Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.
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Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface
Nature Communications Open Access 27 November 2023
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The raw metatranscriptome sequencing data in this study have been deposited in the National Center for Biotechnology Information Sequence Read Archive under the accession numbers SRR22580929-SRR22580947. PacBio reads were deposited to the National Center for Biotechnology Information Sequence Read Archive under access numbers SRR23604162-SRR23604206.
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We would like to acknowledge the crew and entire science party for IODP Expedition 385 for their assistance with sample collection. Without their assistance this study would have been impossible. We thank Dr. Daniel Lizarralde (WHOI) for the edited bathymetric map of Guaymas Basin. We also thank Takeshi Terada and Megumi Becchaku for assisting with cell counting. This study was supported by the National Science Foundation Grant OCE-2046799 to VE, PM, AT, R. Hatzenpichler, and OCE-1829903 to VE, PM, and AT, JSPS KAKENHI JP19H00730 and JP23H00154 to YM, and China Postdoctoral Science Foundation (2022M720039) and Guangdong Natural Resources Foundation (GDNRC30) to Y-LZ.
The authors declare no competing interests.
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Mara, P., Zhou, YL., Teske, A. et al. Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation. ISME J 17, 1907–1919 (2023). https://doi.org/10.1038/s41396-023-01492-z