Arctic peatlands store vast amounts of carbon. As global temperatures increase and environments change in response, the stability of the carbon stored in these habitats has emerged as a pressing concern. Researchers delved deep into the soil microbiome, scrutinizing the functions of thousands of microorganisms in an Arctic peatland ecosystem. Contrary to previous assumptions, the study revealed that many microorganisms metabolize polyphenols. Scientists had believed that this complex class of carbon compounds was inert and an important part of carbon storage. Armed with this new insight, scientists are better equipped to forecast the impacts of climate change on Arctic ecosystems and devise targeted strategies for mitigating these effects.

Peatlands have long intrigued scientists as reservoirs of terrestrial carbon, yet the role of microorganisms in carbon cycling has remained enigmatic. Contrary to past assumptions, this new research challenges the notion that peatland microorganisms exclusively degrade polyphenols under oxygenated conditions using phenol oxidase. Drawing from insights derived from other oxygen-limited environments like the human gut and rumen, where alternative enzymes and pathways metabolize polyphenols, the research team developed a novel computational tool to rapidly profile polyphenol metabolisms in microbial genomes. This software, applied to thousands of microbial genomes sampled from an Arctic peatland, unveiled a surprising diversity of polyphenol-transforming biochemical pathways. Remarkably, certain microorganisms encoded a profusion of these genes, signifying a polyphenol degradation prowess. Furthermore, the findings highlight the adaptability of microbial gene expression to shifts in soil redox conditions across the landscape.

By uncovering this hidden biochemistry, this research pioneers a new understanding of carbon cycling in these climate critical ecosystems. These insights not only expand knowledge of microbial metabolism but also underscore the intricate interplay between microorganisms and carbon dynamics in the face of climate change.

This material was based on work supported by the Department of Energy (DOE) Office of Science, Biological and Environmental Research Program, as well as the National Sciences Foundation Biological Integration Institute. A portion of this research was performed under the DOE Facilities Integrating Collaborations for User Science program and used resources at the Joint Genome Institute and the Environmental Molecular Sciences Laboratory, both DOE Office of Science user facilities.

The microorganisms belong to the genus Acetobacterium and they are commonly found in wastewater environments throughout the world.

Forever chemicals, also known as per- and polyfluoroalkyl substances or PFAS, are so named because they have stubbornly strong carbon-fluorine chemical bonds, which make them persistent in the environment.

The microorganisms discovered by UCR scientists and their collaborators can cleave those stubborn fluorine-to-carbon bonds, they reported Wednesday, July 17, in the journal Science Advances.

“This is the first discovery of a bacterium that can do reductive defluorination of PFAS structures,” said Yujie Men, corresponding author of the study and an associate professor at UCR’s Bourns College of Engineering in the Department of Chemical and Environmental Engineering.

Men cautioned that the bacteria were effective only on unsaturated PFAS compounds, which have double carbon-to-carbon bonds in their chemical structures.

But importantly, the scientists also identified the specific enzymes in these bacteria essential for cleaving the carbon-fluorine bonds. This discovery opens the door for bioengineers to improve these enzymes so they can be effective on other PFAS compounds. (Enzymes are proteins that act as catalysts for biochemical reactions.)

“If we can understand the mechanism, maybe we can find similar enzymes based on the identified molecular traits and screen out more effective ones,” Men said. “Also, if we can design some new enzyme or alter this known enzyme based on the mechanistic understanding, we could be able to make it more efficient and work with a broader range of PFAS molecules .”

Last year, Men published a paper that identified other microorganisms that cleave the carbon-chlorine bond in chlorinated PFAS compounds, which triggers substantial spontaneous defluorination and destroys this group of pollutants. The most recent discovery greatly expands the number of PFAS compounds that can be destroyed biologically. Using bacteria to treat groundwater is cost effective because the microorganisms destroy pollutants before the water reaches wells. The process involves injecting the groundwater with the preferred bacteria species along with nutrients to increase their numbers.

Because PFAS compounds are linked to cancer and other human health maladies, the U.S. Environmental Protection Agency, or EPA, imposed water-quality limits earlier this year that restrict certain forever chemicals to only four parts per trillion in the nation’s tap water, spurring water providers to find PFAS cleanup solutions.

