Volcanic Life Under The Microscope: Scientists Identify Optimal DNA Extraction Method For Microbial Research
June 17, 2025
A research team from Skoltech, the Institute of Physical, Chemical, and Biological Problems of Soil Science of the Russian Academy of Sciences, and other scientific organizations in Russia and the U.S. conducted a study of microbial communities living in extreme conditions in the fumarolic fields of the Elbrus (Russia), Ushkovsky (Russia), and Fuji (Japan) volcanoes. The authors discovered the most efficient technique for separating DNA from microbial samples and demonstrated that the microbial communities of every volcanic region are distinct and influenced by the geochemical conditions of their environment. The findings were published in the Nature Scientific Reports journal.
Volcanoes are one of the most mysterious and captivating places on Earth. Cracks or openings in the Earth's crust on their slopes and at their bases lead to the release of hot gases and steam. These regions are known as fumarolic fields, forming in zones of volcanic activity where magma heats underground water, converting it into vapor. Despite these harsh conditions, life exists even there — archaea and bacteria thrive on fumaroles with interesting adaptational mechanisms that remain largely unexplored.
'Samples collected from fumaroles represent a highly challenging material for DNA extraction. Meanwhile, thermophilic bacteria capable of surviving at extreme temperatures possess intriguing adaptive strategies. Our study provided the first description of microbial communities inhabiting the fumaroles of Elbrus, Ushkovsky, and Mount Fuji. Samples taken from beneath the snow cover on Elbrus exhibited a soil surface temperature of approximately +22.5°C. Summer collections from the Ushkovsky Volcano yielded specimens from a fumarolic area with a surface temperature reaching up to +68.4°C. Fuji samples consisted of frozen sediment deposits. After collection, all samples were preserved at -20°C,' explained lead author Alla Shevchenko, a PhD student in the Life Sciences program at Skoltech.
Researchers used different methods of soil sample pulverization prior to DNA extraction — vertical and horizontal homogenization (mixing). Vertical homogenization proved more effective regarding both DNA yield and detection of archaeal sequences when compared to horizontal homogenization.
'The majority of DNA was extracted via vertical homogenization. Variations in microbial populations correlate with specific features of each volcano. Acidobacteria and Pseudomonas dominate the soils of Elbrus. Ushkovsky fumaroles harbor numerous members of the Crenarchaeota group. Fuji's frozen soil harbors fewer microorganisms overall but retains Actinomyces and additional species of bacteria,' stated Professor Mikhail Gelfand, a study co-author and research supervisor, the vice president for biomedical research at Skoltech.
These findings highlight the significance of selecting an optimal methodology for sample preparation, particularly under extreme conditions. Microorganisms residing within fumaroles serve as sensitive indicators of environmental change. Their adaptability mirrors ecosystem responses to factors like temperature, moisture levels, pH values, and heavy metal concentrations. Changes in the structure and composition of bacterial and fungal colonies could be a sign of global warming, thermal regime shifts, and anthropogenic impacts.
Note:
Skoltech is a private international university in Russia, cultivating a new generation of leaders in technology, science, and business. As a factory of technologies, it conducts research in breakthrough fields and promotes technological innovation to solve critical problems that face Russia and the world. Skoltech focuses on six priority areas: life sciences, health, and agro; telecommunications, photonics, and quantum technologies; artificial intelligence; advanced materials and engineering; energy efficiency and the energy transition; and advanced studies. Established in 2011 in collaboration with the Massachusetts Institute of Technology (MIT), Skoltech was listed among the world's top 100 young universities by the Nature Index in its both editions (2019, 2021). On Research.com, the Institute ranks as Russian university No. 2 overall and No. 1 for genetics and materials science. In the recent SCImago Institutions Rankings, Skoltech placed first nationwide for computer science. Website: https://www.skoltech.ru/.
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June 17, 2025 A research team from Skoltech, the Institute of Physical, Chemical, and Biological Problems of Soil Science of the Russian Academy of Sciences, and other scientific organizations in Russia and the U.S. conducted a study of microbial communities living in extreme conditions in the fumarolic fields of the Elbrus (Russia), Ushkovsky (Russia), and Fuji (Japan) volcanoes. The authors discovered the most efficient technique for separating DNA from microbial samples and demonstrated that the microbial communities of every volcanic region are distinct and influenced by the geochemical conditions of their environment. The findings were published in the Nature Scientific Reports journal. Volcanoes are one of the most mysterious and captivating places on Earth. Cracks or openings in the Earth's crust on their slopes and at their bases lead to the release of hot gases and steam. These regions are known as fumarolic fields, forming in zones of volcanic activity where magma heats underground water, converting it into vapor. Despite these harsh conditions, life exists even there — archaea and bacteria thrive on fumaroles with interesting adaptational mechanisms that remain largely unexplored. 'Samples collected from fumaroles represent a highly challenging material for DNA extraction. Meanwhile, thermophilic bacteria capable of surviving at extreme temperatures possess intriguing adaptive strategies. Our study provided the first description of microbial communities inhabiting the fumaroles of Elbrus, Ushkovsky, and Mount Fuji. Samples taken from beneath the snow cover on Elbrus exhibited a soil surface temperature of approximately +22.5°C. Summer collections from the Ushkovsky Volcano yielded specimens from a fumarolic area with a surface temperature reaching up to +68.4°C. Fuji samples consisted of frozen sediment deposits. After collection, all samples were preserved at -20°C,' explained lead author Alla Shevchenko, a PhD student in the Life Sciences program at Skoltech. Researchers used different methods of soil sample pulverization prior to DNA extraction — vertical and horizontal homogenization (mixing). Vertical homogenization proved more effective regarding both DNA yield and detection of archaeal sequences when compared to horizontal homogenization. 'The majority of DNA was extracted via vertical homogenization. Variations in microbial populations correlate with specific features of each volcano. Acidobacteria and Pseudomonas dominate the soils of Elbrus. Ushkovsky fumaroles harbor numerous members of the Crenarchaeota group. Fuji's frozen soil harbors fewer microorganisms overall but retains Actinomyces and additional species of bacteria,' stated Professor Mikhail Gelfand, a study co-author and research supervisor, the vice president for biomedical research at Skoltech. These findings highlight the significance of selecting an optimal methodology for sample preparation, particularly under extreme conditions. Microorganisms residing within fumaroles serve as sensitive indicators of environmental change. Their adaptability mirrors ecosystem responses to factors like temperature, moisture levels, pH values, and heavy metal concentrations. Changes in the structure and composition of bacterial and fungal colonies could be a sign of global warming, thermal regime shifts, and anthropogenic impacts. Note: Skoltech is a private international university in Russia, cultivating a new generation of leaders in technology, science, and business. As a factory of technologies, it conducts research in breakthrough fields and promotes technological innovation to solve critical problems that face Russia and the world. Skoltech focuses on six priority areas: life sciences, health, and agro; telecommunications, photonics, and quantum technologies; artificial intelligence; advanced materials and engineering; energy efficiency and the energy transition; and advanced studies. Established in 2011 in collaboration with the Massachusetts Institute of Technology (MIT), Skoltech was listed among the world's top 100 young universities by the Nature Index in its both editions (2019, 2021). On the Institute ranks as Russian university No. 2 overall and No. 1 for genetics and materials science. In the recent SCImago Institutions Rankings, Skoltech placed first nationwide for computer science. Website:
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