Key Concepts in Microbial Ecology and Metabolism

Posted on Jan 24, 2026 in Microbiology

Microbiology Key Concepts

Biogeochemical cycles: Involve the oxidation of substrates; cycles are interlinked (Carbon, Nitrogen, Sulfur).
Carbon cycle: Key determinant of ecosystem productivity and water quality.

Autotrophs: Utilize CO₂ as a carbon source.
- Photoautotrophs: Obtain energy from light.
- Chemoautotrophs: Obtain energy from inorganic compounds.
Heterotrophs: Require organic carbon (C).
- Photoheterotrophs: Use light for energy and organic C for carbon.
- Chemoheterotrophs: Use organic C for both energy and carbon (e.g., fungi).
Anaerobic metabolism: Uses non-oxygen electron acceptors. Includes fermentation.
Methane Cycling:
- Methanotrophs: Aerobic methane (CH₄) oxidizers.
- Methanogens: Anaerobic methane (CH₄) producers.

Microbial Loop: A pathway where dissolved organic carbon (DOC) is recycled: DOC → Bacteria → Phage Lysis → Nutrient Release → Cyanobacteria.

Sulfur is a key nutrient, utilized in energy metabolism, and abundant in seawater.
Assimilative Reduction: Sulfate (SO₄²⁻) is converted to organic sulfur (e.g., cysteine) for biomass synthesis.
Dissimilative Reduction: Sulfate (SO₄²⁻) is reduced to hydrogen sulfide (H₂S) to yield energy. This process is anaerobic and produces metal sulfides.
Sulfur Oxidation:
- H₂S → S⁰ → SO₄²⁻. This process is energy-yielding.
- Phototrophs: Examples include purple and green sulfur bacteria.
- Chemolithoautotrophs: These organisms are widely distributed.
Sulfur Reduction: Elemental sulfur (S⁰) is reduced to H₂S, playing a role in both Carbon and Sulfur cycling.
Human Impacts: Burning fossil fuels increases SO₂ emissions, leading to acid rain and subsequent soil and health issues.
Biotechnology Uses: Includes biotreatment of mine drainage and H₂S removal.

Structure: Layered communities stabilized by extracellular polymeric substances (EPS), characterized by steep chemical gradients.
Functions: Perform photosynthesis, fermentation, and respiration.
Significance: Represent ancient life forms, are self-sustaining, and are found in extreme habitats.
Processes: Efficiently recycle waste into resources.
Conservation Example: Shark Bay (hypersaline environment, serving as an early Earth analogue).

Signals: Autoinducers like AHLs (Acyl-Homoserine Lactones) found in the EPS matrix.
Quorum Sensing: A density-dependent signaling mechanism.
- Long-chain signals are typically stable.
- Short-chain signals are typically labile (unstable).
Cross-talk: Communication that occurs between different microbial species (e.g., involving sulfate reducers).

Bifidobacterium: An early colonizer, crucial for pathogen exclusion and immune development.
Development: Significant shift occurs with diet change (~12 months); community stabilizes around age 3.
Structure: Microbes generally do not have direct epithelial contact. Layers include inner mucosa, outer mucosa, and feces.
Functions:
- Produces Short-Chain Fatty Acids (SCFAs): butyrate, acetate, and propionate.
- Involved in the Gut-Brain Axis: communication occurs via the immune system, vagus nerve, and tryptophan metabolism.
Dysbiosis: An imbalance that can lead to disease; antibiotics cause long-term disruption.
Therapies: Includes probiotics, prebiotics, synbiotics, and fecal microbiota transplants (FMT).
Impact of Industrialization: Associated with reduced microbial diversity (bacteria, viruses, and helminths/worms).

Eukarya Origin Hypothesis: Suggests a merger between an archaeon (the host) and a bacterium (which became the mitochondria).
Asgard Archaea: Considered the closest known relatives of eukaryotes.
- They encode “eukaryotic signature proteins” (e.g., actin, components for trafficking, and signaling).
Cultivation Status: Only two species have been successfully cultured; they were found in Shark Bay microbial mats.
Research Note: The Burns Lab sequenced genomes and successfully cultured the strain named “Nelly.”
Metabolism: Mixotrophic, capable of H₂ production, utilizes the Wood–Ljungdahl pathway, and possesses rhodopsins.
Syntrophy: Requires the presence of sulfate reducers; flagellar interactions are likely involved in this relationship.

Deep Ecosystems: Primarily driven by H₂ and chemolithoautotrophy.
Examples:
- Hydrothermal Vents: Feature H₂S oxidation (e.g., Beggiatoa).
- Tube Worms: Exhibit symbiosis with sulfur-oxidizers, utilizing the Calvin cycle.
Columbia River Basalt: Microbes thrive without external organic carbon, contributing to rock weathering.
Significance:
- Serves as an evolutionary model for life existing prior to photosynthesis.
- Involved in natural gas and pollutant degradation.
- A possible analogue for extraterrestrial life.

Culture-Independent Techniques: Include PCR, 16S rRNA gene sequencing, and meta-omics approaches.
Microelectrodes: Used to measure O₂ and Sulfur turnover rates in situ.
High-Throughput Sequencing Methods:
- Taxonomy (16S/ITS): Determines “Who is there.”
- Metagenomics: Determines “What they potentially can do” (genetic potential).
- Metaproteomics: Determines “What they are actively doing” (expressed functions).
Knowledge Gaps: Include “dark matter” microbes, incomplete understanding of Nitrogen cycles, unknown microbial interactions, and the full roles of viruses.