Soil

Soil is a mixture of organic matter, minerals, gases, liquids, and organisms that together support life. Earth's body of soil, called the pedosphere, has four important functions:

as a medium for plant growth
as a means of water storage, supply and purification
as a modifier of Earth's atmosphere
as a habitat for organisms

A, B, and C represent the soil profile, a notation firstly coined by Vasily Dokuchaev (1846–1903), the father of pedology; A is the topsoil; B is a regolith; C is a saprolite (a less-weathered regolith); the bottom-most layer represents the bedrock.

Surface-water-gley developed in glacial till, Northern Ireland.

All of these functions, in their turn, modify the soil and its properties.

The pedosphere interfaces with the lithosphere, the hydrosphere, the atmosphere, and the biosphere.[1] The term pedolith, used commonly to refer to the soil, translates to ground stone in the sense "fundamental stone."[2] Soil consists of a solid phase of minerals and organic matter (the soil matrix), as well as a porous phase that holds gases (the soil atmosphere) and water (the soil solution).[3][4][5] Accordingly, soil scientists can envisage soils as a three-state system of solids, liquids, and gases.[6]

Soil is a product of several factors: the influence of climate, relief (elevation, orientation, and slope of terrain), organisms, and the soil's parent materials (original minerals) interacting over time.[7] It continually undergoes development by way of numerous physical, chemical and biological processes, which include weathering with associated erosion. Given its complexity and strong internal connectedness, soil ecologists regard soil as an ecosystem.[8]

Most soils have a dry bulk density (density of soil taking into account voids when dry) between 1.1 and 1.6 g/cm³, while the soil particle density is much higher, in the range of 2.6 to 2.7 g/cm³.[9] Little of the soil of planet Earth is older than the Pleistocene and none is older than the Cenozoic,[10] although fossilized soils are preserved from as far back as the Archean.[11]

Soil science has two basic branches of study: edaphology and pedology. Edaphology studies the influence of soils on living things.[12] Pedology focuses on the formation, description (morphology), and classification of soils in their natural environment.[13] In engineering terms, soil is included in the broader concept of regolith, which also includes other loose material that lies above the bedrock, as can be found on the Moon and on other celestial objects as well.[14] Soil is also commonly referred to as earth or dirt; some scientific definitions distinguish dirt from soil by restricting the former term specifically to displaced soil.

Functions

Soil is a major component of the Earth's ecosystem. The world's ecosystems are impacted in far-reaching ways by the processes carried out in the soil, from ozone depletion and global warming to rainforest destruction and water pollution. With respect to Earth's carbon cycle, soil is an important carbon reservoir, and it is potentially one of the most reactive to human disturbance[15] and climate change.[16] As the planet warms, it has been predicted that soils will add carbon dioxide to the atmosphere due to increased biological activity at higher temperatures, a positive feedback (amplification).[17] This prediction has, however, been questioned on consideration of more recent knowledge on soil carbon turnover.[18]

Soil acts as an engineering medium, a habitat for soil organisms, a recycling system for nutrients and organic wastes, a regulator of water quality, a modifier of atmospheric composition, and a medium for plant growth, making it a critically important provider of ecosystem services.[19] Since soil has a tremendous range of available niches and habitats, it contains most of the Earth's genetic diversity. A gram of soil can contain billions of organisms, belonging to thousands of species, mostly microbial and largely still unexplored.[20][21] Soil has a mean prokaryotic density of roughly 10⁸ organisms per gram,[22] whereas the ocean has no more than 10⁷ prokaryotic organisms per milliliter (gram) of seawater.[23] Organic carbon held in soil is eventually returned to the atmosphere through the process of respiration carried out by heterotrophic organisms, but a substantial part is retained in the soil in the form of soil organic matter; tillage usually increases the rate of soil respiration, leading to the depletion of soil organic matter.[24] Since plant roots need oxygen, ventilation is an important characteristic of soil. This ventilation can be accomplished via networks of interconnected soil pores, which also absorb and hold rainwater making it readily available for uptake by plants. Since plants require a nearly continuous supply of water, but most regions receive sporadic rainfall, the water-holding capacity of soils is vital for plant survival.[25]

Soils can effectively remove impurities,[26] kill disease agents,[27] and degrade contaminants, this latter property being called natural attenuation.[28] Typically, soils maintain a net absorption of oxygen and methane and undergo a net release of carbon dioxide and nitrous oxide.[29] Soils offer plants physical support, air, water, temperature moderation, nutrients, and protection from toxins.[30] Soils provide readily available nutrients to plants and animals by converting dead organic matter into various nutrient forms.[31]

Composition

Soil profile: Darkened topsoil and reddish subsoil layers are typical in some regions.

