New Study Sheds Light on Ancient Microbial Dark Matter

DRI contributes to international team of scientists that unearths first in-depth look at Omnitrophota, one of the world’s oldest and tiniest bacteria 

DRI’s Duane Moser, Ph.D., is a coauthor on a new study in Nature Microbiology that offers the first detailed analysis of a globally prominent, but poorly characterized type of bacteria belonging to a group scientists refer to as “microbial dark matter.” Formally described here for the first time as the Omnitrophota, the existence of this phylum of bacteria was first inferred from environmental DNA nearly thirty years ago.    

“This paper illuminates the properties and ecological function of a group of ubiquitous, but poorly understood organisms,” said Moser, associate research professor of microbiology.  

Moser’s contribution to the study included identifying field sites and collecting samples, as well as developing an understanding of environmental context. His long-standing research relationship with the lead authors of the study meant that collaborative projects over the years led to a number of useful datasets for the analysis.  

“The research community has followed the Omnitrophota story since the 1990s, when earlier groundbreaking studies that revealed unexpected diversity within Archaea at Obsidian Pool in Yellowstone National Park were expanded to include bacteria,” Moser says. “In those days, full genomes of uncultivable microorganisms were beyond the reach of available technologies, so a conserved gene that encodes an essential structure shared by all cellular life (the 16S rRNA gene) was used to identify novel life and estimate relatedness between organisms.” 

“What scientists found was so different from anything that had been described previously that scientists of the time proposed that Omnitrophota might be a novel phylum within Bacteria (the equivalent of the evolutionary difference between plants and animals). This interpretation has stood the test of time,” Moser continued.  

“Over the past several decades, Omnitrophota has been frequently encountered in aquatic and soil samples worldwide. In our own work in springs, mines, and shallow groundwaters, Omnitrophota have often been among the more prominent microbial groups detected. I sometimes wonder if the sheer abundance and evident diversity of this omnipresent group has intimidated researchers from tackling its formal description. This was an ambitious project that required the combined expertise of a strong team of collaborators.”   

Brian Hedlund, a microbiologist at the University of Nevada, Las Vegas, and lead author of the study, said “Duane’s knowledge of the geology and hydrology of subsurface environments — and how to sample them meaningfully — was really important for this study.” 

Below is the full press release from the University of Nevada, Las Vegas.   

LAS VEGAS – March 16, 2023 – Bacteria are literally everywhere – in oceans, in soils, in extreme environments like hot springs, and even alongside and inside other organisms including humans. They’re nearly invisible, yet they play a big role in almost every facet of life on Earth.  

Despite their abundance, surprisingly little is known about many microorganisms that have existed for billions of years.  

This includes an entire lineage of nano-sized bacteria dubbed Omnitrophota. These bacteria, first discovered based on short fragments of DNA just 25 years ago, are common in many environments around the world but have been poorly understood. Until now.  

An international research team produced the first large-scale analysis of more than 400 newly sequenced and existing Omnitrophota genomes, uncovering new details about their biology and behavior. The team’s findings are reported in the March 16 issue of the journal Nature Microbiology.  

“We now have the most comprehensive view to date of the biology of an entire phylum of microorganisms and the surprising role they play in the Earth’s ecosystems,” said UNLV microbiologist Brian Hedlund, the study’s corresponding author. “There is a finite number of major lineages of life on our planet, and it’s exciting to learn more about organisms that pre-date plants and animals and have been essentially hidden under our noses.”  

The tricky thing with Omnitrophota is that they’re still largely considered microbial dark matter, which means they exist in nature but can’t yet be cultivated as single species in lab studies. Just two species have been microscopically observed, and only very recently.  

To present a comprehensive picture of their biology, scientists compared 349 existing and 72 newly mapped genomes of Omnitrophota. This included a review of publicly available data and new samples collected from geothermal environments, freshwater lakes, wastewater, groundwater, and springs located around the world.   

The team observed that, in most cases, Omnitrophota measure less than 450 nanometers, which places them among the smallest of all known organisms. They also displayed genetic markers consistent with symbiosis – possibly as predators or parasites of other microorganisms, which suggested they would have high metabolic rates. Indeed, when isotope uptake was measured as a proxy for metabolic activity, Omnitrophota were hyperactive.  

