MICR 4040: Biogeochemical cycles

Biogeochemical cycle

The movement and transformation of elements between living organisms and the nonliving environment.

Why are elemental cycles important?

Life depends on available nutrients. Element cycles connect living and nonliving parts of ecosystems, and microbes drive many transformations that affect energy flow and ecosystem stability.

Move, Stick, Change

A framework for element cycling: elements move through environments, stick or become retained in soils, sediments, or biomass, and change through chemical or biological transformations.

How do microbes drive element cycles?

Microbial metabolism catalyzes transformations such as redox reactions, connecting element cycling with energy flow.

Coupled biogeochemical cycles

Element cycles interact rather than operating independently. For example, carbon oxidation can fuel nitrogen reduction during denitrification and sulfur reduction during decomposition.

Carbon oxidation states

Carbon ranges from highly reduced methane (CH₄) to highly oxidized carbon dioxide (CO₂), with organic matter between them. Changes in oxidation state can release or consume energy.

Oxygenic photosynthesis

Light-driven carbon fixation that uses water and releases oxygen. Cyanobacteria and algae perform it. Simplified reaction: CO₂ + H₂O + light → CH₂O + O₂.

Anoxygenic photosynthesis

Light-driven carbon fixation that does not release oxygen. Purple and green sulfur bacteria can use H₂S or H₂ as electron donors.

Chemosynthesis

Carbon fixation powered by energy from chemical oxidation rather than light. It supports ecosystems such as hydrothermal vents.

Aerobic respiration

Breakdown of organic matter using oxygen as the electron acceptor, producing CO₂, water, and energy. It is a highly energy-efficient pathway.

Anaerobic respiration

Respiration that uses electron acceptors other than oxygen, such as nitrate, sulfate, or ferric iron (Fe³⁺). It is important in sediments, wetlands, and anoxic soils.

Fermentation

Energy production without an external electron acceptor. Microbes internally oxidize and reduce organic molecules, producing compounds such as ethanol, lactate, or acetate.

Methanogenesis

Methane production by archaea. Common pathways use acetate or reduce CO₂ with H₂.

Methanotrophy

Microbial consumption and oxidation of methane (CH₄), helping regulate methane in wetlands, sediments, and other environments.

Inorganic carbon pools

Carbon dioxide (CO₂), bicarbonate (HCO₃⁻), and carbonate (CO₃²⁻) occur in water and soil and help buffer these environments.

Microbial weathering

Microbial respiration releases CO₂, which can form carbonic acid. This can speed mineral weathering and release bicarbonate and nutrients.

Keeling Curve

The long-term record of atmospheric CO₂ measured at Mauna Loa. Seasonal rises and falls reflect the balance of photosynthesis and respiration, while the long-term increase is linked to fossil fuel use and land-use change.

Major carbon sinks

Oceans and terrestrial ecosystems store carbon. Ocean uptake includes physical and biological processes; land sinks include soil carbon and biomass.

Ocean biological carbon pump

Phytoplankton take up carbon, and microbes decompose some of that material. Less than 10% of exported carbon is stored in ocean sediments long term, according to the slides.

Why does ocean acidification matter to microbes?

Oceans absorb CO₂, changing water chemistry and affecting microbial communities.

Why are nitrogen and phosphorus important?

Both nutrients can limit biological productivity. Microbes regulate their availability, and agriculture has greatly altered their cycles.

Nitrogen pools and forms

Most atmospheric nitrogen is N₂, which is largely inaccessible to organisms without nitrogen fixation. Reactive forms include ammonia/ammonium, nitrite, nitrate, nitric oxide, and nitrous oxide; organic nitrogen occurs in proteins and amino acids.

Biological nitrogen fixation

Microbial conversion of N₂ into ammonia using nitrogenase. The process requires substantial energy, about 16 ATP per N₂ in the slides.

Nitrogen-fixing microbes

Free-living examples include Azotobacter and Clostridium. Symbiotic examples include Rhizobium, Frankia, and some cyanobacteria.