Components of a loam soil by percent volume

Water (25%)

Gases (25%)

Sand (18%)

Silt (18%)

Clay (9%)

Organic matter (5%)

A typical soil is about 50% solids (45% mineral and 5% organic matter), and 50% voids (or pores) of which half is occupied by water and half by gas.[32] The percent soil mineral and organic content can be treated as a constant (in the short term), while the percent soil water and gas content is considered highly variable whereby a rise in one is simultaneously balanced by a reduction in the other.[33] The pore space allows for the infiltration and movement of air and water, both of which are critical for life existing in soil.[34] Compaction, a common problem with soils, reduces this space, preventing air and water from reaching plant roots and soil organisms.[35]

Given sufficient time, an undifferentiated soil will evolve a soil profile which consists of two or more layers, referred to as soil horizons. These differ in one or more properties such as in their texture, structure, density, porosity, consistency, temperature, color, and reactivity.[10] The horizons differ greatly in thickness and generally lack sharp boundaries; their development is dependent on the type of parent material, the processes that modify those parent materials, and the soil-forming factors that influence those processes. The biological influences on soil properties are strongest near the surface, while the geochemical influences on soil properties increase with depth. Mature soil profiles typically include three basic master horizons: A, B, and C. The solum normally includes the A and B horizons. The living component of the soil is largely confined to the solum, and is generally more prominent in the A horizon.[36]

The soil texture is determined by the relative proportions of the individual particles of sand, silt, and clay that make up the soil. The interaction of the individual mineral particles with organic matter, water, gases via biotic and abiotic processes causes those particles to flocculate (stick together) to form aggregates or peds.[37] Where these aggregates can be identified, a soil can be said to be developed, and can be described further in terms of color, porosity, consistency, reaction (acidity), etc.

Water is a critical agent in soil development due to its involvement in the dissolution, precipitation, erosion, transport, and deposition of the materials of which a soil is composed.[38] The mixture of water and dissolved or suspended materials that occupy the soil pore space is called the soil solution. Since soil water is never pure water, but contains hundreds of dissolved organic and mineral substances, it may be more accurately called the soil solution. Water is central to the dissolution, precipitation and leaching of minerals from the soil profile. Finally, water affects the type of vegetation that grows in a soil, which in turn affects the development of the soil, a complex feedback which is exemplified in the dynamics of banded vegetation patterns in semi-arid regions.[39]

Soils supply plants with nutrients, most of which are held in place by particles of clay and organic matter (colloids)[40] The nutrients may be adsorbed on clay mineral surfaces, bound within clay minerals (absorbed), or bound within organic compounds as part of the living organisms or dead soil organic matter. These bound nutrients interact with soil water to buffer the soil solution composition (attenuate changes in the soil solution) as soils wet up or dry out, as plants take up nutrients, as salts are leached, or as acids or alkalis are added.[41][42]

Plant nutrient availability is affected by soil pH, which is a measure of the hydrogen ion activity in the soil solution. Soil pH is a function of many soil forming factors, and is generally lower (more acid) where weathering is more advanced.[43]

Most plant nutrients, with the exception of nitrogen, originate from the minerals that make up the soil parent material. Some nitrogen originates from rain as dilute nitric acid and ammonia,[44] but most of the nitrogen is available in soils as a result of nitrogen fixation by bacteria. Once in the soil-plant system, most nutrients are recycled through living organisms, plant and microbial residues (soil organic matter), mineral-bound forms, and the soil solution. Both living microorganisms and soil organic matter are of critical importance to this recycling, and thereby to soil formation and soil fertility.[45] Microbial activity in soils may release nutrients from minerals or organic matter for use by plants and other microorganisms, sequester (incorporate) them into living cells, or cause their loss from the soil by volatilisation (loss to the atmosphere as gases) or leaching.

