Chemistry and physics of submerged soil

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The chemistry of submerged soilsPresented byJ.Anandhan,2015672001


contentsIntroductionKinds of submerged soilsCharacteristics of submerged soilsElectro chemical changes in submerged soilsChemical transformations of submerged soilsMineral equilibria in submerged soilsReferences


IntroductionApplications in geochemistry, agriculture, limnology, oceanography and pollution72% of the earth's surface is covered by submerged soils and sedimentsIt is suitable of wet soils for crops, aquatic lives, marine plants and sinks for many nutrients Acts as reservoir for many nutrients




A. WATERLOGGED (GLEY) SOILSsaturated with water for a sufficiently long time annuallyForms horizons like:(a) a partially oxidized A horizon high in organic matter (b) a mottled zone (c) a permanently reduced zone with bluish green colour

(Robinson, 1949)



B. MARSH SOILSFreshwater marsh occur on the fringes of lakes and the networks of streams that feed themIn this the G horizon is blue or greenTypes,Upland (pH 3.5-4.5)Lowland (pH 5.0-6.0)Transitional


Saltwater marsh marshes are found in estuaries, deltas and tidal flats it is green if iron silicates are present and dark grey if pyrites are the main iron minerals


Fresh water marshessalt water marshes


C. PADDY SOILSDeveloped by cultivation practises of paddy (includes puddling, levelling and water stagnation)When irrigated soil undergoes reduction and turns dark grey. Fe, Mn, Si and P become more soluble and diffuse to the surface Moves by diffusion and mass flow to the roots and to the subsoil. When Fe2+ and Mn2+ reach the oxygenated surface, the surface of rice roots, or the oxidized zone below the plough sole they are oxidized and precipitated along with silica and phosphate


It is Sandwiched between the oxidized surface layer and the zone of Fe and Mn illuviation.The root zone of rice with reddish-brown streaks along root channels. When the land is drained at harvest, almost the entire profile above the water table is reoxidized, giving it a highly mottled appearance.Precipitation in the plough layer is not pedologically of any consequence because ploughing and puddling redistribute the deposits


Downward movement of Fe and Mn causes loss of these elements from the topsoil. The eluviated Fe and Mn, along with some phosphate, are deposited below the plow sole to produce an iron-rich B1r horizon overlying a manganese-rich Bmn horizon. Reduction eluviation and oxidative illuviation as the soil forming processes characteristic of paddy soils and have proposed the new term "Aquorizem" at the Great Soil Group level to define soils which have the sequence of reductive eluviation/oxidative illuviation. (Kyuma and Kawaguchi (1966) )A well developed paddy soil has the horizon sequence Apg,/Birg/ B2g/G (Kanno (1957))


Cultivation of Rice


D. SUBAQUATIC SOILSFormed from river, lake, and ocean sediments.Formed by,the sediments are formed from soil components typical soil-forming processes such as hydrolysis, oxidation-reduction, precipitation, synthesis, and exchange of matterdeep sea sediments contain OM and a living bacterial flora


Characters of SUBAQUATIC SOILSthe bacteria in lake and ocean sediments are similar to those in soils the metabolism of subaquatic sediments is similar to those of submerged soilsthe uppermost layers show A horizon differentiation distinct from physical stratification sediments differ in texture, composition, clay mineralogy, organic matter content, and oxidation-reduction level


Characteristics of Submerged SoilsA. Absence of Molecular Oxygen B. Oxidized Mud-Water InterfaceC. Exchanges between Mud and WaterD. Presence of Marsh PlantsE. Soil Reduction


A. Absence of Molecular Oxygen Gas exchange between soil and air is drastically reducedO2 and other atmospheric gases can enter the soil only by molecular diffusion in the interstitial water is 10,000 times slower than diffusion in gas-filled poresWithin a few hours of soil submergence, microorganisms use up the oxygen present in the water or trapped in the soil and render a submerged soil practically devoid of molecular oxygen


Oxygen moves through water layerSoil layer with no oxygen (anaerobic)Thin aerobic soil layer


B. Oxidized Mud-Water InterfaceConcentration of O2 may be high in the surface layer which is a few millimeters thick and in contact with oxygenated waterBelow the surface layer, the O2 concentration drops abruptly to practically zeroThe chemical and microbiological regimes in the surface layer resemble those in aerobic soils


