Week 10

Cycles, Biodegradation and Bioremediation

1 sub-topics · Pages 472–501

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1. The Biogeochemical Cycles

📖 Lecturer's Note

Microorganisms are the primary catalysts of all major biogeochemical cycles — the global pathways by which carbon, nitrogen, sulfur, phosphorus, and other elements cycle between living organisms and the abiotic environment. By catalysing redox transformations — carbon fixation and respiration, nitrogen fixation and denitrification, sulfate reduction and sulfur oxidation — microbial communities regulate the chemical composition of soils, waters, and the atmosphere. Disruption of these cycles through pollution or climate change has profound consequences for ecosystem health and human welfare.

✏️ Fill in the Blank

1. The process by which photosynthetic organisms incorporate atmospheric CO₂ into organic molecules is called _______.

Show Answer Carbon fixation (CO₂ fixation)

2. Biogeochemical cycles are fundamentally driven by microbial _______ reactions in which elements are oxidised or reduced.

Show Answer Redox

3. The anaerobic process by which sulfate-reducing bacteria convert sulfate to hydrogen sulfide is called dissimilatory sulfate _______.

Show Answer Reduction

4. The addition of specialised microbial cultures to a contaminated site to accelerate biodegradation is called bio_______.

Show Answer Augmentation (bioaugmentation)

5. Methane is produced from CO₂ and H₂ (or acetate) by microorganisms called _______.

Show Answer Methanogens

6. The anaerobic decomposition of organic matter to methane and CO₂ by a community of microorganisms is called _______.

Show Answer Methanogenesis (anaerobic digestion)

7. The process by which microorganisms convert nitrate to nitrogen gas is called _______.

Show Answer Denitrification

8. The removal of phosphorus from wastewater using polyphosphate-accumulating microorganisms is called _______ biological phosphorus removal.

Show Answer Enhanced (EBPR)

🔘 Multiple Choice

1. In the nitrogen cycle, the conversion of ammonium (NH₄⁺) to nitrate (NO₃⁻) is called:

  • A) Nitrogen fixation
  • B) Denitrification
  • C) Nitrification
  • D) Ammonification
Show Answer Correct: C) Nitrification

2. Denitrification is problematic in agricultural soils because it:

  • A) Produces toxic ammonium that damages plant roots
  • B) Converts bioavailable nitrate back to N₂ gas, reducing soil fertility
  • C) Acidifies the soil by producing nitric acid
  • D) Converts sulfate to hydrogen sulfide
Show Answer Correct: B) Converts bioavailable nitrate back to N₂ gas, reducing soil fertility

3. Bioremediation uses microorganisms to:

  • A) Synthesise antibiotics from soil contaminated with heavy metals
  • B) Degrade or detoxify pollutants in contaminated environments
  • C) Produce biofuels exclusively from cellulosic waste
  • D) Extract rare earth elements from mine tailings
Show Answer Correct: B) Degrade or detoxify pollutants in contaminated environments

4. The major greenhouse gas produced by methanogenic archaea in waterlogged rice paddies and swamps is:

  • A) CO₂
  • B) N₂O
  • C) CH₄
  • D) H₂S
Show Answer Correct: C) CH₄

5. Polycyclic aromatic hydrocarbons (PAHs) such as naphthalene and phenanthrene are degraded aerobically by bacteria primarily through:

  • A) Direct ring cleavage by hydrolases
  • B) Initial dioxygenase attack introducing two hydroxyl groups, followed by ring cleavage and channelling into central metabolic pathways
  • C) Reduction of the aromatic ring under anaerobic conditions
  • D) Photolysis catalysed by bacterial pigments
Show Answer Correct: B) Initial dioxygenase attack introducing two hydroxyl groups, followed by ring cleavage and channelling into central metabolic pathways

6. Mycorrhizal associations are important in the phosphorus cycle because:

  • A) Mycorrhizal fungi fix atmospheric phosphorus gas into phosphate
  • B) Fungal hyphae extend far beyond the root depletion zone, solubilising and absorbing inorganic phosphate and transferring it to the plant
  • C) Mycorrhizal fungi produce phosphatases that work only in alkaline soils
  • D) They convert organic phosphate to atmospheric P₄ via anaerobic respiration
Show Answer Correct: B) Fungal hyphae extend far beyond the root depletion zone, solubilising and absorbing inorganic phosphate and transferring it to the plant

7. Intrinsic (natural attenuation) bioremediation is preferred over bioaugmentation when:

  • A) The contaminant is rapidly spreading to groundwater and human health risk is high
  • B) Native microbial communities are already actively degrading the contaminant at an acceptable rate and spread is limited
  • C) The contaminant is a chlorinated solvent requiring specialised Dehalococcoides strains
  • D) The site is completely sterile and no indigenous microorganisms are present
Show Answer Correct: B) Native microbial communities are already actively degrading the contaminant at an acceptable rate and spread is limited

8. The global carbon cycle involves a large pool of carbon stored in the deep ocean as dissolved inorganic carbon. How do microorganisms primarily contribute to returning this carbon to the atmosphere?

