🪨Biogeochemistry Unit 7 – Organic Matter Decay and Nutrient Cycling

Key Concepts and Definitions

• Organic matter consists of carbon-based compounds originating from living organisms (plants, animals, microbes)
• Decomposition breaks down complex organic compounds into simpler inorganic forms
  • Involves physical, chemical, and biological processes
• Nutrient cycling recycles essential elements (carbon, nitrogen, phosphorus) between the environment and living organisms
• Biogeochemistry studies the interactions between biological, geological, and chemical processes in ecosystems
• Mineralization releases inorganic nutrients from organic matter during decomposition
  • Makes nutrients available for plant uptake
• Immobilization incorporates inorganic nutrients into microbial biomass
• C:N ratio compares the amount of carbon to nitrogen in organic matter
  • Influences decomposition rates and nutrient availability

Organic Matter Composition

• Organic matter contains a diverse array of compounds (carbohydrates, proteins, lipids, lignin)
• Carbohydrates include sugars, starches, and cellulose
  • Relatively easy for microbes to decompose
• Proteins consist of amino acids and are a major source of organic nitrogen
• Lipids encompass fats, waxes, and resins
  • Hydrophobic nature slows decomposition
• Lignin is a complex polymer that provides structural support in plant cell walls
  • Resistant to microbial breakdown
• Humus is the stable, amorphous end product of decomposition
  • Improves soil structure and nutrient retention
• Composition of organic matter varies among ecosystems (forests, grasslands, wetlands)

Decomposition Processes

• Leaching dissolves soluble compounds from organic matter
  • Transfers nutrients to soil solution or water bodies
• Fragmentation breaks organic matter into smaller pieces
  • Increases surface area for microbial colonization
• Catabolism breaks down complex organic molecules through enzymatic reactions
• Humification converts decomposed organic matter into stable humic substances
• Mineralization releases inorganic nutrients (ammonium, phosphate) from organic compounds
• Volatilization releases gaseous forms of nutrients (ammonia, methane) into the atmosphere
• Decomposition rates vary among different organic matter types
  • Labile compounds (sugars) decompose quickly
  • Recalcitrant materials (lignin) have slower decay rates

Factors Affecting Decay Rates

• Temperature influences microbial activity and enzyme kinetics
  • Higher temperatures generally accelerate decomposition
• Moisture availability affects microbial growth and nutrient diffusion
  • Optimal moisture levels vary among ecosystems
• Oxygen availability determines the dominant decomposition pathways
  • Aerobic respiration occurs in well-aerated soils
  • Anaerobic processes (fermentation, methanogenesis) dominate in waterlogged environments
• Substrate quality refers to the chemical composition of organic matter
  • High-quality substrates (low C:N ratio) decompose faster
• Soil pH influences microbial community composition and enzyme activity
  • Neutral to slightly acidic pH is optimal for most decomposers
• Soil texture affects water and oxygen availability
  • Sandy soils have rapid drainage and aeration
  • Clay soils retain moisture but may limit oxygen diffusion

Nutrient Cycling Overview

• Nutrient cycling involves the transfer of elements between the environment and living organisms
• Biogeochemical cycles include carbon, nitrogen, phosphorus, sulfur, and others
• Plants uptake inorganic nutrients from the soil solution
  • Incorporate nutrients into biomass through photosynthesis and assimilation
• Animals obtain nutrients by consuming plants or other animals
• Decomposition releases nutrients from organic matter back into the environment
  • Completes the cycle and sustains ecosystem productivity
• Nutrient cycling rates vary among ecosystems
  • Depend on factors such as climate, soil properties, and vegetation type
• Human activities (agriculture, fossil fuel combustion) can alter natural nutrient cycles
  • Lead to imbalances and environmental consequences (eutrophication, climate change)

