Deep Subsurface Microbiology

Deep Subsurface Microbiology

• Microbiologists once thought microbial numbers were limited to the top 100 m of Earth's crust.
• Improvements in drilling techniques prove microbial life can extend 3 km into the Earth.
• Deep subsurface microbes live in anoxic, nutrient-depleted surroundings and grow at temperatures above 50°C.
• Microbial activity in sediments and waters greatly influences physical properties.
• Deep subsurface microbiology has applications in carbon sequestration, energy production, bioremediation, astrobiology, and geological research.
• Deep subsurface microorganisms play a role in capturing and storing carbon dioxide for carbon sequestration.
• These microbes contribute to processes like microbial enhanced oil recovery (MEOR) and hydrogen production for energy production.
• Deep subsurface microorganisms are valuable for cleaning up contaminated sites through bioremediation by degrading pollutants in extreme environments.
• Studying these microorganisms helps understand life's potential in extreme environments on Earth and other planets, contributing to astrobiology.
• They provide insights into Earth's history and subsurface processes, aiding natural resource exploration in geological research.
• The term "deep subsurface" refers to intermediate and regional flow systems in microbiology.
• The definition of "deep" depends on the hydrologic framework, not just total depth.
• It's crucial to minimize contamination when retrieving deep subsurface microorganisms.
• Using tracers such as microspheres and perfluorocarbons in drilling fluid can help monitor contamination.
• Steam cleaning equipment and using chlorinated water in drilling muds are techniques to reduce contamination.
• Stripping away external surfaces of sediment cores before sampling is essential.
• Inert gases like nitrogen or argon are used during drilling instead of fluids to minimize contamination.
• Sterilization of drilling fluid or tracers helps prevent contamination.
• Maintaining sterile and non-oxidizing conditions during sample containment is vital.
• Argon-filled bags enclose all tools, and samples are stored in boxes with argon or nitrogen.
• Intense pressure, high temperatures, liveable space, and nutrient availability affect the diversity of microorganisms.
• Temperature is the biggest limitation, increasing with depth in the subsurface.
• The highest temperature generally accepted as liveable for microorganisms is 110°C.
• Oceanic crusts have a temperature increase of about 15°C per kilometer of depth.
• Temperature in oceanic crust results in a maximum liveable depth of about 7 kilometers.
• Continental crust experiences an increase of about 25°C per kilometer.
• Temperature in continental crust results in a maximum liveable depth of approximately 4 kilometers.
• The deep subsurface microbial community has an unexpectedly diverse population.
• Both Bacteria and Archaea have been found at depths of several thousand metres below surface.
• Groundwater flowing through their habitat provides nutrients.
• Long-term isolation in deep subsurface groundwater can lead to allopatric speciation.
• Bacterial and Archaeal species specialize in inorganic substrate oxidation for energy.
• Key energy sources are iron and sulphur oxidation.
• Thermophilic metal oxidizers thrive in the deep subsurface.
• Sedimentary deposits or oil reservoirs host both chemoorganotrophic and chemolithotrophic organisms.
• These ecosystems have microbial densities from single cells to 100 million per gram of rock (102 – 108 cells per ml).
• Cell division can occur as infrequently as once per day, decade, or even century.

Key Organisms

• Lithotrophs obtain energy through the oxidation of soluble inorganic compounds.
• H2 is the primary electron donor used by lithotrophs.
• Reduced sulfur compounds are utilized by microbes to remove H₂ from its mineralized form.
• Examples of lithotrophs: Desulfovibrio profundus, Desulfovibrio aespoeensis, Desulfomicrobium baculatum.
• Other lithotrophic pathways in the deep subsurface are iron [Fe (III)], manganese [Mn (IV)], and arsenic oxidation.
• Genera examples are Geobacter, Thermothrix, Pyrobaculum, Aquifex, Thioploca, and Ferroglobus.
• The carbon source is CO2 trapped in the rocks.
• Heterotrophs face a challenge with organic carbon availability in the subsurface.
• Carbon sources include ancient buried organic matter, hydrocarbons, and dead microbes.
• Energy is derived from reduced inorganic substrates or from hydrocarbons.
• Thermophiles thrive deep in the rocks near the magma layer, and/or within hydrothermal waters deep under the ocean floor.