  • A) By photosynthesis in the deep ocean absorbing CO₂ and releasing O₂
  • B) Through the biological pump failure — microbial respiration of sinking organic matter at depth releases CO₂ which upwells to the surface
  • C) Chemolithotrophs in the deep sea directly convert dissolved CO₂ to CH₄
  • D) Deep sea archaea perform denitrification releasing CO₂
Show Answer Correct: B) Through the biological pump failure — microbial respiration of sinking organic matter at depth releases CO₂ which upwells to the surface

9. Anaerobic oxidation of methane (AOM) in marine sediments involves:

  • A) A single archaeon that oxidises CH₄ aerobically using dissolved O₂
  • B) Syntrophic consortia of archaeal methane-oxidisers (ANME) and sulfate-reducing bacteria that couple CH₄ oxidation to sulfate reduction
  • C) Aerobic methanotrophs that use O₂ delivered by bioturbating organisms
  • D) Fungal decomposers that convert CH₄ to CO₂ via the glyoxylate cycle
Show Answer Correct: B) Syntrophic consortia of archaeal methane-oxidisers (ANME) and sulfate-reducing bacteria that couple CH₄ oxidation to sulfate reduction

10. Phytoremediation uses plants to clean contaminated sites. How do rhizosphere microorganisms enhance phytoremediation of organic pollutants?

  • A) Root exudates chelate heavy metals, removing them from soil permanently
  • B) Rhizosphere bacteria degrade organic contaminants stimulated by root exudate carbon, reducing contaminant uptake into plant tissue
  • C) Plants absorb and volatilise inorganic contaminants directly without microbial help
  • D) Mycorrhizal fungi store toxins in their hyphal vacuoles permanently
Show Answer Correct: B) Rhizosphere bacteria degrade organic contaminants stimulated by root exudate carbon, reducing contaminant uptake into plant tissue

11. Sulfate-reducing bacteria play a key role in the sulfur cycle by:

  • A) Oxidising H₂S to SO₄²⁻ under aerobic conditions
  • B) Reducing SO₄²⁻ to H₂S in anoxic sediments
  • C) Fixing elemental sulfur into organic compounds
  • D) Converting SO₂ to sulfuric acid in the atmosphere
Show Answer Correct: B) Reducing SO₄²⁻ to H₂S in anoxic sediments

12. Recalcitrant compounds like lignin are primarily degraded by:

  • A) Sulfate-reducing bacteria
  • B) Methanogenic Archaea
  • C) White-rot fungi using extracellular peroxidases and laccases
  • D) Nitrite-oxidising bacteria
Show Answer Correct: C) White-rot fungi using extracellular peroxidases and laccases

13. The 'priming effect' in soil microbiology refers to:

  • A) Activation of dormant spores by nutrient addition
  • B) Stimulation of native organic matter decomposition by addition of fresh organic substrate
  • C) Initial lag phase of microbial growth in fresh soil
  • D) Competition between introduced bioaugmentation strains and native microbiota
Show Answer Correct: B) Stimulation of native organic matter decomposition by addition of fresh organic substrate

14. Which process is responsible for the transformation of inorganic mercury (Hg²⁺) to the more toxic methylmercury (MeHg) in aquatic sediments?

  • A) Nitrifying bacteria under oxic conditions
  • B) Sulfate-reducing bacteria and iron-reducing bacteria under anoxic conditions
  • C) Photochemical oxidation in surface waters
  • D) Aerobic methanotrophic bacteria
Show Answer Correct: B) Sulfate-reducing bacteria and iron-reducing bacteria under anoxic conditions

15. In biostimulation for bioremediation, the strategy involves:

  • A) Adding exogenous microorganisms capable of degrading the contaminant
  • B) Adding nutrients (N, P) or electron donors/acceptors to stimulate indigenous microbial activity
  • C) Using plants to take up contaminants (phytoremediation)
  • D) Physically mixing contaminated soil with clean soil
Show Answer Correct: B) Adding nutrients (N, P) or electron donors/acceptors to stimulate indigenous microbial activity

16. The net equation for complete aerobic mineralisation of glucose is:

  • A) C₆H₁₂O₆ → 2C₂H₅OH + 2CO₂
  • B) C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O
  • C) C₆H₁₂O₆ + 4H₂O → 3CH₄ + 3CO₂
  • D) C₆H₁₂O₆ → 3CH₃COOH
Show Answer Correct: B) C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

💬 Open-Ended Questions

1. Describe the role of microorganisms in the carbon cycle. Explain both the processes that fix CO₂ and those that return CO₂ to the atmosphere.