Formation

Soil formation, or pedogenesis, is the combined effect of physical, chemical, biological and anthropogenic processes working on soil parent material. Soil is said to be formed when organic matter has accumulated and colloids are washed downward, leaving deposits of clay, humus, iron oxide, carbonate, and gypsum, producing a distinct layer called the B horizon. This is a somewhat arbitrary definition as mixtures of sand, silt, clay and humus will support biological and agricultural activity before that time. These constituents are moved from one level to another by water and animal activity. As a result, layers (horizons) form in the soil profile. The alteration and movement of materials within a soil causes the formation of distinctive soil horizons. However, more recent definitions of soil embrace soils without any organic matter, such as those regoliths that formed on Mars[46] and analogous conditions in planet Earth deserts.[47]

An example of the development of a soil would begin with the weathering of lava flow bedrock, which would produce the purely mineral-based parent material from which the soil texture forms. Soil development would proceed most rapidly from bare rock of recent flows in a warm climate, under heavy and frequent rainfall. Under such conditions, plants (in a first stage nitrogen-fixing lichens and cyanobacteria then epilithic higher plants) become established very quickly on basaltic lava, even though there is very little organic material. The plants are supported by the porous rock as it is filled with nutrient-bearing water that carries minerals dissolved from the rocks. Crevasses and pockets, local topography of the rocks, would hold fine materials and harbour plant roots. The developing plant roots are associated with mineral-weathering mycorrhizal fungi[48] that assist in breaking up the porous lava, and by these means organic matter and a finer mineral soil accumulate with time. Such initial stages of soil development have been described on volcanoes,[49] inselbergs,[50] and glacial moraines.[51]

How soil formation proceeds is influenced by at least five classic factors that are intertwined in the evolution of a soil. They are: parent material, climate, topography (relief), organisms, and time.[52] When reordered to climate, relief, organisms, parent material, and time, they form the acronym CROPT.[53]

Physical properties

The physical properties of soils, in order of decreasing importance for ecosystem services such as crop production, are texture, structure, bulk density, porosity, consistency, temperature, colour and resistivity.[54] Soil texture is determined by the relative proportion of the three kinds of soil mineral particles, called soil separates: sand, silt, and clay. At the next larger scale, soil structures called peds or more commonly soil aggregates are created from the soil separates when iron oxides, carbonates, clay, silica and humus, coat particles and cause them to adhere into larger, relatively stable secondary structures.[55] Soil bulk density, when determined at standardized moisture conditions, is an estimate of soil compaction.[56] Soil porosity consists of the void part of the soil volume and is occupied by gases or water. Soil consistency is the ability of soil materials to stick together. Soil temperature and colour are self-defining. Resistivity refers to the resistance to conduction of electric currents and affects the rate of corrosion of metal and concrete structures which are buried in soil.[57] These properties vary through the depth of a soil profile, i.e. through soil horizons. Most of these properties determine the aeration of the soil and the ability of water to infiltrate and to be held within the soil.[58]

Soil moisture

Soil moisture refers to the water content of the soil. It can be expressed in terms of volumes or weights. Soil moisture measurement can be based on in situ probes or remote sensing methods.

Water that enters a field is removed from a field by runoff, drainage, evaporation or transpiration.[59] Runoff is the water that flows on the surface to the edge of the field; drainage is the water that flows through the soil downward or toward the edge of the field underground; evaporative water loss from a field is that part of the water that evaporates into the atmosphere directly from the field's surface; transpiration is the loss of water from the field by its evaporation from the plant itself.

Water affects soil formation, structure, stability and erosion but is of primary concern with respect to plant growth.[60] Water is essential to plants for four reasons:

It constitutes 80%-95% of the plant's protoplasm.
It is essential for photosynthesis.
It is the solvent in which nutrients are carried to, into and throughout the plant.
It provides the turgidity by which the plant keeps itself in proper position.[61]

In addition, water alters the soil profile by dissolving and re-depositing minerals, often at lower levels.[62] In a loam soil, solids constitute half the volume, gas one-quarter of the volume, and water one-quarter of the volume[32] of which only half will be available to most plants, with a strong variation according to matric potential.[63]

A flooded field will drain the gravitational water under the influence of gravity until water's adhesive and cohesive forces resist further drainage at which point it is said to have reached field capacity.[64] At that point, plants must apply suction[64][65] to draw water from a soil. The water that plants may draw from the soil is called the available water.[64][66] Once the available water is used up the remaining moisture is called unavailable water as the plant cannot produce sufficient suction to draw that water in. At 15 bar suction, wilting point, seeds will not germinate,[67][64][68] plants begin to wilt and then die. Water moves in soil under the influence of gravity, osmosis and capillarity.[69] When water enters the soil, it displaces air from interconnected macropores by buoyancy, and breaks aggregates into which air is entrapped, a process called slaking.[70]