“Despite how little we collectively knew about Omnitrophota, they’ve long been cited by microbial ecologists. Our goal was to finally drag this lineage out of the dark,” said Cale Seymour, a recent UNLV master’s graduate and the study’s lead author. “The more we learn about their energy conservation pathways and possible lifestyles, the closer we get to our goal of cultivating them in the lab and bringing them into the light.”  

The study, “Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota,” appeared March 16 in the journal Nature Microbiology. Additional collaborating organizations include Bigelow Laboratory for Ocean Sciences, the University of North Alabama, the U.S. Department of Energy’s Joint Genome Institute, Desert Research Institute, Northern Arizona University, Sun Yat-sen University, University of Science and Technology of China, and University of Queensland. 

First-ever layered lake sediment sample extracted from subglacial Antarctica 

Sample gives important details into past dynamics of the Antarctic ice sheet and its cold, dark ecosystems

DRI’s Mark Hausner, Ph.D., is a coauthor on a new study detailing the first layered lake-sediment sample taken from a subglacial lake in Antarctica. Hausner stepped in to assist the project team — dubbed SALSA for Subglacial Antarctic Lakes Scientific Access — after a difficult deployment created challenges in recovering temperature data from their equipment.

“I worked with the team after their return to recover the best temperature data we could,” Hausner says. Although precise temperature observations couldn’t be recovered, Hausner’s expertise with fiber-optic distributed temperature sensing cables enabled him to identify changes in the data that were consistent with other observations. 

“Using multiple observation methods really increases your confidence in what you’re seeing,” he says. “In this case, satellite observations, surface geophysics, and the temperature profile through the ice and into the lake all tell the same story of a lake underneath 1 km of ice that’s switching from draining to filling.”

Below is the full press release from the Colorado School of Mines.

Since the discovery 50 years ago of subglacial lakes in Antarctica — some of the least accessible geological features on Earth — scientists have attempted to extract lake bed sediment to learn about the formation, movement, and past conditions of the ice sheet. Now, a team of researchers with the NSF-funded project Subglacial Antarctic Lakes Scientific Access (SALSA) has successfully done so, recovering the first layered sediments from beneath the modern Antarctic ice sheet.

Their findings from analysis of the sediment sample, published March 9 in Geology, give important insight into the larger dynamics of the Antarctic ice sheet and its history, including when the ice sheet was smaller than its current size. Their work adds to the sedimentary record of knowledge of Antarctica and also holds implications for understanding how Antarctica may contribute to global sea level change.

Previous studies of modern subglacial lakes were limited to the timescale of the modern ice sheet due to the challenge of sampling an environment locked beneath thousands of feet of ice. The sediment sample extracted by the SALSA team will allow researchers to better understand subglacial activity across almost two centuries, instead of merely two decades.

“There are places on Earth that we still haven’t explored,” said Matthew Siegfried, assistant professor of geophysics at Colorado School of Mines and a lead author of the paper. “We have now one sample trying to understand an environment that is one and a half times the size of the continental United States. It’s like pulling up a rock in New Orleans and understanding how the Mississippi River and its entire basin has acted for the past 1,000 years.”

The saga of the SALSA team’s quest to explore subglacial lakes is chronicled in “The Lake at the Bottom of the World,” a feature-length documentary film released across multiple streaming platforms on February 28 by the team in partnership with Metamorph Films. The NSF-funded film gives viewers a close look at how the scientists conducted their work amid harsh Antarctic conditions.

‘Like grabbing a package of soup’

Researchers captured the sediment sample on a field expedition in December 2018. They cleanly bored a hole through over 3500 feet of ice over Mercer Subglacial Lake by filling a modified fire hose with sterilized water at nearly 200 °F and aiming it into the ice. They carefully collected sediment cores through a borehole that was constantly freezing back in using a device modified from its typical use in “normal” lakes to fit in a narrow ice borehole.

While researchers knew that even the mere extraction of the sediment from the lake would be a success, the fact that a sample arrived at the lab intact proved even more gratifying.

“We didn’t expect to find this mushy, fragile sediment under the ice sheet,” Siegfried said. “It was basically like grabbing a package of soup, bringing it up 1100 meters to the surface of the ice, shipping it to America, getting it into a CT scanner in Oregon, and somehow maintaining tiny laminations in the sample.”

Previous sediment samples from beneath the modern West Antarctic Ice Sheet have only consisted of a jumbled mixture of marine muds and rocks left behind when glaciers move over the Earth and do not contain a layered history of the region or ice sheet.