Hint / Guidance Fixation: photosynthesis (Cyanobacteria, algae, plants), chemolithoautotrophy (Calvin cycle). Return: aerobic respiration (most organisms); methanogenesis (CH₄→CO₂ via methanotrophs); fermentation; decomposition. Carbon pools: soil organic matter (largest terrestrial pool); ocean dissolved inorganic C; sedimentary carbon. Wetland drainage → releases stored CH₄ and CO₂; permafrost thaw → massive C release; blue carbon (marine sediments) affected by coastal destruction.

2. What is bioremediation? Compare intrinsic bioremediation, biostimulation, and bioaugmentation. Provide a specific example of each approach.

Hint / Guidance Intrinsic: natural degradation by indigenous microbiome (petroleum-contaminated soil with active alkane degraders — Alcanivorax). Biostimulation: adding nutrients (N, P) or O₂ to enhance indigenous degraders (Exxon Valdez: fertiliser application; benzene-contaminated aquifer: oxygen injection). Bioaugmentation: inoculating site with specialised strains (Dehalococcoides mccartyi for PCE/TCE dechlorination; no indigenous Dehalococcoides present). Factors affecting success: bioavailability of contaminant, electron acceptor availability, soil permeability, toxicity.

3. Trace the fate of a nitrogen atom from atmospheric N₂ to being incorporated into a plant protein and then returned to the atmosphere. Name the microbial processes and key organisms at each step.

Hint / Guidance N₂ fixation (Rhizobium, Azotobacter, Cyanobacteria → NH₃ via nitrogenase); NH₃ assimilation by plant via GS/GOGAT into glutamine/glutamate → protein synthesis; plant dies → decomposition: proteases → amino acids → ammonification: NH₄⁺; nitrification: Nitrosomonas (NH₄⁺→NO₂⁻), Nitrobacter/Nitrospira (NO₂⁻→NO₃⁻); denitrification: Pseudomonas, Paracoccus (NO₃⁻→NO₂⁻→NO→N₂O→N₂). N₂ returns to atmosphere.

4. Describe the key transformations in the sulfur cycle and the microbial groups responsible for each.

Hint / Guidance S⁰/S²⁻ oxidation: aerobic chemolithotrophs (Thiobacillus, Acidithiobacillus): H₂S→S⁰→SO₄²⁻; phototrophic sulfur bacteria (Chlorobium, Chromatium). Dissimilatory sulfate reduction: Desulfovibrio, Desulfobacter: SO₄²⁻ + organic matter → H₂S (anaerobic respiration; produces acid mine drainage by exposing iron sulfides). Assimilatory sulfur reduction: all organisms reduce SO₄²⁻ → S²⁻ for amino acid synthesis. Organic sulfur mineralisation: heterotrophs decompose methionine/cysteine → H₂S. Dimethylsulfoniopropionate (DMSP) cleavage by marine bacteria → DMS → atmospheric SO₂ → cloud condensation nuclei (climate significance).

5. What is acid mine drainage (AMD) and which microorganism is primarily responsible? Explain the biogeochemical mechanisms and the environmental and economic impacts.

Hint / Guidance AMD: highly acidic, metal-rich drainage from mines; pH can reach <1. Primary microorganism: Acidithiobacillus ferrooxidans (formerly Thiobacillus ferrooxidans). Mechanism: (1) Pyrite exposed by mining: FeS₂ + O₂ + H₂O → Fe²⁺ + SO₄²⁻ + H⁺ (chemical); (2) A. ferrooxidans oxidises Fe²⁺ → Fe³⁺ (biological acceleration); (3) Fe³⁺ chemically oxidises more FeS₂ → self-propagating cycle; (4) Fe³⁺ hydrolyses → ochre precipitate. Impacts: destroys aquatic ecosystems; toxic metals (As, Pb, Cd) mobilised; expensive remediation (lime neutralisation); billions in liability. Solution: phytostabilisation, constructed wetlands, sulfate-reducing bacteria passive treatment.

6. Explain how PAH contamination is degraded aerobically by soil bacteria. What limits biodegradation in the field, and how can bioavailability be enhanced?