PFAS compounds came into widespread use in thousands of consumer products starting in the 1940s because of their ability to resist heat, water, and lipids. Examples of PFAS-containing products include fire suppressant foams, grease-resistant paper wrappers and containers such as microwave popcorn bags, pizza boxes, and candy wrappers; also, stain and water repellents used on carpets, upholstery, clothing, and other fabrics; according to the EPA.

The paper’s title is “Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. Drive defluorination of perfluorinated unsaturated carboxylic acids.” Yaochun Yu is the lead author. He was a visiting student scientist and a UCR post-doctoral scientist at UCR before joining the Swiss Federal Institute of Aquatic Science and Technology, or Eawag, in 2022.

In addition to Yu and Men, the co-authors authors are Fengjun Xu, Weiyang Zhao, Calvin Thoma, Shun Che, Jack E. Richman, Bosen Jin, Yiwen Zhu, Yue Xing, and Lawrence Wackett.

Using satellite measurements of cloud cover and the solar radiation reflected by sea ice between 1980 and 2023, the researchers found that the percent decrease in sea ice’s cooling power is about twice as high as the percent decrease in annual average sea ice area in both the Arctic and Antarctic. The added warming impact from this change to sea ice cooling power is toward the higher end of climate model estimates.

“When we use climate simulations to quantify how melting sea ice affects climate, we typically simulate a full century before we have an answer,” said Mark Flanner, professor of climate and space sciences and engineering and the corresponding author of the study published in Geophysical Research Letters.

“We’re now reaching the point where we have a long enough record of satellite data to estimate the sea ice climate feedback with measurements.”

The Arctic has seen the largest and most steady declines in sea ice cooling power since 1980, but until recently, the south pole had appeared more resilient to the changing climate. Its sea ice cover had remained relatively stable from 2007 into the 2010s, and the cooling power of the Antarctic’s sea ice was actually trending up at that time.

That view abruptly changed in 2016, when an area larger than Texas melted on one of the continent’s largest ice shelves.The Antarctic lost sea ice then too, and its cooling power hasn’t recovered, according to the new study. As a result, 2016 and the following seven years have had the weakest global sea ice cooling effect since the early 1980s.

Beyond disappearing ice cover, the remaining ice is also growing less reflective as warming temperatures and increased rainfall create thinner, wetter ice and more melt ponds that reflect less solar radiation. This effect has been most pronounced in the Arctic, where sea ice has become less reflective in the sunniest parts of the year, and the new study raises the possibility that it could be an important factor in the Antarctic, too — in addition to lost sea ice cover.

“The changes to Antarctic sea ice since 2016 boost the warming feedback from sea ice loss by 40%. By not accounting for this change in the radiative effect of sea ice in Antarctica, we could be missing a considerable part of the total global energy absorption,” said Alisher Duspayev, doctoral student in physics and the study’s first author.

The research team hopes to provide their updated estimates of sea ice’s cooling power and climate feedback from less reflective ice to the climate science community via a website that is updated whenever new satellite data is available.

“Climate change adaptation plans should bring aboard these new numbers as part of the overall calculus on how rapidly and how widely the impacts of cryospheric radiative cooling loss will manifest on the global climate system,” said Aku Riihelä, research professor at the Finnish Meteorological Institute and co-author of the study.

The research was funded by the University of Michigan Rackham Graduate School and the Research Council of Finland.

Mark Flanner is also a professor of earth and environmental sciences at the College of Literature, Science, and the Arts.

Opioids are the gold standard of chronic pain treatment, but they come with a host of negative side effects including constipation, addiction potential and respiratory depression that can lead to death. This study, published in Scientific Reports, offers a potential new way to treat acute and chronic pain by reducing the amount of opioid needed for pain relief while also lowering its addiction potential.