Discoveries of Deep Subsurface Microorganisms

• In 2000, researchers discovered an ancient microorganism in a New Mexico salt deposit, 610 meters below ground that was 250 million years old.
• The ancient microorganism was trapped in brine and in a dormant state, waiting for the right conditions to "awaken".
• Metabolically active microbes have been found in subsurface permafrost in the Arctic and Antarctic.
• Permafrost temperatures were -10°C (14°F) or colder for 2-3 million years.
• High populations of viable microbes reside in half-kilometer oceanic sediment cores that are more than 10 million years old.
• In the mid-1990s, novel hyperthermophilic microbes were found in hot oil reservoirs which were 3 kilometers below the North Sea and Alaska's North Slope.
• Scientists initially thought organisms were sour contaminates but realized they occur naturally
• Microbes lived in organic compounds in the oil.
• Strain 121 (Geogemma barossii), discovered in 2003, is a hyperthermophile that can grow at 121°C (250°F).
• A variety of microbes were found in gabbro 750m below the ocean floor including extremophiles.
• Organisms include Chroococcidiopsis and Pseudomonas.

Adaptation

• Microorganisms in the deep subsurface have adapted to nutrient limitations.
• They can reduce inorganic compounds like iron and sulphur from the rocks.
• Some microbes (Thermincola ferriacetica) use molecular hydrogen, iron compounds, and carbon dioxide.
• The heterotrophic species here feed on organic waste from lithoautotrophs and dead cells.
• They can remain viable at minimal metabolic cost, blurring the lines between life and death.
• During water reserve depletion, microorganisms shrink their body size to 1/1000 of original volume for desiccation.
• Dwarfed microbes are called "ultramicro-bacteria".
• Microorganisms enter a dormancy period at this stage.
• Deep subsurface microbes exhibit extreme radiation resistance.
• High radiation levels may act as a renewable energy source.
• Organisms in these communities have improved DNA repair mechanisms due to prevalence of DNA damage.
• Selective pressure has created exceptionally efficient and effective DNA repair mechanisms.

Application of Deep Subsurface Microorganisms

• Deep subsurface microbes are investigated for medical uses, like anti-cancer and anti-AIDS drugs.
• These microorganisms are used in bioaugmentation for ground water cleanup.
• Pollution-eating bacteria metabolize pollutants.
• They can reduce the harm pollutants cause
• Example of a non-adhesive bacteria used in bioaugmentation is Mary deFlaun (Envirogen).
• Deep subsurface environments considered for the storage of nuclear waste underground.

Microorganisms found in Deep Subsurface Environments

• Desulforudis audaxviator was first discovered in a South American gold mine at 2.8km depth.
• The gold mine was the Mponeng gold mine.
• Organism identified by genome analysis but has yet to be cultured.
• It is a gram-positive rod bacterium and possibly thermophilic.
• Found in groundwater exceeding 60°C, groundwater at pH 9, anoxic and nutrient deficient.
• They are motile sporulating chemoautotrophs.
• D. audaxviator grows autotrophically using H2 as the electron donor and CO2 for fixation.
• The organism contains nitrogen fixation genes.
• D. audaxviator has a diet of only a few minerals, consisting of CO2, SO42-, N2, and H2.
• It has traded DNA with Archaea, adapted to high temperatures and no light.
• D. audaxviator has learned to live off of almost nothing because of adaptation.
• D. audaxviator lives in an ecosystem that relies on radioactivity, not sunlight or chemical energy.
• Its genome is 2.35 megabase pairs (Mbp) in size, with 2157 protein-encoding genes.
• The cell has every pathway needed to synthesize all amino acids.