Living microbes discovered in Earth’s driest desert

American Society for Microbiology

Highlights:

• The Atacama Desert is one of the most extreme habitats on Earth.
• Atacama surface soil samples include a mix of DNA from inside and outside living cells.
• A new technique allows researchers to separate external and internal DNA to identify microbes colonizing this hostile environment.
• This approach for analyzing microbial communities could potentially be applied to other hostile environments, like those on other planets. 

Washington, D.C.—The Atacama Desert, which runs along the Pacific Coast in Chile, is the driest place on the planet and, largely because of that aridity, hostile to most living things. Not everything, though—studies of the sandy soil have turned up diverse microbial communities. Studying the function of microorganisms in such habitats is challenging, however, because it’s difficult to separate genetic material from the living part of the community from genetic material of the dead.

A new separation technique can help researchers focus on the living part of the community. This week in Applied and Environmental Microbiology, an international team of researchers describes a new way to separate extracellular (eDNA) from intracellular (iDNA) genetic material. The method provides better insights into microbial life in low-biomass environments, which was previously not possible with conventional DNA extraction methods, said Dirk Wagner, Ph.D., a geomicrobiologist at the GFZ German Research Centre for Geosciences in Potsdam, who led the study.

The microbiologists used the novel approach on Atacama soil samples collected from the desert along a west-to-east swath from the ocean’s edge to the foothills of the Andes mountains. Their analyses revealed a variety of living and possibly active microbes in the most arid areas. A better understanding of eDNA and iDNA, Wagner said, can help researchers probe all microbial processes. 

“Microbes are the pioneers colonizing this kind of environment and preparing the ground for the next succession of life,” Wagner said. These processes, he said, aren’t limited to the desert. “This could also apply to new terrain that forms after earthquakes or landslides where you have more or less the same situation, a mineral or rock-based substrate.” 

Most commercially available tools for extracting DNA from soils leave a mixture of living, dormant and dead cells from microorganisms, Wagner said. “If you extract all the DNA, you have DNA from living organisms and also DNA that can represent organisms that just died or that died a long time ago.” Metagenomic sequencing of that DNA can reveal specific microbes and microbial processes. However, it requires sufficient good-quality DNA, Wagner added, “which is often the bottleneck in low-biomass environments.” 

To remedy that problem, he and his collaborators developed a process for filtering intact cells out of a mixture, leaving behind eDNA genetic fragments left from dead cells in the sediment. It involves multiple cycles of gentle rinsing, he said. In lab tests they found that after 4 repetitions, nearly all the DNA in a sample had been divided into the 2 groups. 

When they tested soil from the Atacama Desert, they found Actinobacteria and Proteobacteria in all samples in both eDNA and iDNA groups. That’s not surprising, Wagner said, because the living cells constantly replenish the store of iDNA as they die and degrade. “If a community is really active, then a constant turnover is taking place, and that means the 2 pools should be more similar to each other,” he said. In samples collected from depths of less than 5 centimeters, they found that Chloroflexota bacteria dominated in the iDNA group. 

In future work, Wagner said he plans to conduct metagenomic sequencing on the iDNA samples to better understand the microbes at work, and to apply the same approach to samples from other hostile environments. By studying iDNA, he said, “you can get deeper insights into the real active part of the community.”
 

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The American Society for Microbiology is one of the largest professional societies dedicated to the life sciences and is composed of over 32,000 scientists and health practitioners. ASM's mission is to promote and advance the microbial sciences.

ASM advances the microbial sciences through conferences, publications, certifications, educational opportunities and advocacy efforts. It enhances laboratory capacity around the globe through training and resources. It provides a network for scientists in academia, industry and clinical settings. Additionally, ASM promotes a deeper understanding of the microbial sciences to diverse audiences.

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Journal

Applied and Environmental Microbiology

 

Of tiny organisms and their giant impact on the ocean

Susanne Neuer receives Petersen Foundation Excellence Professorship

Helmholtz Centre for Ocean Research Kiel (GEOMAR)

The ocean absorbs about a quarter of annual carbon dioxide emissions. One mechanism that facilitates this is known as the biological carbon pump. This process starts with the photosynthesis of tiny microscopic algae, phytoplankton, floating in the sunlit upper layers of the ocean. Professor Dr Susanne Neuer and her team study the Biological Carbon Pump, focusing particularly on the role of plankton organisms in the formation of sinking particles, both in the laboratory and at sea. Since 2004, she has been a Professor of Marine Biogeochemistry at Arizona State University in Tempe, USA. Since 2022, she is also the founding director of the new School of Ocean Futures. For her contributions, she has been awarded the 31st Excellence Professorship of the Prof. Dr Werner Petersen Foundation, which includes €20,000 in funding and a six-week research stay at the GEOMAR Helmholtz Centre for Ocean Research Kiel.