C. Exchanges between Mud and WaterThe presence of this oxygenated surface layer in lake and ocean muds is of the most ecological importance because it acts as a sink for phosphate and other plant nutrients and as a chemical barrier to the passage of certain plant nutrients from the mud to the waterThe surface may use up oxygen faster than it receives it, undergo reduction and release large amounts of nutrients from the lake mud into the water In summer, some lakes undergo thermal differentiation into three layers:Epilimnion Thermocline Hypolimnion


The epilimnion is the surface layer of warm water 10-20 m deep which because of mixing by wind action, is uniform in temperature and is saturated with atmospheric O2 from top to bottom. (Mortimer, 1949).Immediately below this is the thermocline, a layer in which there is a rapid fall in temperature with depth. In this, the concentration of O2 is relatively constant in lakes poor in plant nutrients (oligotrophic lakes), but it decreases with depth in lakes rich in plant nutrients (eutrophic lakes) (Ruttner, 1963). The hypolimnion is the layer of cold stagnant water practically isolated from the epilimnion, except for solids, both organic and inorganic, that sink through it and accumulate on the mud surface. Bacteria in the surface layer use the O2 in it to oxidize the organic matter.



D. Presence of Marsh PlantsPlants growing in submerged soils have two adaptations that enable the roots to ward off toxic reduction products, accumulate nutrients, and grow in an O2 -free medium: O2 transport from the aerial parts and anaerobic respirationIt has been known for quite some time that the roots of marsh plants receive their oxygen from the aerial parts (shoot, air roots or stilt roots) through gas spaces connecting these organs



E. Soil ReductionThe most important chemical difference submerged soil is in a reduced state. Except for the thin, brown, oxidized layer at the surface (and sometimes an oxidized zone in the subsoil), a submerged soil is grey or greenish, has a low oxidation-reduction potential, and contains the reduced counterparts of NO2-, SO42-, Mn4+, Fe3+, and CO2, NH4+, H2S, Mn2+, Fe2+, and CH4


27Oxidation and Reduction in an Aerobic soil Organic matter in soil gives up 4 electrons (e-) which are received by O2. As a result, O2 is reduced. Hydrogen ions (H+) react with the reduced O2 to form water (H2O). 4 e- + O2 + 4 H+ 2 H2O


28Oxidation and Reduction in an Anaerobic SoilElectrons (e-) from organic matter in soil are accepted by nitrate (NO3-) instead of O2. Nitrogen (N) in NO3- is reduced; the N compound becomes nitrogen gas (N2) Hydrogen ions (H+) react with oxygen from NO3- to produce H2O.10 e- + 2 NO3- + 12 H+ 1 N2 + 6 H2O


A change in chemistry results in a change of soil colorbright colors indicate a well-drained soilsubmerged soils change to a gray or blue-green color (often referred to as gley) Reddish-yellowish brown colors are an indication of iron oxides in a well-drained environmentSubmergence causes iron to be reduced resulting in a different iron form and the gley color

Well-drained soil profileReduced soil profile


1. Oxidation-Reduction PotentialOxidation-reduction is a chemical reaction in which electrons are transferred from a donor to an acceptor. The source of electrons for biological reductions is organic matter.Redox potential (Eh) is a quantitative measure of the tendency of a given system to oxidize or reduce susceptible substances. Eh is positive and high in strongly oxidizing systems; Negative in negative and low in strongly reducing systems


Change in free energy

Redox potential is measured using following equation,

Where,Eh = Redox potentialEo = Eh at where Oxi and Red are equalF = Farudays constant


Measurement of Redox potential

Redox meter

Platinum electrode



Clark and Arnon,1960-65


Reaction sequence following submergence

Reaction sequence after draining

Chemical Reduction Sequence of Submergence


N2Mn2+Fe2+NO3-MnO2Fe3+CO2CH4SO4-2H2SH2OSlightly ReducedModerately ReducedStrongly ReducedOxidized

35The boxes represent different chemical compounds in the soil. When the soil is aerated, the chemical compounds in the soil will be represented by the top set of boxes. The bottom set of boxes represent the chemical compounds in the soil after they are reduced. As you click on the slide (in presentation view), you can see the order in which the compounds are reduced and the change in form. The sequence of the compounds from left to right is the order in which they will be reduced starting with oxygen and ending with carbon dioxide.

