🧫Geomicrobiology Unit 4 – Microbial Metabolism & Biogeochemical Cycles

Key Concepts

• Microorganisms play a crucial role in biogeochemical cycles by transforming and recycling elements essential for life (carbon, nitrogen, sulfur, phosphorus, and iron)
• Microbial metabolism drives the flow of energy and matter through ecosystems, linking the biosphere, geosphere, hydrosphere, and atmosphere
• Microbes have evolved diverse metabolic strategies to harness energy from organic and inorganic compounds, including chemotrophy, phototrophy, and lithotrophy
• Redox reactions are central to microbial metabolism, involving the transfer of electrons from reduced donors to oxidized acceptors
• Microbial activity influences the geochemistry of various environments, such as soils, sediments, aquatic systems, and the subsurface
• Understanding microbial metabolism and biogeochemical cycles is essential for addressing environmental challenges (climate change, pollution, and resource management)
• Geomicrobiological research integrates concepts and techniques from microbiology, geology, chemistry, and ecology to study the interactions between microbes and Earth systems

Microbial Energy Generation

• Microbes generate energy through catabolic reactions that break down organic or inorganic compounds, releasing electrons and protons
• Chemotrophs obtain energy by oxidizing chemical compounds, such as organic matter (chemoorganotrophs) or inorganic substances (chemolithotrophs)
  • Chemoorganotrophs utilize organic compounds (glucose, amino acids, or hydrocarbons) as both electron donors and carbon sources
  • Chemolithotrophs oxidize inorganic compounds (hydrogen, sulfur, iron, or ammonia) to generate energy and reduce inorganic carbon for biosynthesis
• Phototrophs harness energy from light using photosynthetic pigments (chlorophylls or bacteriochlorophylls) to drive the synthesis of organic compounds
  • Oxygenic phototrophs (cyanobacteria and algae) use water as an electron donor, releasing oxygen as a byproduct
  • Anoxygenic phototrophs (purple and green bacteria) use alternative electron donors (hydrogen sulfide or hydrogen) and do not produce oxygen
• Lithotrophs obtain energy from the oxidation of inorganic electron donors, such as reduced sulfur, iron, or hydrogen compounds
• Electron transport chains (ETC) couple the oxidation of electron donors to the reduction of terminal electron acceptors, generating a proton motive force that drives ATP synthesis
• Fermentation is an anaerobic process in which organic compounds serve as both electron donors and acceptors, producing ATP through substrate-level phosphorylation

Carbon Metabolism

• Carbon is the backbone of organic molecules and is cycled through various reservoirs (atmosphere, biosphere, hydrosphere, and geosphere)
• Autotrophic microbes fix inorganic carbon (CO2) into organic compounds using energy from light (photoautotrophs) or chemical reactions (chemoautotrophs)
  • The Calvin-Benson-Bassham (CBB) cycle is the most common pathway for CO2 fixation, using the enzyme RuBisCO to incorporate CO2 into ribulose bisphosphate
  • Alternative CO2 fixation pathways include the reverse tricarboxylic acid (rTCA) cycle, the Wood-Ljungdahl pathway, and the 3-hydroxypropionate bicycle
• Heterotrophic microbes obtain carbon and energy from organic compounds, breaking them down through various catabolic pathways
  • Glycolysis is a central pathway that oxidizes glucose to pyruvate, generating ATP and reducing equivalents (NADH)
  • The tricarboxylic acid (TCA) cycle oxidizes acetyl-CoA derived from pyruvate or fatty acids, producing CO2, ATP, and reducing equivalents (NADH and FADH2)
• Methanogenesis is a specialized form of anaerobic respiration in which archaea reduce CO2 or acetate to methane using hydrogen or organic compounds as electron donors
• Methane oxidation is carried out by methanotrophic bacteria, which use methane as both a carbon and energy source, converting it to CO2
• Carbon fixation and respiration processes are tightly coupled in microbial communities, with the products of one group serving as substrates for another

