4.1 Marine bacteria and archaea

The ocean teems with microscopic life. Bacteria and archaea inhabit every nook, from sun-drenched surface waters to the darkest depths. These tiny organisms play outsized roles in marine ecosystems, driving crucial processes like carbon and nitrogen cycling.

Marine microbes have adapted to thrive in diverse ocean environments. Some withstand crushing pressures in the deep sea, while others flourish in scorching hydrothermal vents. Scientists use cutting-edge techniques to study these elusive organisms and unravel their ecological importance.

Marine Bacteria and Archaea

Diversity of marine microorganisms

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• Marine bacteria and archaea inhabit all ocean environments from the surface to the deep sea
  • Estimated over $10^{28}$ bacterial and archaeal cells in the ocean
• Highest abundance and diversity found in the upper ocean layers (epipelagic zone)
  • Sunlit surface waters support high primary productivity providing organic matter for heterotrophic bacteria
• Deep ocean environments (mesopelagic and bathypelagic zones) have lower abundance but still harbor diverse bacterial and archaeal communities
  • Adapted to low nutrient concentrations, high pressure, and absence of sunlight
• Coastal and estuarine environments exhibit high bacterial and archaeal diversity and abundance
  • Influenced by terrestrial inputs of nutrients and organic matter (rivers, runoff)
• Hydrothermal vents and cold seeps support unique bacterial and archaeal communities
  • Chemosynthetic organisms thrive in these extreme environments (high temperatures, toxic chemicals)

Ecological roles of bacteria and archaea

• Carbon cycling
  • Heterotrophic bacteria decompose and remineralize organic matter releasing nutrients back into the water column
  • Chemoautotrophic bacteria and archaea fix inorganic carbon contributing to primary production in the absence of sunlight
• Nitrogen cycling
  • Nitrifying bacteria and archaea oxidize ammonia to nitrite and nitrate
  • Denitrifying bacteria reduce nitrate to nitrogen gas removing bioavailable nitrogen from the ocean
  • Nitrogen-fixing bacteria convert atmospheric nitrogen to ammonia making it available for biological uptake
• Sulfur cycling
  • Sulfate-reducing bacteria reduce sulfate to hydrogen sulfide in anoxic environments (sediments, oxygen minimum zones)
  • Sulfur-oxidizing bacteria oxidize hydrogen sulfide to sulfate coupling this process with carbon fixation
• Degradation of complex organic compounds such as hydrocarbons and pollutants
• Transformation and cycling of trace metals and other elements (iron, manganese)

Adaptations to ocean environments

• Temperature adaptations
  • Psychrophilic bacteria and archaea adapted to cold temperatures in polar regions and the deep sea
  • Thermophilic bacteria and archaea thrive in high-temperature environments like hydrothermal vents
• Pressure adaptations
  • Piezophilic bacteria and archaea adapted to high pressures in the deep ocean
  • Possess specialized membrane lipids and proteins to maintain cell integrity and function
• Nutrient adaptations
  • Oligotrophic bacteria and archaea adapted to low nutrient concentrations in the open ocean
  • Have high surface area-to-volume ratios and efficient nutrient uptake systems
• Light adaptations
  • Photoheterotrophic bacteria use light energy to supplement their organic carbon requirements
  • Rhodopsin-containing bacteria and archaea use light-driven proton pumps for energy production
• Symbiotic adaptations
  • Some bacteria and archaea form symbiotic relationships with marine organisms such as sponges and corals
  • Provide nutrients and chemical defenses in exchange for a stable habitat and organic carbon sources

Methods for studying marine microbes

• Culture-dependent methods
  • Isolation and cultivation of bacteria and archaea on selective media
  • Allows for physiological and biochemical characterization of individual strains
  • Limited by the fact that many marine bacteria and archaea are difficult to culture in the laboratory
• Culture-independent methods
  • Molecular techniques that do not require cultivation of organisms
  • 16S rRNA gene sequencing
    • Identifies and classifies bacteria and archaea based on their evolutionary relationships
    • Provides insights into community composition and diversity
  • Metagenomics
    • Sequencing of total DNA extracted from environmental samples
    • Reveals the metabolic potential and functional diversity of microbial communities
  • Single-cell genomics
    • Isolation and sequencing of individual bacterial or archaeal cells
    • Allows for the study of uncultured organisms and their genomes
  • Other approaches: metatranscriptomics, metaproteomics, stable isotope probing