New Study Investigates the Distribution of Deep Underground Microbial Life

New Study Investigates the Distribution of Deep Underground Microbial Life

Above: DeMMO field team from left to right: Lily Momper, Brittany Kruger, and Caitlin Casar sampling fracture fluids from a DeMMO borehole installation. Credit: Matt Kapust.


Las Vegas, Nev. – Below the Earth’s surface, a zone of life known as the continental deep subsurface is home to large populations of bacteria and archaea, but little is known about how these microbial populations are distributed. To learn whether they are spread evenly across rock surfaces or prefer to colonize specific minerals in the rocks, scientists from Northwestern University and the Desert Research Institute (DRI) went deep inside of a former gold mine in South Dakota and grew biofilms (collections of microorganisms) on rocks. Their results, which published in April in the journal Frontiers in Microbiology, show that the microbes formed “hotspots” around certain minerals in the rocks. Brittany Kruger, Ph.D., Assistant Research Scientist in Biogeochemistry from DRI in Las Vegas, served as field lead for the Northwestern research team at the Sanford Underground Research Facility (SURF), where this study was conducted.

The full text of the paper Rock-Hosted Subsurface Biofilms: Mineral Selectivity Drives Hotspots for Intraterrestrial Life is available from Frontiers in the Environment: https://www.frontiersin.org/articles/10.3389/fmicb.2021.658988/full

The press release below was reposted with permission from Northwestern University in Evanston, IL:


Earth’s crust mineralogy drives hotspots for intraterrestrial life

Northwestern University – Evanston, IL

April 9, 2021 – Below the verdant surface and organic rich soil, life extends kilometers into Earth’s deep rocky crust. The continental deep subsurface is likely one of the largest reservoirs of bacteria and archaea on Earth, many forming biofilms – like a microbial coating of the rock surface. This microbial population survives without light or oxygen and with minimal organic carbon sources, and can get energy by eating or respiring minerals. Distributed throughout the deep subsurface, these biofilms could represent 20-80% of the total bacterial and archaeal biomass in the continental subsurface according to the most recent estimate. But are these microbial populations spread evenly on rock surfaces, or do they prefer to colonize specific minerals in the rocks?

To answer this question, researchers from Northwestern University in Evanston, Illinois, led a study to analyze the growth and distribution of microbial communities in deep continental subsurface settings. This work shows that the host rock mineral composition drives biofilm distribution, producing “hotspots” of microbial life. The study was published in Frontiers in Microbiology.

Hotspots of microbial life

To realize this study, the researchers went 1.5 kilometers below the surface in the Deep Mine Microbial Observatory (DeMMO), housed within a former gold mine now known as the Sanford Underground Research Facility (SURF), located in Lead, South Dakota. There, below-ground, the researchers cultivated biofilms on native rocks rich in iron and sulfur-bearing minerals. After six months, the researchers analyzed the microbial composition and physical characteristics of newly grown biofilms, as well as its distributions using microscopy, spectroscopy and spatial modeling approaches.

The spatial analyses conducted by the researchers revealed hotspots where the biofilm was denser. These hotspots correlate with iron-rich mineral grains in the rocks, highlighting some mineral preferences for biofilm colonization. “Our results demonstrate the strong spatial dependence of biofilm colonization on minerals in rock surfaces. We think that this spatial dependence is due to microbes getting their energy from the minerals they colonize,” explains Caitlin Casar, first author of the study.

Future research

Altogether, these results demonstrate that host rock mineralogy is a key driver of biofilm distribution, which could help improve estimates of the microbial distribution of the Earth’s deep continental subsurface. But leading intraterrestrial studies could also inform other topics. “Our findings could inform the contribution of biofilms to global nutrient cycles, and also have astrobiological implications as these findings provide insight into biomass distributions in a Mars analog system” says Caitlin Casar.

