Recycling in Ecosystems (OCR A-Level Biology A): Revision Notes

Recycling in Ecosystems

Introduction to nutrient recycling

Living organisms require specific chemical elements to construct organic molecules. Six essential elements — carbon, hydrogen, oxygen, nitrogen, sulfur and phosphorus — form the building blocks of biological compounds.

Autotrophic organisms obtain these elements in simple, inorganic forms:

• Carbon, oxygen and hydrogen: absorbed as carbon dioxide ($\mathrm{CO_2}$) and water ($\mathrm{H_2O}$), the substrates for photosynthesis
• Nitrogen: absorbed as nitrate ions ($\mathrm{NO_3^-}$)
• Sulfur: absorbed as sulfate ions ($\mathrm{SO_4^{2-}}$)
• Phosphorus: absorbed as phosphate ions ($\mathrm{PO_4^{3-}}$)

This note examines how carbon and nitrogen cycle through ecosystems, ensuring their constant availability to autotrophs, consumers and decomposers.

Key terminology

Carbon recycling

Carbon reservoirs

Despite atmospheric carbon dioxide representing only $400$ ppm ($0.04\%$ of the atmosphere), this reservoir contains approximately 750,000 million tonnes of carbon. An even larger reservoir exists in the oceans, holding roughly 40 trillion tonnes of dissolved carbon dioxide. The largest carbon store exists in sedimentary rocks like limestone and chalk, formed from calcium carbonate shells of marine organisms, containing approximately 100,000 trillion tonnes.

The carbon cycle

Carbon continuously moves through ecosystems via several interconnected processes.

Carbon atoms absorbed from the atmosphere $350$ million years ago remain locked within fossil fuels. Similarly, sedimentary rocks formed from marine organism shells contain carbon stored over geological timescales. For instance, a massive peatland carbon sink the size of England was discovered in the Republic of the Congo in 2014.

Nitrogen recycling

Forms of nitrogen

Nitrogen appears in many organic molecules, especially proteins and nucleic acids (DNA and RNA). Although dinitrogen ($\mathrm{N_2}$) comprises approximately $80\%$ of the atmosphere, most organisms cannot utilize it directly.

Fixed nitrogen describes nitrogen bonded to other atoms (such as oxygen, hydrogen or carbon), distinguishing it from atmospheric dinitrogen. Most nitrogen enters ecosystems as fixed nitrogen in the form of nitrate ions ($\mathrm{NO_3^-}$), which autotrophs absorb and use to synthesize amino acids. Heterotrophs require fixed nitrogen in the form of amino acids.

Nitrogen use in autotrophs

Autotrophs convert nitrate ions to amino acids through energy-consuming reactions occurring primarily in chloroplasts:

These amino acids are exported from chloroplasts throughout the plant for protein synthesis. Autotrophs also utilize amine groups from amino acids to synthesize purines and pyrimidines for nucleic acid production.

Nitrogen in food chains

Fixed nitrogen within plant biomass enters food chains. Primary consumers digest plant proteins to amino acids, absorb them, and synthesize their own proteins. This process continues through secondary consumers and along both grazing and detritus food chains.

Consumers cannot store amino acids or proteins. Carnivores obtain most energy from proteins, breaking down amino acids not needed for biosynthesis. Deamination removes ammonia from excess amino acid molecules. The remaining carbon skeleton can be respired in the Krebs cycle or converted to glucose for glycogen storage. Aquatic animals typically excrete ammonia directly; mammals convert it to urea, while birds produce uric acid.

Decomposition and ammonification

Decomposers break down excreted and egested materials from animals, plus dead plant and animal bodies. They digest proteins to amino acids, absorb them for biosynthesis, and deaminate excess amino acids, excreting ammonia. Some bacteria utilize urea as an energy source, converting it to ammonia.

Nitrification

Nitrification is the bacterial oxidation of ammonia to nitrate ions, occurring in two distinct stages by different bacteria.

Both Nitrosomonas and Nitrobacter are nitrifying bacteria. They obtain energy from these oxidation reactions. Electrons from ammonia and nitrite ions enter the electron transfer chain, establishing a proton gradient for ATP synthesis via chemiosmosis. This specialized nutrition allows them to fix carbon using energy from these chemical reactions.

Nitrogen fixation

Nitrogen fixation is the conversion of atmospheric nitrogen gas ($\mathrm{N_2}$) into ammonium ions. Only specialized bacteria possess this capability. Breaking the stable nitrogen-nitrogen triple bond requires substantial energy, so nitrogen-fixing bacteria need abundant carbohydrate supplies.

Both bacteria types participate in mutualism with their plant hosts. Host plants supply sugars as an energy source for splitting dinitrogen molecules. In return, bacteria provide fixed nitrogen as ammonium ions or amino acids.

In natural habitats, legumes gain competitive advantage from root bacteria because they do not depend on soil nitrate. Cultivated legumes are grown in crop rotations; after harvest, plant remains are ploughed in to increase soil fixed nitrogen content.

Lightning also fixes nitrogen. During thunderstorms, high temperatures cause nitrogen and oxygen to react, forming nitrogen oxides that produce nitrate ions in soil.

Denitrification

Denitrification converts nitrate ions back to dinitrogen, occurring in anaerobic muds and waterlogged soils. Bacteria such as Pseudomonas survive low oxygen conditions by using nitrate ions as terminal electron acceptors in oxidative phosphorylation when oxygen is scarce. Nitrate is progressively reduced to dinitrogen, which escapes into the atmosphere:

$\mathrm{NO_3^-} \rightarrow \mathrm{NO_2^-} \rightarrow \mathrm{N_2O} \rightarrow \mathrm{N_2}$

Chemistry of nitrogen cycling

Nitrogen exists in nine oxidation states; four are relevant to biosphere cycling:

Form	Oxidation state
Ammonia ($\mathrm{NH_3}$) and ammonium ions ($\mathrm{NH_4^+}$)	$-3$
Dinitrogen ($\mathrm{N_2}$ or $\mathrm{N≡N}$)	$0$
Nitrite ions ($\mathrm{NO_2^-}$)	$+3$
Nitrate ions ($\mathrm{NO_3^-}$)	$+5$

During nitrification, $\mathrm{NH_3}$ and $\mathrm{NO_2^-}$ are oxidized aerobically by nitrifying bacteria. Electrons from these molecules enter the electron transfer chain, establishing a proton gradient for ATP synthesis via chemiosmosis.

Nitrogen fixation requires energy because nitrogen-nitrogen bonds are highly stable. Nitrogen-fixing bacteria therefore require plentiful carbohydrate, obtained by Azotobacter from the rhizosphere and by Rhizobium from within root nodules.