The rate at which a soil can absorb water depends on the soil and its other conditions. As a plant grows, its roots remove water from the largest pores (macropores) first. Soon the larger pores hold only air, and the remaining water is found only in the intermediate- and smallest-sized pores (micropores). The water in the smallest pores is so strongly held to particle surfaces that plant roots cannot pull it away. Consequently, not all soil water is available to plants, with a strong dependence on texture.[71] When saturated, the soil may lose nutrients as the water drains.[72] Water moves in a draining field under the influence of pressure where the soil is locally saturated and by capillarity pull to drier parts of the soil.[73] Most plant water needs are supplied from the suction caused by evaporation from plant leaves (transpiration) and a lower fraction is supplied by suction created by osmotic pressure differences between the plant interior and the soil solution.[74][75] Plant roots must seek out water and grow preferentially in moister soil microsites,[76] but some parts of the root system are also able to remoisten dry parts of the soil.[77] Insufficient water will damage the yield of a crop.[78] Most of the available water is used in transpiration to pull nutrients into the plant.[79]

Soil water is also important for climate modeling and numerical weather prediction. Global Climate Observing System specified soil water as one of the 50 Essential Climate Variables (ECVs).[80] Soil water can be measured in situ with soil moisture sensor or can be estimated from satellite data and hydrological models. Each method exhibits pros and cons, and hence, the integration of different techniques may decrease the drawbacks of a single given method.[81]

Water retention

Water is retained in a soil when the adhesive force of attraction that water's hydrogen atoms have for the oxygen of soil particles is stronger than the cohesive forces that water's hydrogen feels for other water oxygen atoms.[82] When a field is flooded, the soil pore space is completely filled by water. The field will drain under the force of gravity until it reaches what is called field capacity, at which point the smallest pores are filled with water and the largest with water and gases.[83] The total amount of water held when field capacity is reached is a function of the specific surface area of the soil particles.[84] As a result, high clay and high organic soils have higher field capacities.[85] The potential energy of water per unit volume relative to pure water in reference conditions is called water potential. Total water potential is a sum of matric potential which results from capillary action, osmotic potential for saline soil, and gravitational potential when dealing with vertical direction of water movement. Water potential in soil usually has negative values, and therefore it is also expressed in suction, which is defined as the minus of water potential. Suction has a positive value and can be regarded as the total force required to pull or push water out of soil. Water potential or suction is expressed in units of kPa (10³ pascal), bar (100 kPa), or cm H₂O (approximately 0.098 kPa). Common logarithm of suction in cm H₂O is called pF.[86] Therefore, pF 3 = 1000 cm = 98 kPa = 0.98 bar.

The forces with which water is held in soils determine its availability to plants. Forces of adhesion hold water strongly to mineral and humus surfaces and less strongly to itself by cohesive forces. A plant's root may penetrate a very small volume of water that is adhering to soil and be initially able to draw in water that is only lightly held by the cohesive forces. But as the droplet is drawn down, the forces of adhesion of the water for the soil particles produce increasingly higher suction, finally up to 1500 kPa (pF = 4.2).[87] At 1500 kPa suction, the soil water amount is called wilting point. At that suction the plant cannot sustain its water needs as water is still being lost from the plant by transpiration, the plant's turgidity is lost, and it wilts, although stomatal closure may decrease transpiration and thus may retard wilting below the wilting point, in particular under adaptation or acclimatization to drought.[88] The next level, called air-dry, occurs at 100,000 kPa suction (pF = 6). Finally the oven dry condition is reached at 1,000,000 kPa suction (pF = 7). All water below wilting point is called unavailable water.[89]

When the soil moisture content is optimal for plant growth, the water in the large and intermediate size pores can move about in the soil and be easily used by plants.[71] The amount of water remaining in a soil drained to field capacity and the amount that is available are functions of the soil type. Sandy soil will retain very little water, while clay will hold the maximum amount.[85] The available water for the silt loam might be 20% whereas for the sand it might be only 6% by volume, as shown in this table.

Wilting point, field capacity, and available water of various soil textures (unit: % by volume)[90]
Soil Texture	Wilting Point	Field Capacity	Available water
Sand	3.3	9.1	5.8
Sandy loam	9.5	20.7	11.2
Loam	11.7	27.0	15.3
Silt loam	13.3	33.0	19.7
Clay loam	19.7	31.8	12.1
Clay	27.2	39.6	12.4

The above are average values for the soil textures.

