4 Ecosystem Decomposition and Lab Practices

Practical Lab Sessions: Overview and Framework

• Lab Duration and Structure: The upcoming laboratory sessions are scheduled as six-hour blocks. While they may not occupy the entire allotted time, they are intensive and mandatory.

• Session Frequency: Students are required to attend two sessions: one occurring tomorrow and another in two weeks' time.

• Core Objectives: The labs focus on three distinct environmental topics:

  • Ocean Acidification.

  • Net Ecosystem Exchange (NEE).

  • Soil Respiration (Setup phase in the first week, harvest/analysis in the second).

• Resources: All protocols and worksheets are available on the "My Aberdeen" platform for review prior to the class. Professor Graham and the lecturer will provide step-by-step guidance during the sessions.

Experiment 1: Ocean Acidification and Calcareous Organisms

• Theoretical Context: Oceans serve as a critical sink for carbon. Approximately one-third of all anthropogenic (human-induced) carbon dioxide ($CO_2$) is absorbed by seawater.

• Chemical Mechanism:

  • When $CO_2$ enters seawater, it dissociates into carbonic acid ($H_2CO_3$).

  • The presence of carbonic acid increases the concentration of hydrogen ions, leading to a decrease in pH (acidification).

• Quantitative Changes:

  • Measurements indicate that global seawater pH has shifted from approximately $8.2$ in pre-industrial times to $8.1$ currently.

  • Logarithmic Impact: Due to the logarithmic nature of the pH scale, a decrease of $0.1$ units represents a $26\%$ increase in ocean acidity.

• Biological Impact: Acids erode and degrade the structures of calcareous organisms. This includes organisms with calcium carbonate shells and coral reefs composed of carbonates ($CaCO_3$).

• Practical Methodology:

  • The experiment uses seawater samples categorized into three groups: plain seawater, seawater with shells, and carbonated (acidified) seawater with shells.

  • Analytical Technique: Students will use titrations to determine the concentration of dissolved carbonates and bicarbonates in the samples.

  • Goal: Analyze the rate of degradation of the shells by calculating mass changes and chemical shifts in the water, correlating with Graham's lectures on carbon cycling.

Experiment 2: Measuring Net Ecosystem Exchange (NEE)

• Concept: This experiment quantifies the flux of carbon dioxide across an ecosystem, measuring the balance between carbon uptake (photosynthesis) and carbon loss (respiration).

• Mesocosms: Students will observe small-scale contained ecosystems (some with plants and some without) housed in the Science Teaching Hub.

• Instrumentation: Measurements are conducted using an Infrared Gas Analyzer (IRGA), which detects changes in the concentration of $CO_2$ within the contained environment above the soil/plant cores.

• Calculations:

  • Photosynthesis: Carbon uptake by the plants.

  • Respiration: Carbon dioxide released from the soil.

  • NEE Formula Concept: The total exchange of carbon between the system and the atmosphere.

Experiment 3: Soil Respiration Dynamics and Carbon Limitation

• Setup and Incubation: This is an incubation experiment. Soil samples are placed in containers and left in the lab for two weeks.

• Technique: The Potassium Hydroxide (KOH) Trap:

  • $CO_2$ liberated from the soil via microbial respiration is trapped in a solution of $KOH$.

  • The chemical reaction results in the formation of potassium carbonate ($K_2CO_3$).

• Analytical Approach: After two weeks, titrations are performed on the remaining $KOH$. By measuring how much $KOH$ was not converted to $K_2CO_3$, students can calculate the total amount of $CO_2$ respired by the microbes.

• Organic Carbon Limitation and Vmax:

  • Oxygen is rarely a limiting factor in loose container soil; however, organic carbon is a primary bottleneck for microbial activity.

  • Students will add varying quantities of organic carbon to different soil samples to observe how the respiration rate changes.

  • Goal: Plot a curve to calculate the $V_{max}$ (maximum velocity). As more carbon is added, respiration increases until it reaches a plateau where the microbes are saturated and cannot respire any faster, regardless of additional carbon availability.

• Future Algal Ball Experiment: In two weeks, students will also create immobilized freshwater algae "balls" to measure photosynthesis and respiration rates relative to environmental factors.

Foundations of Ecosystem Decomposition: Macro vs. Molecular Scales

• Definition: Decomposition is the process of breaking down organic matter and releasing stored energy and nutrients.

• Macro Scale: Involves the physical conversion of large organic matter into smaller particles, soluble compounds, and gases.

• Molecular Scale: Involves the chemical conversion of complex organic molecules (e.g., carbohydrates, proteins) into simpler forms and eventually into inorganic compounds like ammonium ($NH_4^+$) and carbon dioxide ($CO_2$).

• Energy Dynamics:

  • Each step of breakdown releases energy originally captured via photosynthesis.

  • In the macro scale, the products (small particles) often serve as food or energy sources for other organisms or neighboring ecosystems.

  • At the final molecular stage, once matter is converted to inorganic compounds, very little energy remains for further biological recovery.

• Nutrient Cycling: Decomposition drives biogeochemical cycles. As carbon is broken down, essential elements like nitrogen (e.g., nitrate) are released back into the soil, facilitating new plant growth.

• Mirroring Carbon Fixation: Decomposition is described as the inverse of carbon fixation:

  • Fixation: Inorganic Compounds + Energy (Sunlight) $\rightarrow$ Organic Compounds.

  • Decomposition: Organic Compounds $\rightarrow$ Inorganic Compounds + Released Energy.