Dr h.c. Klaus Wichmann, Chair of the Prof. Dr Werner Petersen Foundation, said: “On behalf of the Foundation, I am very pleased to award another outstanding scientist with an Excellence Professorship today. Since its inception in 2009, the Excellence Initiative has been an indispensable part of our mission to promote scientific excellence in Schleswig-Holstein and to intensify international cooperation. It is an honour for us to continue to support this and I hope that this initiative will set an example for others to follow.”

Professor Dr Katja Matthes, Director of GEOMAR, congratulated the awardee: “I am delighted that we can honour Susanne Neuer with this well-deserved award. With her outstanding research on the biological carbon pump, she has made an invaluable contribution to our understanding of the processes that influence our climate. Professor Neuer has excelled not only as a scientist but also as a mentor. She is a dedicated advocate for the advancement of women in science, having played leading roles with the Association for Women in Science and at Arizona State University. Her expertise and extraordinary achievements have made her a leading voice internationally. We are proud to welcome her to GEOMAR today and look forward to the inspiring contributions she will make during her stay.”

In her laudatio, Professor Dr Anja Engel, Head of the Marine Biogeochemistry Research Division at GEOMAR, emphasised the importance of the awardee's research: "Professor Neuer plays a leading and internationally visible role in marine biogeochemistry, the carbon cycle and particle export. Her highly acclaimed work has contributed significantly to our current understanding of the biological carbon pump in the ocean. Her analyses of ocean time series have laid the foundation for comparative studies of the efficiency of this central mechanism in the carbon cycle".

Insights into the Work of the Ocean’s Biological Carbon Pump

In her keynote lecture, Susanne Neuer discussed the significance of the Biological Carbon Pump for our planet’s climate. A fascinating aspect of this mechanism is the formation of so-called marine snow—sticky aggregates of phytoplankton, bacteria, and other organic matter held together by larger particles such as dust. These aggregates can grow large enough to be visible to the naked eye and form the basis for the transport of carbon into the deep ocean. Planktonic animals such as krill and copepods also contribute to carbon export by releasing phytoplankton particles into the ocean's twilight zone, an area of near darkness where the light barely penetrates.

“The processes initiated by phytoplankton and bacteria in the upper ocean layers of the ocean are a fundamental component of the long-term storage of CO2 and thus play a critical role in the context of climate change,” explained Prof. Neuer. “In the deep ocean, there is a fascinating interplay between microscopic cells that not only remove carbon from the atmosphere, but also sustain life throughout the ocean,” said Neuer. “The next time you look at the ocean, think of all the microscopic life in the water and all that it does for the well-being of our planet.”

Back to the roots: a reunion with Kiel and the chance for new collaborations

Kiel is not new territory for Susanne Neuer: some 40 years ago, she began her training as a marine scientist here at the former Institut für Meeresforschung (IfM), before moving on to the USA for further studies. This is not the first time she has returned to Kiel to talk about her research either. At the invitation of GEOMAR's Women's Executive Board, she gave a talk in 2016 as part of the Marie Tharp Lectures, discussing career issues with young female scientists.

“I am very honoured to receive the Excellence Professorship,” she says, “it will allow me to expand my collaboration with GEOMAR and especially with Prof. Dr Anja Engel and to develop synergies in our research on the biology of the global carbon cycle.” She is particularly looking forward to the exchange with young scientists at GEOMAR. Susanne Neuer: “It is important that the next generation receives special support in their careers so that they can not only be successful, but also make a sustainable contribution to solving environmental problems.”

 

About the Prof. Dr Werner Petersen Foundation

The Prof. Dr Werner Petersen Foundation, based in Schleswig-Holstein, Germany, aims to promote science, research, technology, and culture. A central area of support is the Excellence Initiative, which, in close cooperation with GEOMAR, honours outstanding scientists with international reputations. Through this initiative, leading marine scientists from around the world are invited to come to Kiel as guest scientists for up to six weeks.