Water flow

Water moves through soil due to the force of gravity, osmosis and capillarity. At zero to 33 kPa suction (field capacity), water is pushed through soil from the point of its application under the force of gravity and the pressure gradient created by the pressure of the water; this is called saturated flow. At higher suction, water movement is pulled by capillarity from wetter toward drier soil. This is caused by water's adhesion to soil solids, and is called unsaturated flow.[91][92]

Water infiltration and movement in soil is controlled by six factors:

Soil texture
Soil structure. Fine-textured soils with granular structure are most favourable to infiltration of water.
The amount of organic matter. Coarse matter is best and if on the surface helps prevent the destruction of soil structure and the creation of crusts.
Depth of soil to impervious layers such as hardpans or bedrock
The amount of water already in the soil
Soil temperature. Warm soils take in water faster while frozen soils may not be able to absorb depending on the type of freezing.[93]

Water infiltration rates range from 0.25 cm per hour for high clay soils to 2.5 cm per hour for sand and well stabilized and aggregated soil structures.[94] Water flows through the ground unevenly, in the form of so-called "gravity fingers", because of the surface tension between water particles.[95][96]

Tree roots, whether living or dead, create preferential channels for rainwater flow through soil,[97] magnifying infiltration rates of water up to 27 times.[98]

Flooding temporarily increases soil permeability in river beds, helping to recharge aquifers.[99]

Water applied to a soil is pushed by pressure gradients from the point of its application where it is saturated locally, to less saturated areas, such as the vadose zone.[100][101] Once soil is completely wetted, any more water will move downward, or percolate out of the range of plant roots, carrying with it clay, humus, nutrients, primarily cations, and various contaminants, including pesticides, pollutants, viruses and bacteria, potentially causing groundwater contamination.[102][103] In order of decreasing solubility, the leached nutrients are:

Calcium
Magnesium, Sulfur, Potassium; depending upon soil composition
Nitrogen; usually little, unless nitrate fertiliser was applied recently
Phosphorus; very little as its forms in soil are of low solubility.[104]

In the United States percolation water due to rainfall ranges from almost zero centimeters just east of the Rocky Mountains to fifty or more centimeters per day in the Appalachian Mountains and the north coast of the Gulf of Mexico.[105]

Water is pulled by capillary action due to the adhesion force of water to the soil solids, producing a suction gradient from wet towards drier soil[106] and from macropores to micropores. The so-called Richards equation allows calculation of the time rate of change of moisture content in soils due to the movement of water in unsaturated soils.[107] Interestingly, this equation attributed to Richards was originally published by Richardson in 1922.[108] The Soil Moisture Velocity Equation,[109] which can be solved using the finite water-content vadose zone flow method,[110][111] describes the velocity of flowing water through an unsaturated soil in the vertical direction. The numerical solution of the Richardson/Richards equation allows calculation of unsaturated water flow and solute transport using software such as Hydrus,[112] by giving soil hydraulic parameters of hydraulic functions (water retention function and unsaturated hydraulic conductivity function) and initial and boundary conditions. Preferential flow occurs along interconnected macropores, crevices, root and worm channels, which drain water under gravity.[113][114] Many models based on soil physics now allow for some representation of preferential flow as a dual continuum, dual porosity or dual permeability options, but these have generally been "bolted on" to the Richards solution without any rigorous physical underpinning.[115]

Water uptake by plants

Of equal importance to the storage and movement of water in soil is the means by which plants acquire it and their nutrients. Most soil water is taken up by plants as passive absorption caused by the pulling force of water evaporating (transpiring) from the long column of water (xylem sap flow) that leads from the plant's roots to its leaves, according to the cohesion-tension theory.[116] The upward movement of water and solutes (hydraulic lift) is regulated in the roots by the endodermis[117] and in the plant foliage by stomatal conductance,[118] and can be interrupted in root and shoot xylem vessels by cavitation, also called xylem embolism.[119] In addition, the high concentration of salts within plant roots creates an osmotic pressure gradient that pushes soil water into the roots.[120] Osmotic absorption becomes more important during times of low water transpiration caused by lower temperatures (for example at night) or high humidity, and the reverse occurs under high temperature or low humidity. It is these process that cause guttation and wilting, respectively.[121][122]