“We have been investigating the role of Heat shock protein 90 in regulating opioid signaling in the spinal cord for some time,” said John Streicher, PhD, member of the Comprehensive Center for Pain & Addiction at UArizona Health Sciences and a professor in the College of Medicine — Tucson’s Department of Pharmacology. “This study provides proof of principle that Hsp90 isoform inhibitors are effective at improving opioid pain relief and reducing side effects. This is the critical link that makes our work translationally relevant, giving us a clear path forward to develop a new drug that could benefit millions of people who live with chronic pain.”

Heat shock protein 90 is a chaperone protein that helps other proteins function, including those that promote tumor growth. It has been studied primarily in the context of cancer. Streicher is leading in a long-term effort to investigate its role in opioid receptor activation and pain relief.

Streicher’s prior research showed that Heat shock protein 90 acted upon opioid receptors in the brain differently than in the spinal cord. Inhibiting Hsp90 in the brain blocked the analgesic properties of morphine, meaning the opioid lost its ability to reduce the sensation of pain. But inhibiting Hsp90 in the spinal cord amplified the pain-relieving effects of morphine.

Building on that research, the team tested nonselective Hsp90 inhibitors in mouse models and saw a twofold-to-fourfold increase in the potency of pain relief provided by morphine. At the same time, tolerance was reduced and established tolerance was reversed. Tolerance is a condition where the body gets used to a medication so that more medication or a different medication is needed to achieve the same response.

Early cancer-focused studies, however, found that nonselective Hsp90 inhibitors can cause serious side effects, including macular degeneration. Streicher’s solution was to target individual isoforms of Hsp90, of which there are four.

“Isoforms are different versions of the same thing, like trim packages on a car,” Streicher said. “They are all slightly different and have similar roles, but not identical roles. So these four Hsp90 isoforms are four proteins that we can target individually.”

By using selective inhibitors to target each isoform, they were able to identify and isolate the isoforms that are active in the spinal cord from Hsp90-alpha, the one that is active in the brain. Recent reports have linked Hsp90-alpha with the serious side effect of retinal degeneration.

“We took isoform-selected inhibitors that we got from our collaborator, Brian Blagg, PhD, at the University of Notre Dame, and gave them to mice systemically via IV injection,” Streicher said. “We found that you can give these isoform-selective inhibitors by a translatable route and get the benefits. Pain relief goes up and side effects go down, and presumably we’re going to avoid some of those nasty side effects of the nonselective Hsp90 inhibitors.”

The findings suggest that selective Hsp90 inhibitors could be used as part of a dose-reduction plan in conjunction with opioid therapy prescribed by a physician for chronic pain. The goal is for doctors to be able to prescribe lower amounts of opioids that provide patients with the same pain-relieving benefits and fewer negative side effects.

“What I’m envisioning is you’d be given a pill that is a combination therapy of an opioid with one of these isoform inhibitors,” Streicher said. “The addition of that Hsp90 inhibitor would make the opioid better — it would increase the effectiveness of the pain relief and decrease the side effects.”

Streicher and his team are working to optimize the selective Hsp90 inhibitors to produce a stable drug that can be taken orally.

“Dr. Streicher’s research is an excellent example of the innovative, translational science that is needed to transform health care for pain and addiction,” said Todd Vanderah, PhD, director of the Comprehensive Center for Pain & Addiction, Regents Professor and head of the Department of Pharmacology. “This study is an important step toward developing a novel evidence-based therapy that will provide better treatment options with fewer disruptive side effects, empowering people with chronic pain to thrive.”

The research team included four co-first authors: David Duron, PhD, JD, former doctoral candidate in the Streicher Lab; Parthasaradhireddy Tanguturi, PhD, researcher/scientist in the Department of Pharmacology; former doctoral candidate Christopher Campbell, PhD; and Kerry Chou, former undergraduate student at the UArizona College of Nursing. Other co-authors included Paul Bejarano, and former doctoral candidates Katherin Gabriel, PhD, and Jessica Bowden, DVM, PhD, all of the Department of Pharmacology; Sanket Mishra, PhD, Christopher Brackett, PhD, and Brian Blagg, PhD, of the Department of Chemistry and Biochemistry at the University of Notre Dame’s College of Science; and Deborah Barlow and Karen Houseknecht, PhD, of the Department of Biomedical Sciences at the University of New England’s College of Osteopathic Medicine.

