Meet Graduate Researcher Natasha Sushenko

Meet Graduate Researcher Natasha Sushenko

Meet Natasha Sushenko, Graduate Researcher

May 11, 2021
LAS VEGAS, NEV.

By Kaylynn Perez

Environmental Microbiology
Pathogenic Bacteria
Space

Natasha Sushenko is a graduate research assistant with the Division of Hydrologic Sciences at the Desert Research Institute (DRI) in Las Vegas. She is a Master’s student in Biological Sciences in the School of Life Sciences at the University of Nevada, Las Vegas (UNLV), and is co-mentored by Duane Moser, Ph.D., of DRI and Brian Hedlund, Ph.D., of UNLV. Funding for Natasha’s position is provided by the NASA EPSCOR Rapid Response Research Program. Learn more about Natasha and her graduate research in this interview with DRI’s Behind the Science Blog!

Natasha Sushenko processes samples in the Environmental Microbiology Lab at the Desert Research Institute during a COVID-19 wastewater monitoring study.

Natasha Sushenko processes samples using a biosafety cabinet in the Environmental Microbiology Lab at the Desert Research Institute in December of 2020 during a SARS-CoV-2 wastewater monitoring study. Sushenko is a graduate research assistant with the Division of Hydrologic Sciences at DRI in Las Vegas.

Credit: Ali Swallow/DRI.

DRI: What brought you to DRI?

Sushenko: Dr. Duane Moser spoke in my undergraduate Microbial Ecology class at UNLV, and I was really interested in how his lab studies the deep biosphere, the zone of life that exists far below Earth’s surface. His lab does fascinating research on “microbial dark matter,” yet-to-be-classified microorganisms that live under extreme conditions within the deep biosphere and are difficult to culture in the lab. We kept in touch, and even though I considered leaving Las Vegas to do my graduate studies, the opportunities that he and DRI offered were too good to pass up.

What research projects are you working on? And who at DRI are you working with?

Sushenko: I work in Dr. Moser’s Environmental Microbiology Lab here at DRI. We completed a COVID-19 wastewater monitoring study this winter, but my main research project is a NASA collaboration with the Jet Propulsion Laboratory (JPL). They sent our lab strains of a pathogen (disease-causing bacterium) called Klebsiella pneumoniae that were isolated from the International Space Station (ISS). This microbe is a common cause of hospital-borne pneumonia and other infections, but in this case, it was found living on surfaces on the ISS, including on their space toilet. This pathogen is of particular concern to NASA because it has appeared in multiple samples across several years of microbiome monitoring, and it is growing more prevalent over time. While no astronauts on the space station have gotten sick, future human spaceflight to Mars and beyond may require astronauts to go on trips lasting years before returning to Earth. Because of this, NASA wants to know how pathogens like K. pneumoniae respond and adapt to living in space.

Our goal is to study how this pathogen’s virulence, or ability to cause severe illness, and its resistance to antimicrobial drugs and cleaners changes when exposed to the stresses of microgravity. Microgravity is the condition in space where people or objects appear to be weightless. This is something we can study here on Earth, at DRI, with a machine that simulates microgravity.

Above, left: Natasha Sushenko processes samples using a biosafety cabinet in the Environmental Microbiology Lab at the Desert Research Institute in December of 2020 during a SARS-CoV-2 wastewater monitoring study.

Credit: Ali Swallow/DRI.

Above, right: Natasha Sushenko performs field chemistries on deep borehole samples in the Funeral Mountains near Death Valley on 28-April, 2021. Here Natasha is using a Hach Colorimeter to measure dissolved oxygen, iron, sulfate, and sulfide to test whether increased rates of pumping from a deep well facilitated collection of deeper samples from a geologic fracture zone. Natasha contributed to the DRI-led portion of an NSF-funded collaboration with Bigelow Lab in ME and others focused on applying cutting-edge genomic approaches to the oceans, marine crustal fluids, and the continental subsurface.

Credit: Detra Page/DRI.

DRI: What are your short-term and long-term goals while at DRI?

Sushenko: Right now, I’m on the master’s degree plan, but I’m considering changing to Ph.D. track to continue working on my project to completion and beyond. The issue of the microbiome of the built environment in closed systems like spacecraft will only become more important as agencies and companies explore travel to the moon and Mars. You don’t get opportunities to work with NASA at every institution, and I’m excited that DRI gives me this opportunity.

DRI: Tell us about yourself. What do you do for fun?

The pandemic has cramped a lot of my favorite hobbies, but usually, I love to travel to visit friends, go camping, hike, and just being outside with others. This past year I’ve instead spent more time hanging out with my dog, gardening (indoors and outdoors), and baking.

In her free time, Natasha enjoys hiking and being outside in beautiful areas like the Desolation Wilderness in California.

