Getting genetic with it

DNA from the nests of hibernating lemurs in Madagascar and underwater kelp forests of the Pacific Ocean comes to Argonne National Laboratory for analysis. No genetic sample is too wild for the Environmental Sample Preparation and Sequencing Facility.

You’ve probably probed the upper reaches of your nose to test for COVID-19. You might have even swabbed your cheek or collected your spit to find out who your ancestors were. These tests involve collecting and analyzing genetic material to answer a question.

During the course of the Human Genome Project, an international team of researchers spent nearly 13 years mapping human DNA. Completed in 2003, the project was one of the most audacious scientific endeavors in human history. Now, the processing of human DNA for health care has become fairly routine. You might drop off a sample at a doctor’s office and have your results within a few days or send a vial through the mail and find long-lost relatives in about a month.

But not all genetic samples are as ​“clean” as our spit or as close as our noses. Some samples come from peculiar places or arrive mixed up with fragments of genetic material from multiple, messy sources. For samples like these, unraveling the mysteries of the building blocks of life is still a challenge and an adventure.

“It’s exciting to come to work every day to shed light on the millions and millions of microbes that share our world and shape our lives.” — Sarah Owens, Sequencing Laboratory manager

That’s where the Environmental Sample Preparation and Sequencing Facility (ESPSF) comes in. The ESPSF is part of the Biosciences division at the U.S. Department of Energy’s (DOE) Argonne National Laboratory and specializes in conducting nucleic acid extraction, library preparation and ultrahigh throughput sequencing. Unlike labs that process routine human samples, this team likes some weirdness in their work.

They focus on environmental samples with an emphasis on microorganisms and have received and analyzed DNA from wild places — such as defrosting permafrost, the guts of stink bugs and the bottom of the ocean. This helps scientists all over the world make breakthroughs that save lives and further our understanding of the natural world.

Sarah Owens is the Sequencing Laboratory manager at ESPSF. She says that Argonne is uniquely suited to handle complex genetic analysis.

“Argonne has a culture of openness, a broad range of expertise and an investment in the tools and strategies that give us the ability to find what researchers need,” Owens said.

While Owens said that many of the samples her team analyzes are ​“really cool” she picked her top five favorites to share.

1. Lemur poop. Sure, everybody poops, but not everybody hibernates. In fact, one of the only primates that hibernates is the dwarf lemur of Madagascar. Dwarf lemurs go through seasonal changes as they fatten themselves up for hibernation, hibernate and then become active again. Researchers in Madagascar tracked wild lemurs throughout their hibernation cycle and took rectal swabs from individual lemurs to get samples of their fecal matter. The ESPSF was able to isolate the different strains of bacteria to show the bacterial communities present in dwarf lemur guts before, during and after hibernation. ​“As you can imagine, it’s not easy to get a fecal sample from a hibernating lemur,” Owens said. ​“We’re pleased that the research team trusts our facility to handle these rare samples and to get the results they need in study after study.” Understanding seasonal changes in dwarf lemur metabolism will give researchers insights into the role gut microbes play in human obesity and could lead to new medical treatments and drug discovery. Read the study.
2. Coral reefs. Coral reefs protect coastlines and provide food and shelter for thousands of species of fish, but coral is under extreme risk from warming ocean temperatures and water acidification. Researchers are studying ways that bacteria protect coral from diseases and climate change. The challenge comes in identifying the thousands of individual species of bacteria living in the coral and distinguishing their DNA from that of the coral itself. The microbes and the coral evolved from a shared ancestor and have very similar DNA. The ESPSF was essential in developing a low-cost peptide nucleic acid clamp. During preparation for sequencing, the clamp binds to a targeted sequence of the coral’s DNA and blocks it from replicating. This allows researchers to replicate or amplify more of the bacterial DNA so they can use genes in that DNA to determine the species present in the sample. This research could lead to new antibiotics or new insights into the role coral plays in controlling carbon levels in the environment. It might also help with conservation efforts to protect coral and the species that depend on it for survival. Read the study.
3. Kelp forests. The ocean’s vast underwater forests of bull kelp are an important food source for people around the world and are home to hundreds of marine species, such as sponges, fish, sea birds and otters. But kelp also supports something a little less lovable than otters: millions of different microbes. Researchers collected kelp blades, similar to the leaves of plants, and then cut or swabbed them to get bacterial samples. The ESPSF used a shotgun sequencing technique to identify the wide variety of bacteria on the kelp. This information helped researchers understand what role the microbes play in supporting kelp, such as providing essential vitamins, supporting photosynthesis, balancing carbon levels and reducing the levels of nitrogen that kelp absorbs from the water. ​“This work helps develop understanding of the interplay between microbes and their hosts in an important ecosystem,” Owens said. The research could help kelp forest conservation efforts and provide valuable information to support commercial kelp farming. Read the study.
4. Airborne fungus. Arbuscular mycorrhizal (AM) fungal communities grow in soil, penetrate the roots of plants, and assist plants with exchanging water and nutrients. This relationship helps plants grow larger and protects them against environmental conditions such as drought, salt, disease and pollution. This fungus spreads when spores from the parent organism are dislodged from the soil and moved along by air currents. In cities, there are fewer green spaces and fewer areas for the fungus to reproduce and spread. Over the course of a year, researchers in the city of Chicago captured airborne dust samples from the rooftops of buildings. The ESPSF analyzed the samples to find out how many and which types of AM fungal species were in the air. ​“I’ve always associated AM fungi as being in agricultural systems and below ground,” Owens said. ​“Seeing these fungi in an urban environment and up so high is really neat.” Owens said research like this demonstrates the value of looking at communities and environments from new and different angles. If researchers can increase the amounts of AM fungus in urban areas, they can help increase plant health and biodiversity in urban environments. Read the study.
5. COVID wastewater. It’s not just the fecal matter of dwarf lemurs that can unlock new knowledge. Our own excrement has a story to tell. When humans expel waste, they also shed the genetic material of any microbes and viruses present in their bodies. Those bacteria and viruses make their way into wastewater. Beginning early in the COVID-19 pandemic, the ESPSF worked with a consortium of scientists, public health experts and wastewater management teams to develop ways to track the virus through sewage samples to see how much and which variants are present in a community. According to Owens, finding the right RNA in wastewater provided a host of challenges, including the newness of the virus and the uncertainty of the supply chain. ​“We were learning in real time about the virus that we were trying to study, so there was constant optimization,” Owens said. ​“Plus, wastewater is an incredibly challenging complex matrix. It is filled with many viruses. We needed to carefully select for SARS-CoV-2.” The impact of the ESPSF’s work continues to be seen. ​“Wastewater is now the most consistent way to monitor pathogens, especially those without consistent clinical testing,” Owens said. Read the article.

Whether they’re tracking a pandemic or pioneering new scientific techniques, the team at the Environmental Sample Preparation and Sequencing Facility is always up for a new challenge because unlocking the mysteries of microbiomes can have huge impacts on our environment.

“It’s exciting to come to work every day to shed light on the millions and millions of microbes that share our world and shape our lives,” Owens said.

For additional information on the lab’s equipment, processes and expertise, go to the Environmental Sample Preparation and Sequencing Facility page.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science.

The U.S. Department of Energy’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://​ener​gy​.gov/​s​c​ience.