When a soil is drained, oxygen begins to move into the soil and react with the reduced compounds. The reduced compounds are then oxidized in the reverse sequence starting on the right and moving to the left.

Redox potential of various compounds under submergencePatrick (1964), and Turner and Patrick (1968)


Electrochemical Changes in Submerged SoilsSubmerging a soil brings about a variety of electrochemical changes. These include,(a) a decrease in redox potential, (b) an increase in pH of acid soils and a decrease in pH of alkaline soils, (c) changes in specific conductance and ionic strength, (d) drastic shifts in mineral equilibria,(e) cation and anion exchange reactions, (f) sorption and desorption of ions.


A. Redox PotentialThe low potentials (0.2 to -0.4 V) of submerged soils and sediments reflect this reduced state.The high potentials (0.8 to 0.3 V) of aerobic media, their oxidized condition.


1. Submerged Soils and MudsWhen an aerobic soil is submerged, its Eh decreases during the first few days and reaches a minimum (-0.42 V ).Then it increases, attains a maximum, and decreases again asymptotically to a value characteristic of the soil, after 8-12 weeks of submergenceThe presence of native or added organic matter sharpens and hastens the first minimum, nitrate abolishes it (0.2 V). The rapid initial decrease of Eh is apparently due to the release of reducing substances accompanying oxygen depletion before Mn(IV) and Fe(III) oxide hydrates can mobilize their buffer capacityThe course, rate, and magnitude of the Eh decrease depend on the kind and amount of organic matter, the nature, and content of electron acceptors, temperature, and the duration of submergence(Ponnamperuma, 1955, 1965; Motomura,1962; Yamane and Sato, 1968).


B. pH Decrease of pH in first few days of submergence, then it reaches minimum and increases to a stable value (6.7 7.2)


pH of soils




C. Specific ConductanceThe specific conductance of depends on the kind and concentration of ions present. Ionic strength (I) = CiZiWhere, Ci= concentration of ions (mol/lit) Zi = valence of ionsUnder reduced condition ionic strength was equal to 16 times the specific conductance (k) in mhos/cm at 25C



Chemical Transformations in Submerged SoilsA. CarbonB. NitrogenC. IronD. ManganeseE. SulfurF. PhosphorusG. SiliconH. Trace Elements


47Form of compounds in aerated and submerged soilElementAerated soil (Oxidized)Submerged soil (Reduced)Oxygen (O)Oxygen gas (O2)Water (H2O)Nitrogen (N)Nitrate ion (NO3-)Nitrogen gas (N2)Manganese (Mn)Manganese IV ion (Mn4+)Manganese II ion (Mn2+)Iron (Fe)Iron III ion (Fe3+)Iron II ion (Fe2+)Sulfur (S)Sulfate ion (SO42-)Hydrogen sulfide (H2S)Carbon (C)Carbon dioxide (CO2)Methane (CH4)


A. CarbonThe two main transformations of carbon in nature are photosynthesis and respiration. On the balance between these two processes depend (a) the amount of organic matter that accumulates in soils and sediments, and(b) the quality of streams, lakes, and estuaries. In submerged soils, respiration (decomposition of organic matter) is the main transformation


1. Decomposition of Organic MatterIn well drained soils aerobic microbes will decompose OM to form CO2, NO3-, SO42-. Under submerged condition anaerobic microbes will decompose OM to produce CO2, H2, CH4, NH4+, amines, mercaptans, H2S, and partially humified residues


2. Pyruvic acid metabolismThis will occur in both aerobic and submerged conditions.The precursor is sugars like glucoseC6H12O6 + 2ATP + 2NAD+ 2CH3COCOOH + 4ATP + 2NADH + 8H+ (Pyruvic acid) Under submerged condition Pyruvic acid will transforms,(a) reduction to lactic acid, (b) decarboxylation to CO2 and CH3CHO (c) dissimilation to lactic, butyric and acetic acids and CO2, (d) cleavage to acetic, formic acids, H2, and CO2,(c) carboxylation to oxaloacetic acid (f) condensation with itself or acetaldehyde to give acetylmethylcarbinol