Modeling Decomposition: The Litter Bag and First-Order Decay

• Methodology: The "Litter Bag" approach involves placing organic material in mesh bags, burying them, and retrieving them at intervals to measure mass loss.

• Decay Curves: Decomposition typically follows a negative exponential curve:

  • Phase 1: Rapid Initial Loss: Caused by leaching of soluble compounds and the breakdown of easily degradable material.

  • Phase 2: Gradual Decline: Breakdown of bulk particulate organic matter.

  • Phase 3: Plateau: Only recalcitrant (resistant) material remains.

• Mathematical Model: This is a First-Order Model, meaning the rate of mass loss is proportional to the mass currently present.

• Decomposition Rate ($k$):

  • Represented by the variable $k$, denoting the rate of mass loss over time.

  • Influence Factors: The specific value of $k$ is determined by the type of litter, ambient temperature, and the composition of the local biological community.

Biotic Drivers of Decomposition: The Role of Soil Fauna and Microbes

• Classification of Decomposers:

  • Microorganisms: Bacteria, Archaea, and Fungi. Responsible for molecular-scale decomposition.

  • Invertebrates: Responsible for macro-scale fragmentation (e.g., shredding leaves).

• Invertebrate Exclusion Studies: Research demonstrates that removing invertebrates from a system (e.g., using chemical treatments in streams) leads to a significant decrease in fine particulate organic matter. Without invertebrates to shred large material, microbes cannot access the carbon effectively.

• Earthworm Dynamics:

  • A study on earthworm density showed that decreasing worm populations below natural levels leads to higher retention of carbon (approx. $58\%$ remaining vs. $51\%$ in normal conditions).

  • Stoichiometric Preference: Earthworms preferentially consume nitrogen-rich organic material. High earthworm activity results in a higher Carbon-to-Nitrogen ($C:N$) ratio in the remaining material because the nitrogen is stripped out first.

• Microbial Syntrophy: Decomposition is a "consortium" effort where different organisms work together (syntrophy):

  • Fungi: Predominantly handle complex, recalcitrant polymers and wood (e.g., lignin).

  • Bacteria: More efficient at acquiring nutrients at low concentrations and breaking down monomeric units (sugars, amino acids).

Microbial Metabolism: Net Growth Efficiency (NGE) and Stoichiometry

• Net Growth Efficiency (NGE): Measures the proportion of assimilated carbon incorporated into microbial biomass versus carbon lost to the atmosphere.

  • Formula: $NGE = \frac{\text{Growth}}{\text{Growth} + \text{Respiration}}$

• Implications of Low NGE:

  • Indicates a large net loss of organic matter through respiration.

  • Suggests low retention of nutrients in the system due to high turnover rates.

• Metabolic Stoichiometry:

  • A general biological requirement for microbial biomass is a ratio of $5$ Carbons to $1$ Nitrogen ($5:1$).

  • For every carbon molecule incorporated into biomass, roughly one carbon molecule is lost to respiration.

  • Optimal Degradation Ratio: To successfully build biomass, a microbe ideally needs a ratio of $10$ Carbons to $1$ Nitrogen ($10:1$) in its food source ($5$ for growth, $5$ for energy).

• C:N Ratio Examples:

  • $50:1$ Source: The microbe is nitrogen-limited. It can only use $5$ carbons for biomass and $5$ for respiration. The remaining $40$ carbons are left undecomposed.

  • $10:1$ Source: Balanced. Total decomposition of organic material occurs.

  • $2:1$ Source: Carbon-limited. The microbe decomposes all carbon, using a portion of the nitrogen for biomass and leaving a surplus of inorganic nitrogen in the environment for other organisms.

Intrinsic Factors: Lignin and Chemical Recalcitrance

• Lignin Content: Lignin is the primary structural component of terrestrial vascular plants and the strongest predictor of decomposition rates ($k$).

• Ecological Comparisons:

  • Broadleaf Trees: $k ≈ 0.001$ (Very slow/resistant due to high lignin).

  • Microalgae: $k ≈ 0.1$ (Fast/easily decomposable; no lignin).

  • Seagrasses: More decomposable than trees as lignin is not a major structural component in aquatic flora.

• Why Lignin Resists Decay:

  1. Structural Complexity: It is physically difficult for enzymes to penetrate.

  2. Heterogeneous Polymer: It is made of various repeating units in non-uniform orders, meaning specific enzymes are less effective.

  3. Poor Solubility: Lignin is not water-soluble, protecting it from many microbial enzymes.

  4. Low Energy Yield: Parts of the molecule are already oxidized, providing low energy recovery during catabolism.

• Secondary Metabolites: Plants produce compounds like alkaloids, phenolics, and terpenes. These can act as anti-herbivory agents or chemical inhibitors that decrease the palatability and digestibility of the litter for decomposers.

Extrinsic Factors: Environmental Regulation of Decay

• Temperature: Increased temperature generally accelerates microbial activity and decomposition rates. This is a major concern for climate change regarding Peat Bogs, which are massive carbon stores; rising temperatures may trigger rapid decomposition and massive $CO_2$ release.

• Moisture: Decomposition increases with moisture until the soil becomes saturated. In saturated (waterlogged) conditions, oxygen is depleted, shifting to less efficient anaerobic decomposition.

• pH: Extreme pH levels can inhibit decomposers. For example, Acid Mine Drainage (low pH) significantly disrupts the local microbial community and slows decay.

• Nutrient Supply: The availability of external nutrients (like nitrogen in the soil) can influence which organisms dominate and how effectively they break down carbon-heavy litter.