Indeed, extraterrestrial life could exist in similar subsurface environments where the microorganisms are protected from both radiation and extreme temperatures. Mars, for example, has an iron and sulfur-rich composition similar to DeMMO’s rock formations, which we now know are capable of driving the formation of microbial hotspots below-ground.

 

Ancient ‘quids’ reveal genetic information, clues into migration patterns of early Great Basin inhabitants

Ancient ‘quids’ reveal genetic information, clues into migration patterns of early Great Basin inhabitants

Above: Cave opening at the Mule Springs Rockshelter in southern Nevada’s Spring Mountain Range. Credit: Jeffrey Wedding, DRI.


 

Las Vegas, NV (April 24, 2018): If you want to know about your ancestors today, you can send a little saliva to a company where – for a fee – they will analyze your DNA and tell you where you come from. For scientists trying to find out about ancient peoples, however, the challenge is more complex.

Research published in the journal PLOS ONE by a team of archaeologists and microbiologists from Nevada’s Desert Research Institute (DRI) and Southern Illinois University Carbondale (SIU) showcases the use of modern research methods to uncover clues about the genetic ancestry of Native Americans who inhabited the Desert Southwest during the last thousand years.

“We were surprised by the consistency with which we were able to recover intact human DNA from a common type of plant-based artifact,” explained co-principal investigator Duane Moser, Ph.D., an associate research professor of microbiology at DRI and director of DRI’s Environmental Microbiology Laboratory.

During the Late Holocene Epoch, which began 12,000 to 11,500 years ago and continues through the present, occupants of the Mule Spring Rockshelter in the foothills of the Spring Mountains of southern Nevada commonly gathered agave and yucca plants for food. The artichoke-like hearts and inner leaves of the plants were roasted then chewed to consume the sweet fleshy pulp. This left wads of stringy fibers called ‘quids,’ which were spit out and left behind.

In the late 1960s, researchers from DRI and the University of Nevada, Las Vegas (UNLV) led by Richard Brooks, recovered thousands of quids at the rockshelter. Put into storage for half a century without any consideration for DNA preservation, a DRI-led research team decided to re-examine the quid specimens as possible repositories for ancient DNA.

“The quid’s coarse texture is excellent for capturing skin cells from the mouth, making them the equivalent of the modern-day cheek swab,” explained Susan Edwards, an associate research archaeologist at DRI and co-principal investigator who first thought of applying DNA extraction techniques to the quid samples.

A wad of stringy agave plant fibers commonly called ‘quids’.

A wad of stringy agave plant fibers commonly called ‘quids’. Credit: DRI

The research team used laboratory and computational resources at DRI’s Southern Nevada Science Center in Las Vegas, and later at SIU, to identify changes in the mitochondrial DNA sequences that are maintained in ancestrally related populations called haplogroups. These haplogroups can then be compared to Native American tribes and other ancient DNA lineages.

The study showed that the Mule Spring Rockshelter quid specimens ranged in age from about 350 to 980 years old. Because Mule Spring Rockshelter sits at a crossroads between the southern Great Basin, the Mojave Desert, and the Southwest Puebloan cultures, these results may provide a better timeline for an important but contentiously debated event in human history known as the Numic Spread.

Today’s Numic people contend they have always been here, a position some scientists readily support. However, some evidence suggests that Numic-speaking ancestors of contemporary native peoples spread from southern California throughout the Great Basin about 500 to 700 years ago; a date range which overlaps with the current study. Other studies suggest a much earlier arrival.

This research marks only the second time that scientists have been able to sequence human DNA from plant-based artifacts, expanding upon an approach utilized by Steven LeBlanc of Harvard University.

“Since these materials were also radiocarbon dated, in essence they provide a time-resolved hotel registry for this unique site over a period of hundreds of years,” added Moser.

As an added benefit of utilizing DNA from quid samples (rather than from more traditional sources such as bones or teeth), the research team found that they were able to obtain the information they needed while being respectful of cultural sensitivities.