Werkman and Schlenk (1951),


2. Kinetics of CO21 to 3 tons of CO2 are produced in the ploughed layer of 1 ha of a soil during the first few weeks of submergence (IRRI, 1964). Being chemically active, it forms HCOO-, HCO3- and insoluble CO32-. The excess accumulates as gas.The partial pressure of CO2 in a soil increases after submergence, reaches a peak of 0.2-0.8 atm 1-3 weeks later and declines to a fairly stable value of 0.05-0.2 atmThe decline in Pco2 after 1-4 weeks of submergence is due to escape, leaching, removal as insoluble CO32-, dilution by CH4 produced during the decomposition of organic acids, and bacterial reduction of CO2to CH4


4. Kinetics of Volatile Organic AcidsThe main organic acids found in anaerobic soils and sewage are formic, acetic, propionic, and butyric acids.When a soil is submerged, the concentration of volatile organic acids increases, reaches a peak value of 10-40 mmol/lit in 1-2 weeks and then declines to less than 1 mmol/lit a few weeks later.Soils high in native or added organic matter produce high concentrations of acids (Motomura, 1962). Low temperature retards acid formation slightly, but acid destruction markedly. Thus organic acids persist longer in cold soils than in warm soils. Ammonium sulphate appears to increase acetic acid formation but suppresses the formation of propionic and butyric acids


5. Methane FermentationMethane is the typical end product of the anaerobic decomposition of organic matter. Some of the methane is oxidized bacterially at the surface of paddy soils (Harrison and Aiyer, 1913, 1915) and in the oxygenated strata of lakes (Hutchinson, 1957). Methane formation is ecologically important because it helps the disposal of large amounts of organic matter sedimented in lakes.


Methane is produced by a small group of obligate anaerobes (like Methansarcina inethanica).Methane bacteria function best at temperatures above 30C, but most abundant in natural anaerobic waters, produces methane even at 50C (Ruttner, 1963). Methane bacteria are highly substrate specific and can metabolize only a small number of simple organic and inorganic substances, usually the products of fermentation.


B. NitrogenIn submerged soils, the main transformations are Accumulation of ammonia, Denitrification, Nitrogen fixation.


1. Accumulation of ammoniaAmmonia production in submerged soils follows a roughly asymptotic course and the kinetics of ammonia release can be described by log (A-y) = log A ctWhere, A = mean maximum NH4-N concentration y = actual concentration t days after submergence c = parameter depending on the soil. (Ponnamperuma, 1965)


2. DenitrificationNitrate undergoes two transformations in submerged soils: assimilation or reduction of NO3- with incorporation of the products into cell substancedissimilation or nitrate respiration in which NO3- functions as an alternative to O2 as an electron acceptorRate of denitrification increases with temperature up to 60C.Denitrification will occurs at below the redox potential of 350 mvDenitrification is slow in high OM soils (OM provides C, H and O2 to microbes )Alternate wetting and drying increases denitrification loss


3. N2 fixationBNF is reduction of N2 to NH3.It requires high electron activity or low pEpE = - log aeWhere ae = activity of e-Microbes help in BNF are Nostoc, Anabaena, Ocillatoria, Tolypothrix, Calothrix, Phormidium and some algae speciesSlight alkaline and high P will increase the N- fixationThey fix as much as 22 kg /ha of N2


N transformation in soil


N transformations in aerobic vs anerobic


C. IronThe reduction of iron has important chemical consequences:(a) the concentration of water-soluble iron (Fe2+)increases;(b) pH increases(c) cations are displaced from exchange sites(d) the solubility of phosphorus and silica increases and (e) new minerals are formed.