In her free time, Natasha enjoys hiking and being outside in beautiful areas like the Desolation Wilderness in California. 

Credit: Natasha Sushenko

Additional Information:

For more information on DRI’s Environmental Microbiology Laboratory, please visit: https://www.dri.edu/labs/environmental-microbiology/

For more information on graduate programs at DRI, please visit: https://www.dri.edu/education/graduate-programs/

 

Evaluation of Antibiotic Resistance Genes (ARGs) in the Urban Wetland Ecosystem: Las Vegas Wash

Evaluation of Antibiotic Resistance Genes (ARGs) in the Urban Wetland Ecosystem: Las Vegas Wash

Photo: Duane Moser (left) and Xuelian Bai (right) collect filters from the sampling pump to take back to the lab for analysis.


Research on antibiotic resistance genes at DRI

 

Antibiotic resistance—the ability of bacteria to survive in the presence of antibiotics—is an increasing environmental and public health concern as more antibiotics enter urban waterways and treated wastewater is increasingly used to supplement limited water resources. Current wastewater treatment processes have difficulty removing antibiotics, which also encourages the growth of antibiotic resistance in urban watersheds, such as the Las Vegas Wash.

“Contaminants that are persistent in treated wastewaters that are discarded or reused may lead to health risks for humans,” explains Dr. Xuelian Bai, the principal investigator (PI) of this project that also includes co-PI Dr. Duane Moser and student researcher Rania Eddik-Zein. “The U.S. Centers for Disease Control and Prevention, the World Health Organization, and numerous other global and national agencies recognize antibiotic resistance as a critical challenge.”

 

 

The Las Vegas Wash is a unique watershed that is highly affected by anthropogenic activities and flooding during wet seasons.

“A lot of research has been done to monitor chemical contaminants such as nutrients, heavy metals, and organic contaminants, as well as antibiotics in the Las Vegas Wash and Lake Mead,” Bai says. “However, there is still a lack of information on the presence of microbial contaminants and antibiotic resistance genes [ARGs] in the watershed.”

Understanding the presence and abundance of ARGs in this watershed will provide insight into possible antibiotic resistance developing in the wash.

For this project, the researchers will evaluate the occurrence and prevalence of ARGs in the Las Vegas Wash.

“Resistance to antibiotics is encoded in ARGs, which are segments of DNA that enable bacteria to fight antibiotics,” Bai explains. “The major concerns about antibiotic resistance are the tendency of bacteria to share ARGs through horizontal gene transfer and that efforts to kill resistant bacteria, such as UV or chlorine disinfection in wastewater treatment and drinking water facilities, may not remove ARGs.”

The researchers anticipate that the data from this study will provide insight into the prevalence of ARGs in the wash and provide valuable information that can be used to determine water quality and potential human health concerns in southern Nevada.

First, the researchers will take field samples of water and sediment from the Las Vegas Wash to assess the presence of ARGs in an urban wetland ecosystem.

“Municipal wastewater appears to be a significant reservoir of ARGs,” Bai says. “Many studies have detected ARGs at all stages of the municipal wastewater treatment processes.”

Urban water supplies are particularly susceptible to developing antibiotic resistance because of the concentrated quantities of antibiotics that are released when treated municipal wastewater is discharged into the environment.

“Microorganisms in wastewater discharge can transport ARGs to downstream surface waters used for recreation or sources of drinking water, which can lead to human exposure over local, or even global, scales,” Bai explains. “This is a concern in southern Nevada because five major wastewater treatment plants discharge into the Las Vegas Wash. The Las Vegas Wash then discharges into Lake Mead, which is the primary drinking water supply for the Las Vegas Metropolitan Area.”

 

Researchers carry equipment toward a sampling site at the Las Vegas Wash.

The DRI research team including (from left) Duane Moser, David Basulto, Hai Pham, and Xuelian Bai carry equipment down to the bank of the Lake Mead, one of several sampling sites along the Las Vegas Wash.

 

Lake Mead supplies water to millions of residents in the southwestern United States, so identifying potential antibiotic resistance is increasingly important, especially with the drastic population growth in the region. Effluent discharged from wastewater treatment plants, urban runoff, and floodwaters during wet seasons carry sediment, nutrients, and other contaminants to Lake Mead. This generates several water-quality concerns, particularly about the effects of contaminants on aquatic habitats.

“The Las Vegas Wash provides the full continuum of major freshwater aquatic habitats, includingwetlands, flowing water, lake water, and sediment,” Bai explains. “Wetlands, flowing water, and lake water are defined by aerobic conditions and exposure to photosphere influence. However, sediments almost always go anoxic very quickly below the surface, usually within millimeters in eutrophic systems. The fate of antibiotics and the microbial genes that mediate changes in anaerobes have been relatively understudied.”

