Element Cycles and Environmental Microbiology

Chapter Overview

  • Element Cycles and Environmental Microbiology
  • Major topics include:
    • The carbon cycle and climate change
    • The hydrologic cycle and wastewater treatment
    • The nitrogen cycle
    • The cycles of sulfur, phosphorus, and iron
    • Our built environment
    • Astrobiology

Microbes Cycle Essential Elements

  • All organisms recycle their components back to the biosphere.
  • Partnerships in recycling include:
    • Abiotic: e.g., air, water, minerals
    • Biotic: e.g., predators, decomposers
  • Metabolic interactions are termed biogeochemistry or geomicrobiology.
  • Macroelements cycle through nutrients in both biotic and abiotic components (REDOX reactions).

Sources and Sinks of Essential Elements

  • Biogeochemical cycles include:
    • Biological components: phototrophs and heterotrophs
    • Geological components: volcanoes and oceans
  • Reservoir: The part of the biosphere that contains significant amounts of an element, serving as both a source and sink.
    • Largest reservoir of carbon is found in Earth’s crust, cycling extremely slowly.
    • Major carbon reservoirs include:
    • Marine inorganic carbon (CO2 and carbonates)
    • Atmospheric CO2 (most rapid transfer method)
    • Buried fossil fuels
  • Largest nitrogen reservoirs include:
    • Atmospheric N2 and Earth’s crust
    • Nitrogen cycles extremely slowly through the biosphere.
  • As elements cycle from sources to sinks, microbial metabolism modifies redox states.
  • Microbes throughout the biosphere recycle carbon, nitrogen, sulfur, and other life-essential elements.
  • Human activity profoundly alters all geochemical cycles.

The Carbon Cycle and Climate Change

  • All food webs involve the influx and efflux of carbon.
  • The most accessible carbon reservoir is the atmosphere.
  • Industrial burning of fossil fuels disrupts balance between atmospheric reservoir and larger reservoirs like the ocean.
  • Current increase in CO2 levels at an annual rate of 2 ppm.

Atmospheric Greenhouse Gases

  • 40% increase in atmospheric CO2 since the Industrial Revolution.
    • Highly soluble, dissolves in oceans (500 billion tons).
    • Modulates the greenhouse effect:
    • 0.75 °C increase during the 20th century.
    • Estimated 1.1-6.4 °C increase for the 21st century.
  • Warmed oceans lead to:
    • More stratified waters
    • Slowing nutrient transfer
    • Decreased ocean productivity
    • Expansion of oxygen minimum zones
    • Acidification of ocean waters (down 0.1 pH, predict 0.3-0.4 more by 2100).

Oxidation-State Changes during Carbon Flux

  • Microbial metabolism generates redox changes based on oxygen presence, notable reactions include:
    • Organic matter oxidation
    • Oxygenic photosynthesis
    • Chemolithotrophy
    • Respiration: varies between oxic and anoxic environments.

Methods to Measure Element Cycling

  • Chemical and spectroscopic analysis: Atmospheric CO2 measured via infrared absorption spectroscopy.
  • Radioisotope incorporation: CO2 flux measured by the uptake of 14C-labeled substrates.
  • Stable isotope ratios: The 14N/15N ratio indicates denitrifiers.

Carbon Cycling in Ecosystems

  • Marine Carbon Cycling:
    • Largest aerobic ecosystem is the photic zone of oceans where photosynthesis exceeds heterotrophy, driven by the biological carbon pump.
  • Terrestrial Carbon Cycling:
    • Aerobic: Oxygenated soil layers facilitate microbial fixation of CO2 into biomass, producing O2 and organic compounds.
    • Anaerobic: Lower cycling rates in reduced environments, involving fermentation and anaerobic respiration.

The Global Carbon Balance and Temperature Change

  • The balance of biological CO2 fixation and release determines atmospheric CO2 levels.
  • CO2 release has accelerated since the industrial age, corroborated by ice cores from polar glaciers.
    • Climate modeling indicates 1 °C increase since 1800.
    • Microbes influence temperature increase through various pathways.
  • Radiative forcing: Difference between sunlight absorbed by Earth and energy radiated to space. Defined as:
    • Balance of biological fixation and release by combustion and catabolism.
    • Oceans dissolve over half of the CO2 from the atmosphere, which reacts to create carbonic acid, lowering ocean pH.

