🧫Geomicrobiology Unit 9 – Microbes in Sedimentary Processes

Key Concepts and Terminology

• Sedimentary processes involve the deposition, accumulation, and lithification of sediments over time
• Microbes play crucial roles in sedimentary environments by influencing chemical, physical, and biological processes
• Biogeochemical cycling refers to the transfer of elements between the biosphere, atmosphere, hydrosphere, and lithosphere mediated by microbial activities
• Microbial metabolism encompasses the chemical reactions that microorganisms use to obtain energy and nutrients for growth and reproduction
  • Includes processes such as photosynthesis, chemosynthesis, fermentation, and respiration
• Diagenesis is the process by which sediments are transformed into sedimentary rocks through compaction, cementation, and recrystallization
• Microbial mats are layered communities of microorganisms that form in aquatic environments and can trap and bind sediments
• Stromatolites are layered sedimentary structures formed by the trapping, binding, and cementation of sediments by microbial mats

Microbial Diversity in Sediments

• Sedimentary environments harbor diverse microbial communities adapted to various physical and chemical conditions
• Bacteria and archaea are the most abundant microorganisms in sediments due to their ability to survive in extreme conditions (high pressure, low oxygen, limited nutrients)
• Microbial diversity in sediments is influenced by factors such as organic matter availability, redox gradients, and sediment composition
• Techniques such as 16S rRNA gene sequencing and metagenomics have revealed the presence of novel microbial lineages in sediments
  • These techniques allow for the identification and characterization of microbes without the need for cultivation
• Microbial communities in sediments exhibit vertical stratification, with different groups of microbes occupying specific depth horizons based on their metabolic requirements
• Interactions between different microbial groups (syntrophy, competition) shape the structure and function of sedimentary microbial communities
• Viruses (bacteriophages) play important roles in regulating microbial populations and facilitating horizontal gene transfer in sediments

Sedimentary Environments and Microbes

• Microbes are found in a wide range of sedimentary environments, including marine, lacustrine, and terrestrial settings
• Marine sediments, such as those in the deep sea and coastal regions, are characterized by high pressure, low temperature, and limited organic matter input
  • These conditions favor the growth of specialized microbial communities adapted to oligotrophic conditions
• Lacustrine sediments (lake sediments) often exhibit seasonal variations in microbial community composition due to changes in temperature, nutrient availability, and mixing patterns
• Terrestrial sediments, such as those in soils and subsurface environments, host diverse microbial communities involved in the decomposition of organic matter and weathering of minerals
• Extreme sedimentary environments, such as hot springs, hypersaline lakes, and subglacial sediments, support unique microbial communities adapted to harsh conditions
• Microbes in sedimentary environments are involved in the formation of various geological features, such as microbialites, carbonate deposits, and iron-rich sediments
• The study of microbes in ancient sedimentary rocks (paleomicrobiology) provides insights into the evolution of life and past environmental conditions on Earth

Microbial Metabolic Processes

• Microbial metabolism in sediments is driven by the availability of electron donors (organic matter, reduced inorganic compounds) and electron acceptors (oxygen, nitrate, sulfate, iron)
• Aerobic respiration is the most energetically favorable metabolic process and occurs in the presence of oxygen
  • Microbes use oxygen as the terminal electron acceptor to oxidize organic matter or reduced inorganic compounds
• In the absence of oxygen, microbes utilize alternative electron acceptors for anaerobic respiration, following a sequence based on energy yield (nitrate, manganese, iron, sulfate, carbon dioxide)
• Fermentation is a metabolic process that occurs in the absence of external electron acceptors, where organic compounds serve as both electron donors and acceptors
  • Fermentation products (short-chain fatty acids, alcohols) can be further utilized by other microbes in the community
• Chemolithotrophy involves the use of inorganic compounds (hydrogen, sulfur, iron) as energy sources for microbial growth
• Phototrophy, particularly in shallow sedimentary environments, involves the use of light energy to drive the fixation of carbon dioxide into organic compounds
• Syntrophic interactions between different microbial groups allow for the complete degradation of complex organic compounds in sediments
  • Example: Fermentative bacteria break down complex organic matter into simpler compounds, which are then utilized by methanogens to produce methane