Root extension is vital for plant survival. A study of a single winter rye plant grown for four months in one cubic foot (0.0283 cubic meters) of loam soil showed that the plant developed 13,800,000 roots, a total of 620 km in length with 237 square meters in surface area; and 14 billion hair roots of 10,620 km total length and 400 square meters total area; for a total surface area of 638 square meters. The total surface area of the loam soil was estimated to be 52,000 square meters.[123] In other words, the roots were in contact with only 1.2% of the soil. However, root extension should be viewed as a dynamic process, allowing new roots to explore a new volume of soil each day, increasing dramatically the total volume of soil explored over a given growth period, and thus the volume of water taken up by the root system over this period.[124] Root architecture, i.e. the spatial configuration of the root system, plays a prominent role in the adaptation of plants to soil water and nutrient availabiity, and thus in plant productivity.[125]

Roots must seek out water as the unsaturated flow of water in soil can move only at a rate of up to 2.5 cm per day; as a result they are constantly dying and growing as they seek out high concentrations of soil moisture.[126] Insufficient soil moisture, to the point of causing wilting, will cause permanent damage and crop yields will suffer. When grain sorghum was exposed to soil suction as low as 1300 kPa during the seed head emergence through bloom and seed set stages of growth, its production was reduced by 34%.[127]

Consumptive use and water use efficiency

Only a small fraction (0.1% to 1%) of the water used by a plant is held within the plant. The majority is ultimately lost via transpiration, while evaporation from the soil surface is also substantial, the transpiration:evaporation ratio varying according to vegetation type and climate, peaking in tropical rainforests and dipping in steppes and deserts.[128] Transpiration plus evaporative soil moisture loss is called evapotranspiration. Evapotranspiration plus water held in the plant totals to consumptive use, which is nearly identical to evapotranspiration.[127][129]

The total water used in an agricultural field includes surface runoff, drainage and consumptive use. The use of loose mulches will reduce evaporative losses for a period after a field is irrigated, but in the end the total evaporative loss (plant plus soil) will approach that of an uncovered soil, while more water is immediately available for plant growth.[130] Water use efficiency is measured by the transpiration ratio, which is the ratio of the total water transpired by a plant to the dry weight of the harvested plant. Transpiration ratios for crops range from 300 to 700. For example, alfalfa may have a transpiration ratio of 500 and as a result 500 kilograms of water will produce one kilogram of dry alfalfa.[131]

Soil gas

The atmosphere of soil, or soil gas, is very different from the atmosphere above. The consumption of oxygen by microbes and plant roots, and their release of carbon dioxide, decrease oxygen and increase carbon dioxide concentration. Atmospheric CO₂ concentration is 0.04%, but in the soil pore space it may range from 10 to 100 times that level, thus potentially contributing to the inhibition of root respiration.[132] Calcareous soils regulate CO₂ concentration by carbonate buffering, contrary to acid soils in which all CO₂ respired accumulates in the soil pore system.[133] At extreme levels CO₂ is toxic.[134] This suggests a possible negative feedback control of soil CO₂ concentration through its inhibitory effects on root and microbial respiration (also called 'soil respiration').[135] In addition, the soil voids are saturated with water vapour, at least until the point of maximal hygroscopicity, beyond which a vapour-pressure deficit occurs in the soil pore space.[34] Adequate porosity is necessary, not just to allow the penetration of water, but also to allow gases to diffuse in and out. Movement of gases is by diffusion from high concentrations to lower, the diffusion coefficient decreasing with soil compaction.[136] Oxygen from above atmosphere diffuses in the soil where it is consumed and levels of carbon dioxide in excess of above atmosphere diffuse out with other gases (including greenhouse gases) as well as water.[137] Soil texture and structure strongly affect soil porosity and gas diffusion. It is the total pore space (porosity) of soil, not the pore size, and the degree of pore interconnection (or conversely pore sealing), together with water content, air turbulence and temperature, that determine the rate of diffusion of gases into and out of soil.[138][137] Platy soil structure and soil compaction (low porosity) impede gas flow, and a deficiency of oxygen may encourage anaerobic bacteria to reduce (strip oxygen) from nitrate NO₃ to the gases N₂, N₂O, and NO, which are then lost to the atmosphere, thereby depleting the soil of nitrogen.[139] Aerated soil is also a net sink of methane CH₄[140] but a net producer of methane (a strong heat-absorbing greenhouse gas) when soils are depleted of oxygen and subject to elevated temperatures.[141]