Chemical Equations

  • The equilibrium of carbonic acid in the ocean is represented by:
    CO_2 + H_2O
    ightleftharpoons H_2CO_3
    ightleftharpoons HCO_3^{-} + H^{+}
    ightleftharpoons CO_3^{2-} + 2H^{+}

Arctic Methanogens and Global Warming

  • Methane, although a minor atmospheric component (0.00017%), has 25 times the radiative force of CO2.
  • Permafrost contains thawed dead plant matter, accelerating decomposition and methane release.
    • Bacterial fermentation produces acetate and CO2, feeding methanogens for methane production.

The Hydrologic Cycle and Wastewater Treatment

  • The hydrologic (water) cycle involves cyclic exchange between the atmosphere and biosphere, characterized by:
    • Water precipitating as rain and returning to air via evaporation.
    • Interactions with the carbon cycle.
  • Human communities utilize the hydrologic cycle for water supply and wastewater management.
  • Biochemical oxygen demand (BOD): Rate of dissolved oxygen depletion indicates organic matter concentration in wastewater, thus reflecting hydrologic and carbon interactions.

Oxygen Minimum Zones (OMZ)

  • OMZs represent hypoxic regions where oxygen levels drop due to accelerated microbial respiration from carbon runoff.
    • E.g. the Oregon coast sees fish dying as oxygen depletes.

Wastewater Treatment Process

  • Aims to decrease BOD and human pathogens before discharging water back into rivers.
  • Treatment steps include:
    • Preliminary treatment: Removes solid debris.
    • Primary treatment: Uses fine screens and sedimentation tanks.
    • Secondary treatment: Microbial decomposition of organic material.
    • Tertiary treatment: Chemical methods like chlorination for pathogen removal.

Alternative Methods

  • Wetland restoration: Filters wastewater naturally similar to treatment plants.
  • Artificial wetlands: Local community solutions for agricultural runoff management.

The Global Nitrogen Cycle

  • Nitrogen, a major element cycled primarily through microbial processes:
    • Nitrogen features the most oxidation states among biological elements.
    • It cannot cycle without prokaryotes and is greatly perturbed by human activity.

Sources of Nitrogen

  • Nitrogen is primarily found as atmospheric N2 (79% of the atmosphere), but this molecule is stable and requires extensive energy for assimilation.
    • Artificial nitrogen fixation aids in fertilizer production via the Haber process.

The Nitrogen Triangle

  • The nitrogen cycle can be visualized as:
    • Fixation: Biological uptake of atmospheric N2.
    • Nitrification: Transformation of NH4+ through NO2– to NO3–.
    • Denitrification: Conversion back to N2 or N2O.

Key Processes in the Nitrogen Cycle

  1. Nitrification: Conversion of Ammonium (NH4+) to Nitrate (no2-) and Nitrate (NO3-).
    • Example bacteria: Nitrosomonas (NH4+ to NO2−) and Nitrobacter (NO2− to NO3−).
  2. Nitrogen fixation: Catalyzed by nitrogenase, capable of incorporating N2 into usable forms.
  3. Denitrification: Reduction of nitrates leading to N2 or N2O production, particularly prevalent in hypoxic conditions.

Anaerobic Ammonium Oxidation

  • Anammox reaction occurs in anoxic habitats, significant for returning N2 to the atmosphere:
    NH_4^{+} + NO_2^{-}
    ightarrow N_2 + 2H_2O
  • Conducted by specialized bacteria, especially in planctomycete groups.

Biogeochemical Cycles

  • Discussion and thought questions regarding climate change impacts on carbon/nitrogen cycles.

Sulfur, Phosphorus, and Metals

  • Key elements partaking in crucial biochemical cycles affecting both biosphere and human environments, focusing on:
    • The sulfur cycle
    • The phosphorus cycle
    • The iron cycle

The Sulfur Cycle

  • Consists of a “sulfur triangle” with various oxidation states from H2S to SO4^2-.
    • Competing sulfur reactions and their environmental impacts, including corrosion in sewers.

The Phosphate Cycle

  • Phosphate primarily exists in a fully oxidized state, rapidly assimilated in ecosystems but precipitating as insoluble salts in sediments.

The Iron Cycle

  • Iron cycles through oxidized (Fe3+) and reduced forms (Fe2+), emphasizing the role of bacteria in both anoxic and oxic environments.

Astrobiology

  • The study of life beyond Earth, hypothesis regarding microbial life in extraterrestrial environments.
    • Focus on Mars and features similar to Earth that could have supported life.
  • Evidence of biogenic activity sought through biosignatures.

Key Questions in Astrobiology

  • Investigates whether life could exist on other planets, with emphasis on conditions for Earth-like life and microbial existence in extreme environments.

NASA Perseverance Mission

  • Launched to seek biosignatures in geological records on Mars, understanding historic climates and possibilities for past life.