Subterranean Eukaryotes

Rori Stuart ‘22, 8/23/2020, Life Sciences

Figure 1: The image above shows the fungus Alternaria, a member of the Ascomycota phylum, the Alternaria sp., one of the more abundantly found phyla by Saitoh and the rest of the Horonobe Underground Research team.

Source: Wikimedia Commons

Life can survive in a wide array of environments. Microbial eukaryotes, organisms with membrane-bound nuclei like plants and animals, can be found from deep-sea sediments to human lungs.1,2 Deep-sea sedimentary fungi dominate eukaryotic life in their environment whereas the Pneumocytis fungus lives with low numbers in the lower respiratory tract.1,2 Since eukaryotic life has been found in highly disparate environments, the Saitoh and their team endeavored to learn whether these organisms can live far underground in terrestrial environments3.

The researchers collected their samples at the Horonobe Underground Research Facility, in Hokkaido, Japan, from -250m (Rock 1) and -270m (Rock 2). The samples were isolated and pulverized so that the 18S-rRNA (18 subunit ribosomal ribonucleic acid) could be extracted and amplified via a polymerase chain reaction (PCR) assay. The amplified rRNA was then placed into an E. coli plasmid and sequenced for taxonomic and phylogenetic analysis. Once the analysis was complete, several different phyla were detected in the deep-subterranean environment sampled. These organisms were included in the Amoebozoa, Heterolobosea, Chlorophyta, Basidiomycota, and Ascomycota phyla. To determine the abundance of these fungi, quantitative PCR was used, with 4.7 ± 0.4 × 103 and 3.6 ± 0.1 × 103 copies of 18S rRNA/g of rock, for Rocks 1 and 2 respectively, being found.3

The Horonobe Underground Research Facility is in an area dominated by sedimentary rock with little groundwater flow, indicating that the eukaryotes found in the study were present since the initial deposition of these sediments. There is a lack of movement of cells into the area due to this lack of groundwater flow; however, some members of Chlorophyta, a taxon filled with organisms which typically rely on light to create chemical energy, were present, potentially indicating that some species have evolved to live in the absence of light. These Chlorophyta, while present, were not the dominant form of eukaryotic life, but rather the Basidiomycota and Ascomycota phyla, which accounted for 72.8% of the eukaryotes found.3

Although the abundance of eukaryotes deep below ground are far lower compared to the surface, there is still a wide variety of different eukaryotic species in deep subterranean environments.3 The results of the study conducted by Saitoh and their team were not dissimilar from another study, conducted by Edgcomb and their team Beaudoin, Gast, Biddle, and Teske which also found large populations of Basidiomycota and, to lesser extents, Ascomycota.1 Green algal and plant genetic material were found in both studies as well; however, this was identified as contamination in the Edgcomb et al. study unlike with the Saitoh et al. study where these genetic materials were believed to represent inhabitants of these deep subterranean environments.1,3 Despite the Saitoh and their team’s reasonable inability to fully grasp the potential biodiversity of the deep subterranean biome, due to the sheer scope of the ecosystem being studied, they showed a great diversity of eukaryotes in an understudied region of the biosphere.


[1] Edgcomb, Virginia P., Beaudoin, David, Gast, Rebecca, Biddle, Jennifer F., Teske, Andreas. 2011. “Marine Subsurface Eukaryotes: The Fungal Majority.” Environmental Microbiology 13(1):172-183.

[2] Zimmer, Carl. 2013. “Getting to Know Your Inner Mushroom.” National Geographic, May 22.

[3] Saitoh, Yoshimoto, Hirano, Shin-ichi, Nagaoka, Toru, Amano Yuki. 2019. “Genetic Survey of Indigenous Microbial Eukaryotic Communities, Mainly Fungi, in Sedimentary Rock Matrices of Deep Terrestrial Subsurface.” Ecological Genetics and Genomics 12.


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