Nitrogen Cycle

• Nitrogen is an essential component of proteins, nucleic acids, and other biomolecules, and its availability often limits biological productivity
• The nitrogen cycle involves several microbially-mediated transformations: nitrogen fixation, nitrification, denitrification, and ammonification
• Nitrogen fixation is the conversion of atmospheric N2 to ammonia (NH3) or ammonium (NH4+), carried out by specialized bacteria and archaea (diazotrophs)
  • Diazotrophs possess the nitrogenase enzyme complex, which reduces N2 to NH3 using ATP and reducing equivalents
  • Symbiotic nitrogen fixation occurs in the root nodules of legumes, where rhizobia bacteria provide fixed nitrogen to the plant in exchange for carbon compounds
• Nitrification is the oxidation of ammonia to nitrite (NO2-) and then to nitrate (NO3-) by chemolithotrophic bacteria and archaea
  • Ammonia-oxidizing bacteria (AOB) and archaea (AOA) use ammonia as an electron donor and oxygen as an electron acceptor, producing nitrite
  • Nitrite-oxidizing bacteria (NOB) oxidize nitrite to nitrate using oxygen as an electron acceptor
• Denitrification is the reduction of nitrate to nitric oxide (NO), nitrous oxide (N2O), and finally to N2, carried out by facultative anaerobic bacteria under low oxygen conditions
  • Denitrifiers use nitrate as a terminal electron acceptor in the absence of oxygen, coupling its reduction to the oxidation of organic compounds or hydrogen
• Ammonification is the conversion of organic nitrogen compounds (proteins, amino acids) to ammonia through microbial decomposition
  • Ammonifying bacteria and fungi release ammonia as a byproduct of their metabolism, which can then be assimilated by plants or other microbes

Sulfur Cycle

• Sulfur is an important element in proteins (cysteine and methionine), coenzymes (coenzyme A, biotin), and other biomolecules
• The sulfur cycle involves the transformation of sulfur compounds between various oxidation states (-2 to +6) through microbial metabolism
• Sulfate reduction is the anaerobic respiration process in which sulfate (SO42-) serves as a terminal electron acceptor, producing hydrogen sulfide (H2S)
  • Sulfate-reducing bacteria (SRB) couple the oxidation of organic compounds or hydrogen to the reduction of sulfate, generating ATP through chemiosmosis
  • SRB are important in anoxic environments (sediments, wetlands, and the subsurface) and can contribute to the formation of metal sulfide minerals
• Sulfide oxidation is carried out by chemolithotrophic and phototrophic bacteria, converting H2S or other reduced sulfur compounds to elemental sulfur (S0) or sulfate
  • Colorless sulfur bacteria (Thiobacillus, Beggiatoa) use oxygen or nitrate as electron acceptors to oxidize H2S, S0, or thiosulfate (S2O32-) to sulfate
  • Purple and green sulfur bacteria use H2S or S0 as electron donors in anoxygenic photosynthesis, producing sulfate or S0 as end products
• Sulfur disproportionation is a process in which certain bacteria (Desulfocapsa, Desulfobulbus) simultaneously oxidize and reduce S0 or thiosulfate, producing sulfate and H2S
• Microbial sulfur transformations play a key role in the formation of sedimentary sulfide minerals (pyrite, FeS2) and the mobilization of metals in acid mine drainage environments