“The distinct advantage of this genetic technique, is that it does not require the sampling of human remains” said Scott Hamilton-Brehm, lead author on the study and assistant professor of microbiology at SIU who completed his postdoctoral research at DRI.

In the future, the team hopes to continue this work by targeting additional quids from the Mule Spring Rockshelter collection, with the possibility of corroborating evidence of older dates for habitation of the site suggested by prior studies of more traditional cultural artifacts. Plans are in the works to perform similar studies on quids from other Great Basin sites to glean additional information about the movements of ancient peoples and utilize more powerful analytical approaches to obtain greater DNA sequence coverage than was obtained by this pilot study.

“We look forward to learning more about Native American presence in the Great Basin and Southwest area, and how the data compares over time,” added Lidia Hristova, a graduate of the UNLV Anthropology Program who conducted much of the hands-on DNA extraction from the samples while working as an undergraduate research assistant at DRI and studying at UNLV.

The full study, “Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA,” is available online from  PLOS ONE: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194223 

Mule Spring Rockshelter is a protected cultural resource located on BLM-managed lands. DRI access to the Mule Spring collection was granted under permit and loan agreement. 

Tim Crosby, Communications and Marketing Strategist at SIU Carbondale contributed to this press release. 

Additional photos available upon request.  

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The Desert Research Institute (DRI) is a recognized world leader in investigating the effects of natural and human-induced environmental change and advancing technologies aimed at assessing a changing planet. For more than 50 years DRI research faculty, students, and staff have applied scientific understanding to support the effective management of natural resources while meeting Nevada’s needs for economic diversification and science-based educational opportunities. With campuses in Reno and Las Vegas, DRI serves as the non-profit environmental research arm of the Nevada System of Higher Education. For more information, please visit  www.dri.edu.

Meet Brittany Kruger, Ph.D.

Meet Brittany Kruger, Ph.D.

Brittany Kruger, Ph.D., is a staff research scientist in geobiology with the Division of Hydrologic Sciences at the Desert Research Institute in Las Vegas, NV. She specializes in the study of microbes that live in deep underground environments, such as those found inside of deep mines. Brittany is a Minnesota native, and holds a Ph.D. and Master’s Degree in Water Resources Science from the University of Minnesota, Duluth. Her work has taken her to diverse environments, including Lake Superior, Lake Malawi in Africa, Woods Hole, MA, Japan, and a mile-deep abandoned gold mine in South Dakota. She has been a member of the DRI community since 2014, when she moved to Las Vegas for a position in Dr. Duane Moser’s Environmental Microbiology Lab. In her free time, Brittany enjoys rock climbing in Red Rock Canyon and making trips into the Sierras.


DRI: What do you do here at DRI?
BK: I am a staff scientist here at DRI. I support a number of different projects that focus on deep biosphere life, which essentially means we try and examine life as deep as we can access it underground. Specifically, we look for microbial life and try and understand how those organisms are functioning given the stresses that they encounter deep underground.

DRI: How do you access deep underground environments?
BK: There are a couple different ways you can access the deep biosphere. One way is to actually go there – you can go down in deep mines, for example. In that scenario we can actually bring instruments and equipment down with us. One of our most recently active field sites is an old gold mine in South Dakota, where we are able to go about a mile underground.

Another option to access subsurface life is to use deeply drilled wells that access water or aquifers that are very far underground. This is the approach that we use at active field sites in the Death Valley and Armargosa Valley areas. There aren’t a lot of places in the world where you can access the very hottest, deepest part of the earth quite as easily as we can in this area, because that surface layer of the earth is a little bit thinner here, particularly in the Death Valley region.

Brittany Kruger collects samples from an underground mine site.

Brittany Kruger collects samples from an underground mine site.