Hint / Guidance Aerobic PAH degradation: naphthalene→1,2-dihydronaphthalene (dioxygenase) → salicylate → catechol → TCA cycle. Bacteria: Pseudomonas putida (naphthalene dioxygenase); Rhodococcus, Burkholderia for 4-ring PAHs. High-molecular-weight PAHs (pyrene, benzo[a]pyrene) more recalcitrant. Limitations: (1) Bioavailability: PAHs adsorb tightly to soil organic matter → inaccessible; (2) Co-metabolism required for some PAHs; (3) O₂ limitation in deep soil; (4) Toxicity at high concentrations. Enhancement: biosurfactant production (Pseudomonas rhamnolipids) increases solubility; surfactant addition; biostimulation with oxygen; landfarming (aeration + nutrient addition).

7. What is co-metabolism in biodegradation? Give a specific example and explain its significance for bioremediation.

Hint / Guidance Co-metabolism: transformation of a non-growth-supporting compound by enzymes induced by a different (growth) substrate; organism gains no benefit. Classic example: Methylosinus trichosporium (methanotroph) — methane monooxygenase (MMO) also oxidises TCE (trichloroethylene) to TCE-epoxide → spontaneous breakdown → non-toxic products. Organism grows on methane; co-metabolises TCE. Significance: many chlorinated solvents cannot support growth alone; co-metabolic degradation by methanotrophs/propane-oxidisers important. Limitation: product inhibition; enzyme competition by growth substrate; not enough reducing equivalents. Used in TCE-contaminated aquifer remediation by methane injection.

8. Describe the process of anaerobic digestion in four stages. What are the end products, and what is the significance of each microbial group?

Hint / Guidance Stage 1 — Hydrolysis: extracellular hydrolases (cellulases, proteases, lipases) from Firmicutes/Bacteroidetes break polymers to monomers. Stage 2 — Acidogenesis: fermentative bacteria produce acetate, propionate, butyrate, H₂, CO₂. Stage 3 — Acetogenesis: syntrophic acetogens oxidise propionate/butyrate → acetate + H₂ (Syntrophobacter, Syntrophomonas); H₂ must be removed by methanogens (interspecies H₂ transfer — rate-limiting step). Stage 4 — Methanogenesis: hydrogenotrophic methanogens (Methanobacterium: CO₂ + H₂ → CH₄); acetoclastic methanogens (Methanosarcina: CH₃COO⁻ → CH₄ + CO₂). End products: biogas (55–70% CH₄, 30–45% CO₂); digestate (nutrient-rich fertiliser). Significance: renewable energy, waste treatment, GHG reduction.

9. Outline the key processes in the phosphorus cycle. Why is phosphorus often the limiting nutrient in freshwater ecosystems, and how does eutrophication occur?

Hint / Guidance P cycle: unlike C/N, no significant atmospheric pool. Weathering of rocks releases PO₄³⁻; plants/microbes assimilate → organic P; decomposition/mineralisation releases PO₄³⁻; sedimentation into lake sediments; geological uplift returns rock. Microbial roles: phosphate-solubilising bacteria (Bacillus megaterium, Pseudomonas) produce gluconic acid → solubilise rock phosphate; polyphosphate accumulating organisms (Accumulibacter in enhanced biological phosphorus removal). Eutrophication: agricultural P runoff → P enriches lake → Cyanobacterial blooms (N-fixers can fix N when N:P low); algal death → decomposition → O₂ depletion → fish kills; toxin production (microcystins). P is limiting in freshwater (low natural weathering; high retention in sediments).

10. How do mycorrhizal fungi contribute to nutrient cycling and carbon storage in forest soils? What would be the ecological consequences of losing mycorrhizal networks?

Hint / Guidance Nutrient cycling: ectomycorrhizal fungi produce organic acid exudates that weather rock minerals releasing Ca, K, Mg, P; extend effective absorbing surface area 100-fold; transfer limiting nutrients (especially P, N) to trees in exchange for 10–30% of photosynthate (phloem sugars). Carbon storage: mycorrhizal networks decompose slowly → contribute to stable soil organic matter pool; glomalin (AM fungi) major soil aggregate stabiliser. Common mycorrhizal networks ('wood wide web'): interconnect trees; may transfer C from surplus to shaded individuals. Consequences of loss: reduced tree growth; nutrient limitation; increased soil erosion (loss of aggregation); reduced carbon sequestration; forest regeneration failure after disturbance (mycorrhizal propagule banks depleted).

11. Describe the microbial nitrogen cycle in detail. Include all key transformations, the microorganisms responsible, and the environmental conditions required for each.