“In a 2001 paper published after a decade of subglacial drilling efforts in Antarctica, glaciologist Barclay Kamb somewhat unenthusiastically summarizes that everywhere the project sampled sediments, they found the same uninteresting, sticky, gray mixture,” said Ryan Venturelli, assistant professor of geology and geological engineering at Colorado School of Mines and a lead author on the paper.

“We found that, too. But above that same sticky, gray stuff, we found something different for the first time.”

Understanding subglacial movement

CT imagery of the sample showed a pattern of contrasts that indicated the subglacial lake was filling and draining with water before the scientists’ observational record. This finding offers insight into how long water has been moving under this part of Antarctica — movement that has implications for how the ice sheet moves and contributes to sea level rise. The life cycle of subglacial lakes derived from these contrasts also will enable researchers to better identify how carbon, nutrients and dissolved gasses are transported through the subglacial system to the global ocean.

“We use sediments from normal (subaerial) lakes all the time to build records of regional changes in climate. Subglacial lakes are different, because they are sealed by an overlying ice sheet that shields them from changing seasons and changing climate. Any variation in the subglacial sediment record is driven by changes to the overlying ice sheet and associated water system,” Venturelli said.

“Thanks to satellites that have helped us spy on Antarctica from space since 2003, we have a deep understanding of subglacial lake activity in the modern record, but the sediments we collected as part of SALSA give us an idea of how persistent these features are on a much longer timescale — hundreds of years. It’s our first insight into the life cycle of an active subglacial lake, and that is really exciting,” Venturelli added.

Significance of the sampling effort

The findings shared in Geology come amid more groundbreaking publications from the SALSA team based on the sediment samples they retrieved from Mercer Subglacial Lake. In February, researchers published work in ISME Communications that examined and compared microbial communities in the sediment to other regions under the ice; their work indicated an extensive subglacial ecosystem that is biogeochemically and evolutionarily linked through ice sheet behavior and the transport of microbes, water and sediments. Forthcoming research out soon in AGU Advances, also led by Venturelli, constrains the Antarctic subglacial carbon cycle for the first time and indicates how details of the cycle can be used to estimate how much smaller the West Antarctic Ice Sheet was in the last few thousand years.

“Knowing the dynamics of the ice sheet in the past is critical for predicting how it may respond to changes in the future, but this information has also helped to better understand the connectedness of these ecosystems to processes on the surface and regions beneath deep Antarctic ice that have yet to be explored,” said Brent Christner, a microbiologist at the University of Florida and SALSA Project team member.

Arsenic Contaminates Private Drinking Water Wells Across the Western Great Basin 

A New Study Maps Risk of Elevated Arsenic Levels in Groundwater Wells Across Northern Nevada, Northeastern California, and Western Utah

In the arid and drought-stricken western Great Basin, sparse surface water means rural communities often rely on private groundwater wells. Unlike municipal water systems, well water quality in private wells is unregulated, and a new study shows that more than 49 thousand well users across the region may be at risk of exposure to unhealthy levels of arsenic in drinking water.  

Led by researchers at DRI and the University of Hawai’i Cancer Center and published February 16th in Environmental Science and Technology, the study used data from groundwater wells across the western Great Basin to build a model to predict the probability of elevated arsenic in groundwater, and the location and number of private well users at risk. According to the study, the Carson Desert basin (including the town of Fallon, Nevada), Carson Valley (Minden and Gardnerville, Nevada), and the Truckee Meadows (Reno), have the highest population of well users at risk. The new study builds on previous research showing that 22% of 174 domestic wells sampled in Northern Nevada had arsenic levels exceeding the EPA guideline.  

“What we are finding is that in our region, we have a high probability for elevated arsenic compared to most other regions in the country,” said Daniel Saftner, M.S., a hydrogeologist at DRI and lead author of the study. “And we are seeing that geothermal and tectonic processes that are characteristic of the Great Basin contribute to the high concentrations of naturally occurring arsenic in the region’s groundwater.”   

The region’s mountains are also primary sources of arsenic. “As the arsenic-rich volcanic and meta-sedimentary rocks that form the mountains erode, sediment is transported to the valleys below,” says Steve Bacon, Ph.D., DRI geologist and study co-author. Water percolating through the valley floor then carries arsenic into the groundwater. Deeper, older groundwater and geothermal waters tend to have a higher arsenic concentration and can migrate upward along faults and mix with shallow groundwater. 