Soil atmosphere is also the seat of emissions of volatiles other than carbon and nitrogen oxides from various soil organisms, e.g. roots,[142] bacteria,[143] fungi,[144] animals.[145] These volatiles are used as chemical cues, making soil atmosphere the seat of interaction networks[146][147] playing a decisive role in the stability, dynamics and evolution of soil ecosystems.[148] Biogenic soil volatile organic compounds are exchanged with the aboveground atmosphere, in which they are just 1–2 orders of magnitude lower than those from aboveground vegetation.[149]

We humans can get some idea of the soil atmosphere through the well-known 'after-the-rain' scent, when infiltering rainwater flushes out the whole soil atmosphere after a drought period, or when soil is excavated,[150] a bulk property attributed in a reductionist manner to particular biochemical compounds such as petrichor or geosmin.

Solid phase (soil matrix)

Soil particles can be classified by their chemical composition (mineralogy) as well as their size. The particle size distribution of a soil, its texture, determines many of the properties of that soil, in particular hydraulic conductivity and water potential,[151] but the mineralogy of those particles can strongly modify those properties. The mineralogy of the finest soil particles, clay, is especially important.[152]

Chemistry

The chemistry of a soil determines its ability to supply available plant nutrients and affects its physical properties and the health of its living population. In addition, a soil's chemistry also determines its corrosivity, stability, and ability to absorb pollutants and to filter water. It is the surface chemistry of mineral and organic colloids that determines soil's chemical properties.[153] A colloid is a small, insoluble particle ranging in size from 1 nanometer to 1 micrometer, thus small enough to remain suspended by Brownian motion in a fluid medium without settling.[154] Most soils contain organic colloidal particles called humus as well as the inorganic colloidal particles of clays. The very high specific surface area of colloids and their net electrical charges give soil its ability to hold and release ions. Negatively charged sites on colloids attract and release cations in what is referred to as cation exchange. Cation-exchange capacity (CEC) is the amount of exchangeable cations per unit weight of dry soil and is expressed in terms of milliequivalents of positively charged ions per 100 grams of soil (or centimoles of positive charge per kilogram of soil; cmol_c/kg). Similarly, positively charged sites on colloids can attract and release anions in the soil giving the soil anion exchange capacity (AEC).

Cation and anion exchange

The cation exchange, that takes place between colloids and soil water, buffers (moderates) soil pH, alters soil structure, and purifies percolating water by adsorbing cations of all types, both useful and harmful.

The negative or positive charges on colloid particles make them able to hold cations or anions, respectively, to their surfaces. The charges result from four sources.[155]

Isomorphous substitution occurs in clay during its formation, when lower-valence cations substitute for higher-valence cations in the crystal structure.[156] Substitutions in the outermost layers are more effective than for the innermost layers, as the electric charge strength drops off as the square of the distance. The net result is oxygen atoms with net negative charge and the ability to attract cations.
Edge-of-clay oxygen atoms are not in balance ionically as the tetrahedral and octahedral structures are incomplete.[157]
Hydroxyls may substitute for oxygens of the silica layers, a process called hydroxylation. When the hydrogens of the clay hydroxyls are ionised into solution, they leave the oxygen with a negative charge (anionic clays).[158]
Hydrogens of humus hydroxyl groups may also be ionised into solution, leaving, similarly to clay, an oxygen with a negative charge.[159]

Cations held to the negatively charged colloids resist being washed downward by water and out of reach of plants' roots, thereby preserving the fertility of soils in areas of moderate rainfall and low temperatures.[160][161]

There is a hierarchy in the process of cation exchange on colloids, as they differ in the strength of adsorption by the colloid and hence their ability to replace one another (ion exchange). If present in equal amounts in the soil water solution:

Al³⁺ replaces H⁺ replaces Ca²⁺ replaces Mg²⁺ replaces K⁺ same as NH⁴⁺ replaces Na⁺[162]

If one cation is added in large amounts, it may replace the others by the sheer force of its numbers. This is called law of mass action. This is largely what occurs with the addition of cationic fertilisers (potash, lime).[163]