Other Biogeochemical Cycles

• The phosphorus cycle involves the microbial transformation of phosphorus compounds between organic and inorganic forms
  • Phosphate-solubilizing bacteria (Pseudomonas, Bacillus) release inorganic phosphate from insoluble mineral phosphates or organic phosphorus compounds
  • Polyphosphate-accumulating organisms (PAOs) store excess phosphate as intracellular polyphosphate granules, which can be released under anaerobic conditions
• The iron cycle is driven by the redox transformations of iron between ferrous (Fe2+) and ferric (Fe3+) states, mediated by microorganisms
  • Iron-reducing bacteria (Geobacter, Shewanella) use Fe3+ as a terminal electron acceptor in anaerobic respiration, producing Fe2+
  • Iron-oxidizing bacteria (Acidithiobacillus, Leptospirillum) oxidize Fe2+ to Fe3+ using oxygen or nitrate as electron acceptors, contributing to the formation of iron oxide minerals
• The manganese cycle involves the microbial oxidation and reduction of manganese between Mn2+ and Mn4+ states
  • Manganese-oxidizing bacteria (Leptothrix, Pseudomonas) oxidize Mn2+ to Mn4+, forming manganese oxide minerals
  • Manganese-reducing bacteria (Shewanella, Geobacter) reduce Mn4+ to Mn2+ in anaerobic respiration, coupled to the oxidation of organic compounds or hydrogen
• Microbial transformations of other elements (selenium, arsenic, mercury) also play important roles in their biogeochemical cycling and environmental fate

Environmental Impacts

• Microbial metabolism and biogeochemical cycles have significant impacts on the environment, both locally and globally
• Microbial nitrogen fixation and nitrification contribute to the availability of nitrogen for plant growth, but excessive nitrogen inputs can lead to eutrophication and water quality issues
• Denitrification and anaerobic ammonium oxidation (anammox) remove fixed nitrogen from ecosystems, helping to counterbalance nitrogen fixation and maintain nitrogen limitation
• Microbial sulfur and iron transformations influence the formation and dissolution of minerals, affecting soil and sediment structure, porosity, and geochemistry
• Sulfate reduction in anaerobic environments can lead to the production of hydrogen sulfide, which is toxic to many organisms and can cause corrosion of infrastructure
• Methanogenesis in wetlands, rice paddies, and the guts of ruminants contributes to the emission of methane, a potent greenhouse gas
• Methane oxidation by methanotrophic bacteria helps to mitigate methane emissions, acting as a biological filter
• Microbial carbon fixation (primary production) and respiration are major drivers of the global carbon cycle, influencing atmospheric CO2 levels and climate
• Microbial interactions with pollutants (hydrocarbons, heavy metals) can lead to their degradation or immobilization, contributing to bioremediation efforts

Lab Techniques and Applications

• Cultivation-based techniques involve the isolation and growth of microorganisms in the laboratory using selective media and growth conditions
  • Enrichment cultures are used to select for specific functional groups of microbes (methanogens, sulfate reducers) by providing favorable substrates and conditions
  • Pure cultures allow the study of individual microbial species and their metabolic capabilities, but many environmentally relevant microbes are difficult to cultivate
• Molecular techniques enable the study of microbial communities without the need for cultivation, based on the analysis of nucleic acids (DNA, RNA)
  • 16S rRNA gene sequencing is used to identify and classify microorganisms based on the sequence of this conserved gene, providing insights into community composition and diversity
  • Metagenomics involves the sequencing of total DNA extracted from an environmental sample, allowing the exploration of the metabolic potential of microbial communities
  • Metatranscriptomics and metaproteomics provide information on the actual expression of genes and proteins in microbial communities, indicating active metabolic processes
• Stable isotope probing (SIP) tracks the incorporation of isotopically labeled substrates (13C, 15N) into microbial biomolecules, enabling the identification of microbes responsible for specific metabolic activities
• Geochemical analyses (ion chromatography, mass spectrometry) are used to measure the concentrations and isotopic composition of metabolic reactants and products, providing insights into microbial activity and biogeochemical processes
• Microscopy techniques (fluorescence in situ hybridization, electron microscopy) allow the visualization and spatial analysis of microbial cells and their associations with minerals or other organisms
• Geomicrobiological knowledge and techniques are applied in various fields, including:
  • Bioremediation of contaminated soils, groundwater, and wastewater
  • Enhanced oil recovery and biogenic methane production
  • Biomining and bioleaching of metals from ores
  • Carbon sequestration and climate change mitigation
  • Astrobiology and the search for life on other planets