In acid soils high in OM and Fe will increases to 600 ppm within 1-6 weeks after submergenceFe2O4.nH2O Fe3+ Fe2+ (Clay)Fe2+ diffuses and mass flow to the surface of soil and also to plant roots where oxidise and forms precipitates under the plough soleGrey colour mottles due to FeS2Paddy soils contains hydrated magnetite (Fe2O4.nH2O) along with some hydrtrolilite (FeS.nH2O)


D. ManganeseIn submerged soils Mn2+ availability is increased by conversion of Mn(IV) oxides into Mn(II) ions or carbonatesThese Mn2+ ions moves to the oxygenated interfaces in soils by mass flow and diffusionWhen co2 concentrations in soil increases Mn2+ precipitated as MnCO3


E. Sulphur In aerated soils,Elemental S is converted into SO42-, sulphides and organic sulphur compoundsReduction of SO42- and incorporation into plant tissues as elemental S.In submerged soils,SO42- to sulphide ,Other S containing compounds into H2S (forms bad ordous )And used by S reducing microbes like Desulfovibrio


F. PhosphorusPhosphorus in valence states from +5 to -3 The forms are phosphite, hypophosphite, phosphine and phosphate in anaerobic media.Soils having forms like,(a) iron(III) and aluminum phosphates (in acid soils)(b) phosphates adsorbed or co-precipitated with Fe(IlI) and Mn(IV) hydrous oxides (c) phosphates held by anion exchange on clay and hydrous oxides, (d) calcium phosphates (in neutral & alkali soils)(e) organic phosphates. The increase in concentration of water-soluble P on soil submergence (Stumm and Morgan, 1970)


Sandy clay (pH= 7.6)14. Clay(pH= 4.6)25. Sandy loam(pH= 4.8)26. Clay loam(pH= 7.6)27. Clay(pH= 6.6)


G. SiliconIn soils occurs as crystalline and amorphous silicaAlso as silicates, adsorbed or co-precipitated with hydrous oxides of Al, Fe(III)and Mn(IV), and also dissolved in the soil solution.Dissolved silica is present as monomeric Si(OH) 4. The concentration of Si(OH) 4, in equilibrium with amorphous silica at 25C is 120-140 ppm as SiO2, and is independent of pH 2 to 9.Submergence will slightly increases (due to release by Fe3+ ions and higher CO2 concentration) and then decreases the Si concentrations ( decrease in Pco2).


H. Trace ElementsSubmergence will increase availability of Co, Cu and Zn.Increase in pH of acid soils lower the solubility of nutrients due to release of Sulphide which forms precipitatesThe elements in reduced layer will moves towards to the oxidised layer


Mineral Equilibria in Submerged Soils

A. Redox Systems B. Carbonate Systems


A. Redox Systems Reduction sequences as follows under submerged condition of soil, O2, NO3-, Mn4+, Fe3+, SO42-, CO2, N2 and H+.These each are associated with H+ ions and Electrons.They includes systems like,The O2 H2O systemThe N2 systemThe Mn systemThe Fe systemThe sulphur system


B. Carbonate Systems It includes,(a) high concentrations of CO2 (b) the presence of the divalent cations, Fe2+, Mn2+, Ca2+ and Mg2+ in most soils, CaCO3 in calcareous soils and NaHCO3 in sodic soils (c) intimate contact between solid, solution, and gas phases(d) virtual isolation of the system from the surroundings. Thus sodic soils behave like NaHCO3, calcareous soils like CaCO3, ferruginous soils like Fe3O4nH20, and manganiferrous soils likeMnCO3 when submerged and equilibrated with CO2.(Ponnamperuma et al., 1969)


It includes the systems like,The Na2CO3 H2O CO2 systemThe CaCO3 H2O CO2 systemThe MnCO4 H2O CO2 systemThe FeCO3 H2O CO2 system


Physical changes of submerged soils


Drastically retards gas exchange between soil and air

Stabilizes soil temperature

Causes swelling of colloids

Destroys aggregates Reduces permeability

Effects of flooding


Retardation of gas exchange

Oxygen deficiency - The moment a soil is flooded, its oxygen supply is virtually cut off. Oxygen can enter the soil only by molecular diffusion in the interstitial water. The process is 10,000 times slower than in gas-filled pores.

Thus the oxygen diffusion rate suddenly decreases when a soil reaches saturation by water. Within a few hours of flooding, microorganisms use up the oxygen present in the water or trapped in the soil and render a submerged soil practically devoid of molecular oxygen.

A flooded soil, however, is not uniformly devoid of oxygen: the oxygen concentration may be high in the surface layer which is a few millimeters thick and in contact with oxygenated water.


The thickness of the layer represents a balance between diffusion from the flood water and oxygen consumption by the soil.

