Subsurface Microbiomes: Global Study Compares Surface/Subsurface Microbes and Terrestrial/Marine Subsurface Microbes

     In case you were wondering, there are microbes that live deep in the Earth and are found in mines, aquifers, and deep-seafloor boreholes. The first global study to catalog these microbes is underway. The study looks at microbes up to 4375 m (14,354 ft or 2.72 miles) below ground and up to 491 m (1,611ft) below the seafloor. The study is led by scientists at the Marine Biological Laboratory (MBL), Woods Hole, Massachusetts. Part of the Woods Hole Oceanographic Institute. According to Phys.org:

“This discovery points to vast, untapped, subsurface reservoirs of diversity for bioprospecting new compounds and medicinals, for understanding how cells adapt to extremely low-energy environments, and for illuminating the search for extraterrestrial life."

     It is generally assumed that deeper into the Earth, there is less energy available and generally less microbial biodiversity. However, that is not always the case, especially among Archaean species of microbes.

"But we show that in some subsurface environments, the diversity can easily rival, if not exceed, diversity at the surface. This is particularly true for marine environments and for microbes in the Archaea domain," says Emil Ruff , lead researcher of the project.  

     The study took eight years to complete. Researchers compared terrestrial and marine subsurface microbes. They found that terrestrial and marine subsurface microbes vary in composition as they do above the surface, but that their levels of diversity are similar. Biological selection pressures are different for terrestrial and marine microbes.

"The first time scientists broadly realized there is a huge reservoir of microbes right under our feet, kilometers deep in rock and below the seafloor, was the mid-1990s," Ruff says. Scientists now estimate between 50–80% of Earth's microbial cells live in the subsurface, where energy availability can be orders of magnitude less than on the sunlit surface.

     With the low availability of energy, the microbes’ life processes are very slow. Some microbes can take 1000 years for a simple cell division. The slow pace is due to low energy availability.  

     If Mars had water, as it appears it did, then there is a possibility of finding subsurface microbes on the planet. Thus, understanding Earth’s subsurface microbes could help in exploring Martian subsurface microbes.

     The study analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments.

     Microbes have evolved to survive temperature extremes greater than 122°C or lower than −20°C, and from ambient pressures up to pressures greater than those of abyssal oceanic trenches. Although most of Earth’s microbial biomass is on the surface, it is also interesting to note that subsurface archaeal and bacterial biomass is greater than on the surface. According to the paper in Science Advances:

“Microbes can also increase cellular lifespan by slowing genome transcription or actively expressing mRNA for DNA repair enzymes. Among many other processes acetogenesis, methanogenesis; hydrogen, methane, and sulfur oxidation; fermentation of microbial biomass and necromass; symbiosis; serpentinization; and even radiolysis might contribute to the subsistence of deep life. While a portion of cells persist in a dormant state, many organisms actively metabolize but often with generation times of decades to centuries.”

     Previous studies noted that factors such as salinity, pH, and the availability of nutrients were among the major drivers of microbial community (microbiome) variance. The new study compares both surface and subsurface microbiomes, but also terrestrial and marine subsurface microbiomes.

     The figures below from the paper show sample sites, diversity, and species richness. As noted, certain archaeal and bacterial species lineages are most prevalent in the subsurface, including Lokiarchaeia, Bathyarchaeia, Hadarchaeia, and Caldatribacteriota. They also note that “it is likely that the subsurface holds a substantial degree of uncharted phylogenetic and likely metabolic diversity.” It was also found that species differ the most according to depth – generally, the deeper a species is found, the more it is different from surface species. They also noted that there are many differences in subsurface environmental, energy, oxygen, and other conditions that often do not correlate directly with depth.

 

 

 

References:

 

First global study provides insights into Earth's subsurface microbiomes. Science X staff. December 18, 2024. First global study provides insights into Earth's subsurface microbiomes

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide. S. Emil Ruff, Isabella Hrabe de Angelis, Megan Mullis, Jérôme P. Payet, Cara Magnabosco, Karen G. Lloyd, Cody S. Sheik, Andrew D. Steen, Anna Shipunova, [...] , and Frederick Colwell +11 authors Authors. Science Advances. 18 Dec 2024. Vol 10, Issue 51. A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide | Science Advances