —18^oC for the more widespread C3 plants and 28^oC for C4 plants— are already being exceeded in nature, but saw no temperature check on respiration. This means that in many biomes, continued warming will cause photosynthesis to decline while respiration rates rise exponentially, tipping the balance of ecosystems from carbon sink to carbon source and accelerating climate change.

“Different types of plants vary in the details of their temperature responses, but all show declines in photosynthesis when it gets too warm,” said NAU co-author George Koch.

Right now, less than 10 percent of the terrestrial biosphere experiences temperatures beyond this photosynthetic maximum. But at the current rate of emissions, up to half the terrestrial biosphere could experience temperatures beyond that productivity threshold by mid-century—and some of the most carbon-rich biomes in the world, including tropical rainforests in the Amazon and Southeast Asia and the Taiga in Russia and Canada, will be among the first to hit that tipping point.

“The most striking thing our analysis showed is that the temperature optima for photosynthesis in all ecosystems were so low,” said Vic Arcus, a biologist at the University of Waikato and co-author of the study. “Combined with the increased rate of ecosystem respiration across the temperatures we observed, our findings suggest that any temperature increase above 18^oC is potentially detrimental to the terrestrial carbon sink. Without curbing warming to remain at or below the levels established in the Paris Climate Accord, the land carbon sink will not continue to offset our emissions and buy us time.” 

Funding for this research was provided by the National Aeronautics and Space Administration (grant NNX12AK12G), National Science Foundation (NSF) East-Asia Pacific Summer Institute Fellowship (1614404), the Royal Society of New Zealand Foreign Partnership Programme (EAP- UOW1601) and the New Zealand Marsden Fund (grant 16-UOW-027). This work used eddy covariance data acquired and shared by the FLUXNET community, including AmeriFlux, AfriFlux, AsiaFlux, CarboAfrica, CarboEuropeIP, CarboItaly, CarboMont, ChinaFlux, Fluxnet-Canada, GreenGrass, ICOS, KoFlux, LBA, NECC, OzFlux-TERN, TCOS-Siberia, and USCCC networks.