Flooded Soils

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When the pore spaces in soils are saturated with water, oxygen dissolved in water is gradually depleted because oxygen is used as terminal electron acceptor for respiration by some aerobes and the facultative anaerobes. This results in anaerobic condition of soils. This anoxic condition can be found in soil aggregates and pollutants plume. Under anoxic condition, some microbes can use alternative electron acceptors such as nitrate, iron, sulfate, and carbon dioxide.


In general, flooded soil condition occurs due to seasonal flooding or agricultural activity. The flooded soils condition can be often converted into non-flooded soil condition by the water level fluctuation and drainage. Through this variation of soil condition, various gases are emitted into the atmosphere or environmental factors, such as redox potential (Eh), pH, acidity, alkalinity, and salinity, are continuously changed. As explained in the introduction, microorganism can use alternative terminal electron acceptor when dissolved oxygen is absent. They successively use electron acceptor according to the order of electron acceptor utilization based on electron tower. The order change of electron acceptor utilization is observed in soil aggregates and pollutant plume. (Figure aggregates and pollutant plume)

Oxidation/reduction (redox) reaction

Electron tower

Electron tower theory explains the utilization order of electron acceptor for respiration. Depending on the type of electron acceptors used by microorganisms, microbes can be classified into the strict aerobes, obligate anaerobes, and facultative anaerobes. The strict aerobes can not live under anoxic condition; on the contrary, obligate anaerobes can never use oxygen as electron acceptor. However, facultative anaerobes can live in both aerobic and anaerobic condition. If oxygen is plentiful, they tend to use oxygen because microorganisms gain much energy from reducing oxygen rather than other electron acceptors. When there is no more available oxygen in solution, they start to use nitrate as electron acceptor. Thus, obligate anaerobes and facultative anaerobes use alternative electron acceptor in the order of electron acceptor having more reducing energy. Oxygen is most efficient electron acceptor, while carbon dioxide has the less reducing energy. (figure electron tower)

Variation of pH and Eh


Neutral pH soil

When soil is saturated with water, pH drops at first due to organic acid produced from fermentation. Then, pH gradually starts to rise because H+ is consumed via respiration of the aerobes and anaerobes. The half reactions of hydrogen consumption are as follow;

Aerobic respiration: ½ O2 + 2e- + 2H+ -> H2O (by facultative anaerobe and aerobes)

Iron reduction: Fe(OH)3 + 3 H+ + 2e- -> Fe2+ + 2H2O (by Iron reducing bacteria)

Denitrification: 2NO3- + 12 H+ +10e- -> N2+6H2O (by Denitrifier)

Sulfate reduction: SO42- + 10H+ +8e- -> H2S + 4H2O (by sulfate reducing bacteria)

Methane production: CO2 + 8 H+ + 8e- -> CH4 +2 H2O (by Methanogeous)

Manganese reduction: MnO2 + 4H+ + 2e- ->Mn2+ + 2H2O (by Manganese reducing bacteria)


decreasing in Eh(V) with soil depth

Exchange of atmospheric gases


Aerobic respiration: ½ O2 + 2e- + 2H+ -> H2O (by facultative anaerobe and aerobes)

Carbon dioxide



Solubility/mobility of mineral

Effects on life

Plant nutrient availability

Microorganism activity


Key Microorganisms

The role of microorganisms under flooded soil

nitrate reducing bacteria

Methaneous bacteria

Ion reducing bacteria

Sulfate reducing bacteria

Manganese reducing bacteria

Current Research


Edited by students of Kate Scow