Microbial Diversity in the Deep Biosphere and Their Industrial Applications

The deep biosphere, comprising subsurface microbial ecosystems situated deep beneath Earth's surface, represents one of the least understood and most intriguing microbial environments on our planet. In this Research Topic on the deep biosphere, our emphasis is on in situ subsurface environments accessed via cores, boreholes, observatories, mines, and aquifers. These unique communities have evolved adaptations that enable survival under various environmental stresses. Stressors can include energy and nutrient limitation, redox stratification, low permeability and restricted fluid flux, physical isolation, and temperature conditions governed primarily by geothermal gradients. Pressure can also be relevant as lithostatic and/or pore-fluid pressure associated with burial depth.

Technological breakthroughs in genomic and metagenomic methods have significantly advanced our understanding of the biodiversity and complex ecological strategies employed by these microbes. However, major gaps remain regarding the precise diversity, adaptive physiology, metabolic flexibility under persistent energy limitation, rates and controls on activity, and the biogeochemical roles of these communities.

Addressing these knowledge gaps, this Research Topic aims to thoroughly investigate the biodiversity, ecological functions, survival mechanisms, and industrially relevant metabolic capabilities of microbial communities within deep aquatic and terrestrial subsurface ecosystems. By leveraging state-of-the-art analytical techniques, including omics-based approaches, we seek to reveal key adaptive strategies, metabolic pathways, and novel biological compounds produced by these microorganisms. Insights from such studies not only deepen our fundamental knowledge of life in Earth’s deep subsurface, but also unlock opportunities for industrial applications in biotechnology, bioremediation, pharmaceuticals, and sustainable bioenergy.

We welcome contributions of Original Research, Reviews, Perspective, Methods and Opinion articles exploring, but not limited to, the following themes:

• Characterization and taxonomy of microbial diversity within deep subsurface habitats;

• Metabolic pathways and physiological adaptations underlying the resilience of extremophiles in deep subsurface environments;

• Ecological interactions and functional roles of deep biosphere microbial communities;

• Biotechnological potential of deep biosphere microbes for industrial applications in bioremediation, pharmaceuticals, bioenergy production, and beyond;

• Discovery, characterization, and engineering of novel microbial-derived enzymes and bioactive metabolites;

• Studies exploring subsurface biosphere as a model for extraterrestrial life.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Deep biosphere, subsurface microbial ecosystems, deep marine biosphere, terrestrial subsurface, microbial survival mechanisms, deep subsurface biodiversity, deep earth microbiology, astrobiology applications

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.