Mineralization (ammonification)

Microbial decomposition converts organic nitrogen, such as proteins and amino acids, into ammonium (NH₄⁺), making nitrogen available to plants.

Immobilization

Microbes take up ammonium or nitrate and incorporate nitrogen into their biomass. It can temporarily reduce nitrogen available to plants, especially when the substrate has a high carbon-to-nitrogen ratio.

Nitrification

Microbial oxidation of ammonium to nitrite and then nitrate. Some Nitrospira can perform both steps through complete ammonia oxidation, or comammox.

Denitrification

Reduction of nitrate through nitrite and gaseous intermediates to nitrogen gas (N₂). It removes reactive nitrogen from ecosystems and can release nitrous oxide (N₂O).

Anammox

Anaerobic process in which microbes combine ammonium and nitrite to produce nitrogen gas (N₂).

DNRA

Dissimilatory nitrate reduction to ammonium: microbes reduce nitrate to ammonium, retaining reactive nitrogen in the ecosystem.

Nitrogen cascade

The movement of reactive nitrogen through air, land, and water, where it can cause multiple environmental effects.

Human impacts on the nitrogen cycle

Haber–Bosch fertilizer production, fossil fuel combustion, and nitrogen-fixing crops add or redistribute reactive nitrogen. Excess nitrogen can contribute to pollution and eutrophication.

Phosphorus cycle basics

Phosphorus is essential for DNA, ATP, and cell membranes. It has no major gaseous pool, and its global cycle is slow, involving rock weathering and ocean burial.

Main source of phosphorus

Weathering of apatite minerals releases phosphate (PO₄³⁻), which can move through erosion and water flow and often binds strongly to soils and sediments.

How do microbes make phosphorus available?

Microbes secrete phosphatases to release phosphorus from organic matter and produce organic acids or other compounds that help solubilize mineral phosphorus.

Mycorrhizal fungi and phosphorus

Mycorrhizal fungi extend the area from which plant roots can take up phosphorus and can help weather minerals. Plants supply the fungi with carbon.

Phosphorus enrichment in water

Excess phosphorus can cause cyanobacterial blooms, including toxic blooms, and shift aquatic communities toward phytoplankton dominance.

Human impacts on the phosphorus cycle

Mining phosphate for fertilizer and agricultural runoff redistribute phosphorus. Legacy soil phosphorus can continue feeding waterways and contributing to eutrophication.

Sulfur cycle

Many microbes transform sulfur between reduced sulfide and oxidized sulfate. Key processes include sulfate reduction, sulfur oxidation, and anoxygenic photosynthesis.

Sulfate reduction

Anaerobic microbial process that uses sulfate and organic matter to produce hydrogen sulfide (H₂S). It is common in sediments, and H₂S can be toxic and react with metals.

Sulfur oxidation

Microbial oxidation of H₂S to sulfate can provide energy for carbon fixation. It occurs in places such as hydrothermal vents and oxygen-poor boundaries.

Anaerobic methane oxidation with sulfate

A microbial process that couples methane consumption with sulfate reduction in marine sediments, helping limit methane emissions.

Metals as microbial nutrients

Iron, manganese, copper, zinc, and molybdenum can serve as essential enzyme cofactors. Microbes can acquire metals using compounds such as siderophores.

Microbial iron cycling

Iron oxidizers convert Fe²⁺ to Fe³⁺, while iron reducers convert Fe³⁺ to Fe²⁺. These transformations affect minerals, soil fertility, and ocean productivity.

Microbial detoxification of toxic elements

Microbes can change, export, or otherwise detoxify toxic elements such as arsenic, cadmium, and mercury. Some transformations can also increase harm, such as mercury methylation and subsequent bioaccumulation in fish.

Selenium and arsenic cycling

Microbes transform selenium and arsenic between chemical forms and can use some forms as electron donors or acceptors. These processes affect contamination and detoxification.

Human impacts across element cycles

Fertilizers alter nitrogen and phosphorus cycles; fossil fuel burning raises CO₂; mining and pollution affect sulfur and metals. These changes can cause eutrophication, acid mine drainage, and bioaccumulation.