DRI: We understand that some of your research has implications for life on other planets. Can you tell us about that?
BK: One of the projects that I’ve been focusing on since I started here at DRI is the NASA Astrobiology Life Underground Project. I have served as continental fieldwork coordinator for that project since joining DRI. We try to access the deep biosphere in multiple locations to install experimentation and collect samples, and we use what we learn about the way microbes are metabolizing and surviving in those locations to help us understand how life might be functioning on other planets that experience the same or similar stressors, like extreme heat, temperature, pressure, radiation, lack of sunlight, etc.

Right now, we’re installing experiments that focus on better understanding exactly what chemical reactions microbes are using to live in these deep environments.  If you think about it, the majority of life that we understand well, the life on the surface of the planet, uses sunlight for energy at some point in their food chain. But these microbes deep underground do not.  Instead they’re able to rely on dissolved metals or other compounds to produce the energy they need to live. Sometimes they need to be in actual physical contact with these compounds, and attach to those surfaces to live.  It’d be similar to us having to go touch a rusty car in order to breathe. So we’re installing various mineral materials into these deep biosphere environments and studying the microbial populations that colonize them.

As an additional component to that project, we also work closely with members of the SHERLOC instrument team at the NASA Jet Propulsion Laboratory, who are developing an instrument slated to fly on the Mars 2020 Rover that uses Raman and Luminescence scanning to detect organics and chemicals. A lot of the field samples and experiment results are analyzed with that instrument to learn more about our samples and to help provide background data for the instrument prior to its Mars deployment.

Brittany Kruger collects samples from an underground mine site.

Brittany Kruger collects samples from an underground mine site.

DRI: What is it like to work deep underground?
BK: It’s great. I love it. I’m always excited to go down. It’s absolute pitch black, and it gets hotter the deeper you go. At our hottest underground site, it is something like 90 degrees and 90 percent humidity. It is uncomfortable to be there for a long time, for sure. But the facility we work in does a really good job of trying to mitigate air flow while we’re there to keep that a little more comfortable.

One of the best parts is also spending time with the old miners. I go to South Dakota every few months, and spend multiple days underground accessing our sites in what was once the Homestake Gold Mine.  Mining has ceased in the facility, and the entire mine has now been dedicated solely to science and is called the Sanford Underground Research Facility.  So it’s a really unique facility where people who previously mined the workings are now employed as underground guides for scientists. There are extremely high-level physics labs located about a mile underground on the deepest accessible level. You’d never know you were underground in those labs; they’re like any state of the art aboveground facility.

But, that’s not where we want to go – we want to go to the far away, dirty, dark, hot places where it’s not maintained and where we can access the unaltered water flowing out of the mine wall. So, we get to hang out with the old miners that know the mine, and know how to access those places and know how to do it safely. So that’s fantastic – we get to see some really exciting things and some really awesome old history. It’s fun.

Brittany Kruger collects samples from an underground mine site.

Brittany Kruger collects samples from an underground mine site.

 

New research improves prospects for imperiled Devils Hole Pupfish in captivity

New research improves prospects for imperiled Devils Hole Pupfish in captivity

Above: Researchers Joshua Sackett (left) and Duane Moser (right) of DRI help National Park Service officials move scaffolding infrastructure during a routine sampling visit to Devils Hole on December 13, 2014. Credit: Jonathan Eisen.


DRI study finds key differences between artificial habitat and the real Devils Hole

Las Vegas, NV (Tuesday, March 20, 2018): In a first-of-its kind study of comparing the microbiology of Devils Hole with that of a constructed scale replica at the Ash Meadows Fish Conservation Facility (AMFCF), a team of scientists from the Desert Research Institute (DRI) in Las Vegas discovered key differences in nutrient levels and species composition that may be impacting the ability of the highly endangered Devils Hole Pupfish (Cyprinodon diabolis) to survive in captivity.