Bacteria have developed special defense mechanisms to protect themselves against viruses, which by no means infect only humans. As part of these so-called CRISPR-Cas systems, a CRISPR ribonucleic acid (crRNA), which serves as a “guide RNA,” recognizes regions of a foreign genome, such as viral DNA. The CRISPR-associated (Cas) nuclease, directed by a crRNA, then renders it harmless by cutting it like a pair of scissors. Humans have exploited this strategy: “CRISPR, often referred to as ‘gene scissors’, is the basis of many molecular technologies,” says Chase Beisel, head of the RNA Synthetic Biology department at the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg. The institute is a site of the Braunschweig Helmholtz Centre for Infection Research (HZI) in cooperation with the Julius-Maximilians-Universität (JMU) of Würzburg, where Beisel holds a professorship.

The diagnostic platform LEOPARD, developed by Beisel’s lab in cooperation with JMU in 2021, also leverages CRISPR as a technology. LEOPARD has the potential to detect a variety of disease-related biomarkers in just one test. The approach is based on reprogramming RNA factors, so-called tracrRNAs. Those RNAs are naturally involved in helping produce guide RNAs used by Cas9 and different Cas12 nucleases. “LEOPARD focused on Cas9. However, CRISPR-Cas systems also include another diverse set of nucleases, called Cas12,” explains Beisel. While both Cas9 and Cas12 cut DNA targets, Cas12 can increase the output signal by performing cuts on “collateral” DNA. This can make detection technologies more sensitive and, therefore, more efficient.

The team led by Chase Beisel has now extended the unique features of LEOPARD to Cas12. The researchers have named the resulting method PUMA (Programmable tracrRNAs Unlock protospacer-adjacent Motif-independent detection of ribonucleic Acids by Cas12 nucleases). The details of their findings are the subject of a paper in the journal Nature Communications.

Overcoming hurdles

Although Cas12 nucleases are widely used in molecular diagnostics, two major limitations have persisted: Cas12-based technologies have been restricted to DNA targets, and a specific recognition sequence called a PAM, short for protospacer-adjacent motif, is required to identify the target molecule.

PUMA elegantly addresses these challenges. Like LEOPARD, this new method also relies on tracrRNAs. “Using PUMA, we can reprogram the tracrRNAs. This allows us to decide which RNA biomarker becomes a guide RNA. This guide RNA, in turn, directs Cas12 to a DNA molecule that we provide and activates the gene scissors,” explains the study’s first author, Chunlei Jiao. Chunlei Jiao, a former graduate student and postdoctoral researcher in the Beisel lab, was also involved in the development of LEOPARD. He recently started a professorship at the National University of Singapore. “DNA cutting then tells us which biomarker was present in the sample, such as biomarkers specific to different pathogens,” adds Beisel.

The novel method therefore enables the detection of RNA biomarkers using CRISPR nucleases that can normally only recognize DNA. “This is particularly important for molecular biomarkers that can only be found at the RNA level. This includes RNA viruses, for example,” says Beisel. And yet, PUMA does not require a specific recognition sequence: The PAM is contained in the DNA target molecule provided. Since the researchers provide the target molecule, they can also introduce truncated DNA. As a result, they were able to significantly increase the speed of the method.

Several birds, one stone

“PUMA has the potential to become a flexible and precise tool for RNA detection,” concludes Beisel. Finally, the team demonstrated the potential of the method by identifying five bacterial pathogens associated with acute sepsis. Their detection relied on a single universal, reprogrammed tracrRNA, which provides a simplified means of differentiating between various types of bacteria. This opens up a wide range of potential applications in medicine: “The new technology represents a novel form of CRISPR diagnostics that enables reliable molecular testing at the point of care — whether for the identification of viral or bacterial pathogens or the detection of cancer biomarkers,” says Jiao.

The research team is already planning its next steps: “Our goal is to achieve a multiplexed readout similar to that of LEOPARD and to expand the range of applications for the technology,” says Beisel, who also anticipates broad use in the research community: “We hope that our study will spur further exploration of tracrRNA reprogramming.”