Biogeochemical Cycling

• Microbes in sediments play critical roles in the cycling of carbon, nitrogen, sulfur, and other elements
• The carbon cycle in sediments involves the degradation of organic matter by heterotrophic microbes and the production of methane by methanogens
  • Methanogenesis is a key process in anaerobic sediments, contributing to the global methane budget
• Nitrogen cycling in sediments includes processes such as nitrogen fixation, nitrification, denitrification, and anaerobic ammonium oxidation (anammox)
  • These processes are mediated by specialized groups of microbes and influence the availability of nitrogen for biological productivity
• Sulfur cycling in sediments is driven by sulfate-reducing bacteria, which use sulfate as an electron acceptor for the oxidation of organic matter
  • The production of hydrogen sulfide by sulfate reducers can lead to the formation of metal sulfide minerals (pyrite) and the development of euxinic conditions
• Iron cycling in sediments involves the reduction of ferric iron (Fe(III)) to ferrous iron (Fe(II)) by iron-reducing bacteria
  • The formation of iron-rich sediments (banded iron formations) in the geologic past is attributed to the activity of iron-oxidizing bacteria
• Microbes in sediments also participate in the cycling of other elements, such as phosphorus, manganese, and trace metals, through various redox reactions and biomineralization processes

Microbial Influence on Sediment Formation

• Microbes contribute to the formation and stabilization of sediments through various processes, such as trapping and binding of particles, biomineralization, and alteration of sediment properties
• Microbial mats and biofilms, composed of extracellular polymeric substances (EPS), help to trap and bind sediment particles, promoting sediment accumulation and stability
• Biomineralization processes, such as the precipitation of calcium carbonate or iron oxides, can lead to the formation of microbially-induced sedimentary structures (MISS)
  • Examples include stromatolites, thrombolites, and microbially-induced carbonate precipitation
• Microbial activities can alter the physical and chemical properties of sediments, such as porosity, permeability, and pH, influencing diagenetic processes and the preservation of sedimentary features
• The production of biosurfactants by microbes can enhance the mobilization and transport of hydrocarbons in sediments, with implications for oil and gas exploration
• Microbial degradation of organic matter in sediments contributes to the formation of petroleum and natural gas reserves over geologic time scales

Research Methods and Techniques

• A combination of field-based and laboratory-based approaches is used to study microbes in sedimentary processes
• Sampling techniques, such as coring and drilling, are employed to obtain sediment samples from various depths and environments
  • Special precautions (aseptic techniques, anaerobic sampling) are necessary to maintain the integrity of microbial communities during sampling
• Geochemical analyses, including measurements of pH, redox potential, and concentrations of various chemical species, provide insights into the biogeochemical conditions in sediments
• Microscopy techniques, such as scanning electron microscopy (SEM) and transmission electron microscopy (TEM), allow for the visualization of microbial cells and their associations with sediment particles
• Cultivation-based approaches involve the isolation and characterization of microbes from sediments using selective media and growth conditions
  • However, the majority of microbes in sediments are difficult to cultivate using standard laboratory techniques
• Molecular techniques, such as 16S rRNA gene sequencing, metagenomics, and metatranscriptomics, enable the study of microbial diversity and function in sediments without the need for cultivation
  • These techniques provide insights into the metabolic potential and active processes within microbial communities
• Stable isotope probing (SIP) allows for the identification of microbes actively involved in specific biogeochemical processes by tracking the incorporation of isotopically labeled substrates
• Geochemical modeling and reactive transport modeling are used to simulate and predict the interactions between microbial activities and sedimentary processes over time and space

Real-World Applications and Case Studies

• Understanding the role of microbes in sedimentary processes has important implications for various fields, including environmental management, energy exploration, and climate change studies
• Bioremediation strategies employ microbes to degrade contaminants (hydrocarbons, heavy metals) in sediments, helping to restore impacted environments
  • Example: The use of sulfate-reducing bacteria to immobilize heavy metals in acid mine drainage
• Microbial enhanced oil recovery (MEOR) techniques involve the injection of microbes or their products into oil reservoirs to improve oil production and recovery
  • Example: The use of biosurfactant-producing bacteria to enhance oil mobilization in low-permeability reservoirs
• The study of microbial communities in sediments can provide insights into past climate conditions and environmental changes, as preserved in the sedimentary record
  • Example: The analysis of lipid biomarkers and isotopic signatures in sediment cores to reconstruct past ocean temperatures and productivity
• Microbial processes in sediments have implications for the global carbon cycle and climate change, particularly through the production and consumption of greenhouse gases (methane, carbon dioxide)
  • Example: The potential release of methane from thawing permafrost sediments and its impact on global warming
• The discovery of novel microbial lineages and metabolic capabilities in sediments can lead to the development of new biotechnological applications, such as the production of biofuels or the synthesis of novel compounds
  • Example: The identification of enzymes from sedimentary microbes that can degrade recalcitrant organic compounds or tolerate extreme conditions