Carbon Cycle in Organic Matter Decay

• Carbon is a key component of organic matter
• Photosynthesis fixes atmospheric CO2 into plant biomass
• Decomposition releases CO2 back into the atmosphere through microbial respiration
• Methanogenesis produces methane (CH4) under anaerobic conditions
  • Methane is a potent greenhouse gas
• Dissolved organic carbon (DOC) leaches from organic matter into soil solution or water bodies
  • Can be transported or further decomposed
• Soil organic carbon (SOC) represents the largest terrestrial carbon pool
  • Consists of various fractions with different turnover rates
• Stabilization mechanisms protect SOC from decomposition
  • Include physical protection, chemical interactions, and microbial efficiency

Nitrogen and Phosphorus Cycling

• Nitrogen is a limiting nutrient in many ecosystems
• Decomposition of organic matter releases organic nitrogen
• Ammonification converts organic N to ammonium (NH4+)
  • Mediated by heterotrophic microbes
• Nitrification oxidizes ammonium to nitrite (NO2-) and then to nitrate (NO3-)
  • Carried out by autotrophic bacteria (Nitrosomonas, Nitrobacter)
• Denitrification reduces nitrate to gaseous forms (N2O, N2) under anaerobic conditions
  • Results in nitrogen loss from the ecosystem
• Phosphorus is another essential nutrient for living organisms
• Decomposition releases organic P from plant and microbial biomass
• Mineralization converts organic P to inorganic phosphate (PO4-)
  • Makes P available for plant uptake
• Phosphorus can be immobilized by adsorption to soil particles or precipitation with metals
  • Reduces P availability in the soil solution

Microbial Role in Decomposition

• Microorganisms are the primary drivers of decomposition
• Bacteria and fungi secrete extracellular enzymes to break down organic matter
  • Specific enzymes target different compounds (cellulases, proteases, lignases)
• Microbial succession occurs during decomposition
  • Community composition changes as substrate quality and environmental conditions evolve
• Bacteria dominate early stages of decomposition
  • Rapidly colonize and consume labile compounds
• Fungi are important decomposers of recalcitrant materials (lignin, cellulose)
  • Produce powerful oxidative enzymes
• Protozoa and nematodes graze on bacterial and fungal populations
  • Release nutrients through their waste products
• Microbial biomass serves as a temporary nutrient sink
  • Immobilizes nutrients during growth and turnover
• Microbial diversity influences decomposition rates and nutrient cycling efficiency
  • Functional redundancy ensures process stability

Environmental Implications

• Decomposition and nutrient cycling are critical for ecosystem functioning
  • Sustain plant growth and productivity
• Changes in decomposition rates can affect carbon storage and climate regulation
  • Accelerated decomposition may increase atmospheric CO2 levels
• Nutrient imbalances can lead to environmental problems
  • Excess nitrogen and phosphorus cause eutrophication in aquatic ecosystems
• Land-use changes (deforestation, agriculture) alter organic matter inputs and decomposition dynamics
  • Can deplete soil organic carbon stocks and fertility
• Climate change affects decomposition processes
  • Warmer temperatures may accelerate decay rates
  • Altered precipitation patterns influence moisture availability
• Invasive species can disrupt native decomposer communities
  • Affect nutrient cycling and ecosystem stability
• Understanding decomposition and nutrient cycling informs sustainable land management practices
  • Helps maintain soil health and productivity

Research Methods and Techniques

• Litterbag experiments measure decomposition rates in the field
  • Organic matter is enclosed in mesh bags and retrieved over time
• Reciprocal litter transplants assess the influence of environmental factors on decomposition
  • Litter is exchanged between different ecosystems or treatments
• Stable isotope tracers (13C, 15N) track the fate of nutrients through decomposition pathways
• Respirometry quantifies CO2 production during decomposition
  • Indicates microbial activity and carbon mineralization rates
• Enzyme assays measure the activity of specific extracellular enzymes involved in decomposition
• Phospholipid fatty acid (PLFA) analysis characterizes microbial community composition
  • Different microbial groups have distinct PLFA profiles
• Molecular techniques (DNA sequencing, qPCR) provide insights into microbial diversity and functional genes
• Spectroscopic methods (FTIR, NMR) analyze the chemical composition of organic matter during decomposition
• Mathematical models simulate decomposition and nutrient cycling processes
  • Help predict ecosystem responses to environmental changes