It increases in thickness as the crop matures. Below the surface layer, the oxygen concentration drops abruptly to practically zero.

The brown color of the oxygenated layer, its chemical properties, and its oxidation-reduction potential undergo a similar abrupt change with depth in submerged soils. The root zone of rice is practically free of molecular oxygen (Ponnamperuma 1972). Retardation of gas exchange


Accumulation of carbon dioxideThe presence of a layer of water also drastically cuts down the escape of soil gases. Carbon dioxide, methane, hydrogen, and nitrogen produced in the soil tend to accumulate, build up pressure, and escape as bubbles.

The partial pressure of carbon dioxide in a soil increases after submergence and reaches a peak of 0.2 0.8 bars 1-3 weeks later. Carbon dioxide injury to rice may occur on acid soils low in iron, in organic soils, and cold soils.


Stabilization of soil temperature The effects of flooding on soil temperature follow from three important thermal properties of water its high specific heat, high latent heat of vaporization, and a higher thermal conductivity than soil material.

The high specific heat prevents violent temperature fluctuation. The high heat of vaporization tends to keep flooded soils cooler than dry soils.


The cooling effect is used to reduce high temperature injury in hot locations while the stabilizing effect is used to prevent low temperature injury at night.

Standing water markedly influences the microclimate of the first 50 cm above the soil surface (Nagai 1958). Introduction of cold or warm water into the field rapidly changes the temperature of soil, air, and plants.

Low soil temperatures retard mineralization of organic nitrogen and phosphorus and favor the accumulation of carbon dioxide, organic acids, and excess water-soluble iron in flooded soils (Cho and Ponnamperuma 1971, Ponnamperuma 1976).

Stabilization of soil temperature


The adverse effects of low soil and water temperatures are present in tropical soils above 1000 m and in soils irrigated by cold, mountain streams.Low water temperature reduces germination, retards growth, and depresses grain yield. Grain yield is reduced if the water temperature is less than 17 degrees C during the active tillering and meiotic stages. Rice with panicle primordia above the water level suffered less yield reduction (IRRI 1980).

Stabilization of soil temperature


Swelling of colloids When a dry soil is flooded, soil colloids absorb water and swell. The rate of water sorption and volume increase of mineral soils depend on the clay content, type of clay mineral, and the nature of the adsorbed cations. Swelling is usually complete in one to three days.

The higher the clay content the greater the swelling. The expanding-lattice type of clays (montmorillonite and beidellite) swell more than the fixed-lattice type (kaolinite and halloysite). Sodium clays swell more than calcium and potassium clays.


When a puddled soil is dried, it shrinks and the decrease in volume equals the volume of water lost.

Deep cracks are common in puddled rice fields after draining and drying.

They cause heavy loss of water by percolation during reflooding (Wickham and Singh 1978).

Swelling of colloids


Consistency As the moisture content of a soil increases the cohesion of water films around soil particles causes them to stick together rendering the soil plastic. At this moisture content soils are easily puddled.

At higher moisture contents (as in flooded soils), cohesion decreases rapidly, making tillage easy. But penetration increases and soil strength decreases, rendering the use of heavy machinery impractical on flooded soils.


Destruction of soil aggregatesWhen a dry soil is flooded, the aggregates become saturated with water. During the process, internal air pressure disrupts the aggregates (Baver et al 1972). Swelling of colloids and dissolution of cementing agents, such as iron oxide, further decrease aggregate stability.

Sodic soils show marked aggregate breakdown on flooding, whereas soils high in iron and aluminum oxides and organic matter suffer little aggregate destruction (Sanchez 1976). On soil drying and oxidation, reaggregation occurs through soil cracking and cementing by higher oxides of iron.


Reduction of permeability (percolation rate) Flooding decreases percolation rate in soils of low permeability even without puddling. This has been attributed to dispersion of soil particles, swelling, aggregate destruction, and clogging of pores by microbial slime.

In porous, non-swelling soils, flooding (by providing a greater head of water) increases percolation (Wickham and Singh 1978).


ReferencesThe Chemistry of Submerged Soils, F.N. Ponnamperuma, Advances in Agronomy, Vol. 24Physical changes in flooded soils, F.N. Ponnamperuma


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