The researchers anticipate that the field sampling and the lab studies conducted for this project—which include microcosm and microbial community experiments, and DNA analysis—will allow them to specifically identify southern Nevada water issues.

“We will detect and quantify target ARGs in water samples collected upstream and downstream along the Las Vegas Wash, as well as target ARGs in sediment samples collected from the Las Vegas Wash wetlands,” Bai says. “We will also determine the fate and spread of ARGs in the aquatic ecosystems, and assess the effects of elevated antibiotic concentrations on the ecosystem.”

Because evaluating ARGs in surface water and sediment has not been fully studied locally or globally, this project will address local water issues in Nevada and provide useful antibiotic resistance data about urban watersheds that can be used worldwide.

This story was originally written for the Nevada Water Resources Research Institute (NWRRI) July 2019 Newsletter. Success and the dedication to quality research have established DRI’s Division of Hydrologic Sciences (DHS) as the Nevada Water Resources Research Institute (NWRRI) under the Water Resources Research Act of 1984 (as amended). The work conducted through the NWRRI program is supported by the U.S. Geological Survey under Grant/Cooperative Agreement No. G16AP00069.

Meet Josh Sackett, Ph.D.

Meet Josh Sackett, Ph.D.

Josh Sackett, Ph.D., is a postdoctoral researcher with the Division of Hydrologic Sciences at the Desert Research Institute in Las Vegas. Josh specializes in the study of microbes that inhabit Earth’s deep subsurface environments. He grew up in southwestern Colorado, and holds bachelor’s and master’s degrees in Biology from University of Colorado Denver, and a Ph.D. in Biological Sciences from University of Nevada, Las Vegas. Josh has been a member of the DRI community since 2014, when he moved to Las Vegas for a position working in DRI’s Environmental Microbiology Laboratory. In his free time, he enjoys hiking and exploring Mount Charleston and other natural areas around Las Vegas.  


 

What do you do here at DRI? 

I am a microbial ecologist and postdoctoral researcher with the Environmental Microbiology Lab at DRI. Some of my graduate work took place out in Amargosa Valley, Nevada, where we were looking for differences in the microbial community between Devils Hole and the Ash Meadows Fish Conservation Facility. We learned that the lack of cyanobacteria in the fish conservation facility may be impacting the survival of the Devils Hole Pupfish, which is critically endangered.

Right now, I am studying microbes such as bacteria and archaea that inhabit Earth’s deep subsurface fluids, which we access primarily through deep wells and mine shafts. We’re looking at the genetic material of these microbes using a technique called single-cell genomics where we isolate individual microbes, sequence their genomes, and learn about their potential role in their environment based on what genes are present.

What do you hope to learn about these deep subsurface organisms? 

We’re interested in how organisms live life independent of sunlight. These organisms are usually anaerobic (able to live without oxygen, some requiring the complete absence of oxygen), and they live a different lifestyle than most organisms that you think of. Humans, for example, we breathe oxygen and we metabolize organic carbon; these organisms don’t necessarily do that. So, learning about how these organisms live in the absence of oxygen, sunlight, or in environments where organic carbon is scarce gives us insight into potential for life on other planets where oxygen and dissolved organic carbon are likely limiting or not present at all.

Our research has potential for biotechnological applications as well. Sometimes, organisms that live in unique or austere environments are capable of degrading certain compounds, such as contaminants, or produce enzymes that are of interest to the scientific community.

Josh Sackett, Ph.D.

Josh Sackett, Ph.D., is a postdoctoral researcher with the Division of Hydrologic Sciences at DRI’s campus in Las Vegas.

Where does your research take place? 

One of our study sites, called BLM1, is located in Inyo County, near Amargosa Valley, Nevada. It’s a 2,500-foot deep well, which really isn’t all that deep. However, the earth’s crust is actually really thin in this area, so you don’t have to drill very deep to access hot fluids. Because of this, BLM1 serves as a stellar field site for investigating life in the subsurface. We also have a study site located along the Juan De Fuca Ridge, off the coast of Washington State, and we plan to look at microbial activity in sediments and fluids from that environment.

How did you end up here at DRI? 

I was born and raised in southwest Colorado, in a little town near Durango. I moved to Denver for my bachelor’s and master’s degrees. After that, I was searching for a laboratory to do my Ph.D. research in, and came across Duane Moser’s lab. I was interested in the plethora of projects he had going on, and I thought I could gain a lot of research experience and exposure to many different topics in his lab.

Initially, I wanted to be a physician. However, I caught the microbiology bug — no pun intended —  as an undergraduate student, and I’ve been hooked ever since. I really became interested in it because I’m interested in how microbes influence biogeochemical cycling, or how microbes contribute to earth’s processes, on a global scale.

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.

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.