“We were interested in taking a closer look at the chemical and biological factors that control productivity at both sites,” said Duane Moser, Ph.D., an associate research professor of microbiology at DRI who has been involved with research at Devils Hole since 2008. “In studying both, we could gain some insights into how well the artificial refuge actually replicates Devils Hole, and in turn, offer recommendations for ways to make the refuge a better habitat for the pupfish.”

Devils Hole Pupfish (population 115 in autumn 2017) are an iridescent blue, one-inch-long pupfish. They are native only to Devils Hole, an isolated water-filled cavern of unknown depth located in a detached unit of Death Valley National Park within the Ash Meadows National Wildlife Refuge in Amargosa Valley, Nevada. Devils Hole is an extreme environment, with water temperatures and dissolved oxygen concentrations near their lethal limits for most fishes.

Since 2013, scientists have been trying to establish a backup population of these endangered fish in a constructed tank at the AMFCF, which is located a short distance west of Devils Hole. Although the facility was designed to match the climate, water chemistry and physical dimensions of an area of shallow shelf habitat in Devils Hole, the pupfish have had only limited success reproducing and surviving in this artificial environment.

In 2015, Moser and a team of researchers from DRI set out to learn if there were other factors that might be impacting the success of these fish. Their new study, published in the March edition of PLOS One, characterizes and compares water chemistry and microbial communities between Devils Hole and the AMFCF.

Although water temperature and dissolved oxygen at the AMFCF are intentionally maintained at values that are slightly lower and higher, respectively, from those of Devils Hole, this work shows that the nutrient balance between the two sites is also very different, with AMFCF being strongly nitrogen limited – about five times lower than that of Devils Hole.

In the microbial communities, which contribute to the distribution and availability of dissolved nutrients in the water and are also a food source for the pupfish, the research team discovered more than 2,000 microbial species from 44 distinct phyla present in the water at Devils Hole. They detected similar levels of species diversity at AMFCF, but found that different bacterial phyla were dominant at each site. These differences may relate to the observed differences in nitrogen concentrations.

“Nitrogen levels have an effect on the types of organisms that you’ll find, and the types of metabolisms that they have,” said Joshua Sackett, a graduate research assistant with the Desert Research Institute and doctoral student in the School of Life Sciences at the University of Nevada, Las Vegas. “We found a lot fewer of at least one major category of primary producers – the cyanobacteria – in the AMFCF compared to Devils Hole, and we think that’s due to differences in nutrient concentration.”

One of the strengths of the comparative power of this study is that the data from each site were gathered on the same day. This study highlights the potential importance of considering water chemistry and microbiology when constructing artificial fish habitats – and the team hopes that the information will provide a valuable contribution to the continued survival of the Devils Hole Pupfish in captivity.

“This work revealed very different microbial populations, which we infer might correspond to large differences in nutrient dynamics between the sites – especially in terms of nitrogen,” Moser said. “Consequently, some relatively modest tweaks in how the refuge is operated could potentially improve the prospects for continued survival of one of Earth’s most imperiled fishes.”

The full version of the study – A comparative study of prokaryotic diversity and physicochemical characteristics of Devils Hole and the Ash Meadows Fish Conservation Facility, a constructed analog – is available online: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0194404

For more information about DRI, visit www.dri.edu

Photo caption: Researchers Joshua Sackett (left) and Duane Moser (right) of DRI help National Park Service officials move scaffolding infrastructure during a routine sampling visit to Devils Hole on December 13, 2014. Credit: Jonathan Eisen.

Additional photos are available upon request.

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The Desert Research Institute (DRI) is a recognized world leader in investigating the effects of natural and human-induced environmental change and advancing technologies aimed at assessing a changing planet. For more than 50 years DRI research faculty, students, and staff have applied scientific understanding to support the effective management of natural resources while meeting Nevada’s needs for economic diversification and science-based educational opportunities. With campuses in Reno and Las Vegas, DRI serves as the non-profit environmental research arm of the Nevada System of Higher Education. For more information, please visit www.dri.edu.