Hint / Guidance N₂ fixation (anaerobic nitrogenase): Rhizobium, Azotobacter, Cyanobacteria; N₂ → NH₄⁺. Ammonification: decomposers (Bacillus, Pseudomonas) mineralise organic N → NH₄⁺. Nitrification (oxic): Nitrosomonas: NH₄⁺ → NO₂⁻; Nitrobacter: NO₂⁻ → NO₃⁻; comammox Nitrospira: NH₄⁺ → NO₃⁻. Denitrification (anoxic, organic C): Paracoccus, Pseudomonas; NO₃⁻ → NO₂⁻ → NO → N₂O → N₂. Anammox (anoxic): Candidatus Brocadia; NH₄⁺ + NO₂⁻ → N₂. Dissimilatory NO₃⁻ reduction to NH₄⁺ (DNRA, anoxic): retains N in ecosystem. N₂O: greenhouse gas and ozone depleter, produced by nitrification and denitrification.

12. What is co-metabolism in biodegradation? Why is it important for the degradation of compounds like trichloroethylene (TCE) and polychlorinated biphenyls (PCBs)?

Hint / Guidance Co-metabolism: transformation of a non-growth-supporting compound by enzymes produced for a different (growth) substrate; no energy or carbon benefit to the organism. TCE: methanotrophs (Methylosinus) express methane monooxygenase (MMO) to oxidise CH₄; MMO fortuitously oxidises TCE to TCE-epoxide (toxic intermediate; kills some cells). PCBs: Burkholderia and others grow on biphenyl; biphenyl dioxygenase also oxidises PCB congeners (lower chlorinated). Limitations: inducer substrate must be present; toxic intermediate may kill organism; slow rates. Strategy: bioaugmentation with specialised strains + biostimulation with growth substrate.

13. Explain how microorganisms are involved in the geochemical cycling of iron and what implications this has for the availability of nutrients in aquatic systems.

Hint / Guidance Iron cycle: Fe³⁺ (ferric, insoluble) ↔ Fe²⁺ (ferrous, soluble). Iron-reducing bacteria (IRB, e.g., Geobacter, Shewanella): anaerobic respiration using Fe³⁺ as terminal electron acceptor → Fe²⁺ release. Iron-oxidising bacteria (e.g., Gallionella, Acidithiobacillus): aerobic/microaerobic oxidise Fe²⁺ → Fe³⁺ + energy. At redox interfaces (sediment-water): reductive dissolution releases Fe²⁺ + adsorbed phosphate; upward diffusion into oxic zone → re-oxidation to Fe(OH)₃ and P re-adsorption. Ocean: Fe is limiting micronutrient for phytoplankton; Fe fertilisation experiments (HNLC regions) increase productivity → carbon pump. Acid mine drainage: Acidithiobacillus catalyses pyrite oxidation → H₂SO₄ + Fe³⁺.

14. How does the phosphorus cycle differ from the nitrogen and carbon cycles in terms of microbial involvement and environmental reservoirs?

Hint / Guidance Key difference: no gaseous phase; P does not cycle through atmosphere. Reservoirs: lithosphere (apatite minerals), soils, water, biomass. Microbial roles: (1) Phosphate solubilisation — organic acids (gluconate) and phosphatases release P from mineral/organic forms; (2) Mineralisation — phosphatases cleave organophosphate (phytate, phospholipids) → Pi; (3) Luxury uptake/EBPR — polyphosphate-accumulating organisms (PAO, e.g., Candidatus Accumulibacter) cycle between anaerobic (P release + PHA storage) and aerobic (massive P uptake as polyphosphate); (4) P immobilisation in biomass. Unlike N cycle: no reduction (P stays +5 oxidation state in biota). Long-term recycling requires geological uplift of marine sediments — very slow (>10⁶ yr).

15. Describe the role of fungi in terrestrial carbon cycling and compare their strategies with those of bacteria.

Hint / Guidance Fungi: hyphal growth allows translocation of C and N across cm–m distances; ectomycorrhizal and AM fungi supply P/N to plants (up to 90% of plant P via mycorrhizae) in exchange for photosynthate (~20% of plant C); saprotrophic Basidiomycetes (white-rot) uniquely degrade lignin via ligninases/peroxidases/laccases; brown-rot fungi modify cellulose; fungi dominate in acidic, dry, high C:N soils. Bacteria: more diverse metabolic repertoire; dominate in wet, nutrient-rich soils; faster response to soluble substrates; denitrification. Fungi often form stable large aggregates (macroaggregates); bacterial EPS forms microaggregates. Together: fungi prime soil organic matter; bacteria rapidly mineralise products.
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