“We really wanted to better understand the unique geologic factors that contribute to high arsenic in this study,” Saftner says. “It’s important for us to think about the role of the environment as it pertains to human health – where we live can influence what our long-term health looks like.”  

To train and test the predictive model, the research team used data collected through the Healthy Nevada Project, including water samples from 163 domestic wells primarily located near Reno, Carson City, and Fallon. These data were supplemented with 749 groundwater samples compiled from the USGS National Water Information System. The model uses tectonic, geothermal, geologic, and hydrologic variables to predict the probability of elevated arsenic levels across the region.  

Although the U.S. EPA has set an arsenic concentration guideline of 10 µg/L for public drinking water, previous research has shown a range of health effects from long-term exposure to levels above 5 µg/L. Using this concentration as the benchmark, the model and map show that much of the region’s groundwater – particularly in western and central Nevada – is predicted to have more than a 50% probability of elevated arsenic levels.  

“Community members can use our arsenic hazard map to see what the risk is at their location, which might motivate them to test their well water,” says Monica Arienzo, Ph.D., associate research professor at DRI and study co-author. “Then, if they have high levels of arsenic or other contaminants, they can take steps to reduce their exposure, such as installing a water treatment system.”  

The findings from this study are potentially useful for a range of different applications. “The results can be useful for water utilities or water managers who tap similar shallow aquifers for their water supply,” says Saftner, “as well as irrigation wells that source water from these aquifers.”   

The research team plans to use their model to take a closer look at the health impacts of prolonged arsenic exposure. “Through the Healthy Nevada Project, genetic data and health records are paired with environmental data to help determine whether there are associations between the levels of arsenic in a community’s groundwater and specific health outcomes,” stated Joe Grzymski, Ph.D., research professor at DRI and principal investigator of the project.  

Map showing the hydrographic basin boundaries and predicted average population density with arsenic ≥5 μg/L in (a) the entire western Great Basin; (b) Truckee Meadows (Reno area), Lemmon Valley, and Cold Spring Valley; (c) Carson Valley (Minden and Gardnerville areas); and (d) Carson Desert (Fallon area).

Credit: DRI.

Predicted probability of arsenic ≥5 μg/L in alluvial aquifers of the western Great Basin, including (a) mean probability of arsenic ≥5 μg/L, (b) 95% confidence upper bound, and (c) 95% confidence lower bound. Bedrock aquifers and lakes are shown in gray and were not included in the arsenic hazard assessment.

Credit: DRI.

More information:

The full study, “Predictions of Arsenic in Domestic Well Water Sourced from Alluvial Aquifers of the Western Great Basin, USA,” is available from Environmental Science and Technology: https://doi.org/10.1021/acs.est.2c07948 

Study authors include: DRI researchers Daniel Saftner, Steve Bacon, Monica Arienzo, Erika Robtoy, Karen Schlauch, Iva Neveux, and Joseph Grzymski, as well as Michele Carbone with the University of Hawaii Cancer Center. 

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About DRI

The Desert Research Institute (DRI) is a recognized world leader in basic and applied environmental research. Committed to scientific excellence and integrity, DRI faculty, students who work alongside them, and staff have developed scientific knowledge and innovative technologies in research projects around the globe. Since 1959, DRI’s research has advanced scientific knowledge on topics ranging from humans’ impact on the environment to the environment’s impact on humans. DRI’s impactful science and inspiring solutions support Nevada’s diverse economy, provide science-based educational opportunities, and inform policymakers, business leaders, and community members. With campuses in Las Vegas and Reno, DRI serves as the non-profit research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.

About the University of Hawaiʻi Cancer Center

The University of Hawaiʻi Cancer Center through its various activities, including scientific research and clinical trials, adds more than $57 million to the Oʻahu economy.  It is one of only 71 research institutions designated by the National Cancer Institute.  An organized research unit within the University of Hawaiʻi at Mānoa, the UH Cancer Center is dedicated to eliminating cancer through research, education, patient care and community outreach with an emphasis on the unique ethnic, cultural, and environmental characteristics of Hawaiʻi and the Pacific.  Learn more at https://www.uhcancercenter.org.  Like us on Facebook at https://www.facebook.com/UHCancerCenter.  Follow us on Twitter @UHCancerCenter.