As the soil solution becomes more acidic (low pH, meaning an abundance of H⁺, the other cations more weakly bound to colloids are pushed into solution as hydrogen ions occupy exchange sites (protonation). A low pH may cause hydrogen of hydroxyl groups to be pulled into solution, leaving charged sites on the colloid available to be occupied by other cations. This ionisation of hydroxyl groups on the surface of soil colloids creates what is described as pH-dependent surface charges.[164] Unlike permanent charges developed by isomorphous substitution, pH-dependent charges are variable and increase with increasing pH.[42] Freed cations can be made available to plants but are also prone to be leached from the soil, possibly making the soil less fertile.[165] Plants are able to excrete H⁺ into the soil through the synthesis of organic acids and by that means, change the pH of the soil near the root and push cations off the colloids, thus making those available to the plant.[166]

Cation exchange capacity (CEC)

Cation exchange capacity should be thought of as the soil's ability to remove cations from the soil water solution and sequester those to be exchanged later as the plant roots release hydrogen ions to the solution. CEC is the amount of exchangeable hydrogen cation (H⁺) that will combine with 100 grams dry weight of soil and whose measure is one milliequivalents per 100 grams of soil (1 meq/100 g). Hydrogen ions have a single charge and one-thousandth of a gram of hydrogen ions per 100 grams dry soil gives a measure of one milliequivalent of hydrogen ion. Calcium, with an atomic weight 40 times that of hydrogen and with a valence of two, converts to (40/2) x 1 milliequivalent = 20 milliequivalents of hydrogen ion per 100 grams of dry soil or 20 meq/100 g.[167] The modern measure of CEC is expressed as centimoles of positive charge per kilogram (cmol/kg) of oven-dry soil.

Most of the soil's CEC occurs on clay and humus colloids, and the lack of those in hot, humid, wet climates, due to leaching and decomposition, respectively, explains the apparent sterility of tropical soils.[168] Live plant roots also have some CEC, linked to their specific surface area.[169]

Cation exchange capacity for soils; soil textures; soil colloids[170]
Soil	State	CEC meq/100 g
Charlotte fine sand	Florida	1.0
Ruston fine sandy loam	Texas	1.9
Glouchester loam	New Jersey	11.9
Grundy silt loam	Illinois	26.3
Gleason clay loam	California	31.6
Susquehanna clay loam	Alabama	34.3
Davie mucky fine sand	Florida	100.8
Sands	------	1–5
Fine sandy loams	------	5–10
Loams and silt loams	-----	5–15
Clay loams	-----	15–30
Clays	-----	over 30
Sesquioxides	-----	0–3
Kaolinite	-----	3–15
Illite	-----	25–40
Montmorillonite	-----	60–100
Vermiculite (similar to illite)	-----	80–150
Humus	-----	100–300

Anion exchange capacity (AEC)

Anion exchange capacity should be thought of as the soil's ability to remove anions (e.g. nitrate, phosphate) from the soil water solution and sequester those for later exchange as the plant roots release carbonate anions to the soil water solution. Those colloids which have low CEC tend to have some AEC. Amorphous and sesquioxide clays have the highest AEC,[171] followed by the iron oxides. Levels of AEC are much lower than for CEC, because of the generally higher rate of positively (versus negatively) charged surfaces on soil colloids, to the exception of variable-charge soils.[172] Phosphates tend to be held at anion exchange sites.[173]

Iron and aluminum hydroxide clays are able to exchange their hydroxide anions (OH⁻) for other anions.[174] The order reflecting the strength of anion adhesion is as follows:

H₂PO₄⁻ replaces SO₄²⁻ replaces NO₃⁻ replaces Cl⁻

The amount of exchangeable anions is of a magnitude of tenths to a few milliequivalents per 100 g dry soil.[170] As pH rises, there are relatively more hydroxyls, which will displace anions from the colloids and force them into solution and out of storage; hence AEC decreases with increasing pH (alkalinity).[175]

Reactivity (pH)

Soil reactivity is expressed in terms of pH and is a measure of the acidity or alkalinity of the soil. More precisely, it is a measure of hydrogen ion concentration in an aqueous solution and ranges in values from 0 to 14 (acidic to basic) but practically speaking for soils, pH ranges from 3.5 to 9.5, as pH values beyond those extremes are toxic to life forms.[176]

At 25 °C an aqueous solution that has a pH of 3.5 has 10^−3.5 moles H⁺ (hydrogen ions) per litre of solution (and also 10^−10.5 mole/litre OH⁻). A pH of 7, defined as neutral, has 10⁻⁷ moles of hydrogen ions per litre of solution and also 10⁻⁷ moles of OH⁻ per litre; since the two concentrations are equal, they are said to neutralise each other. A pH of 9.5 has 10^−9.5 moles hydrogen ions per litre of solution (and also 10^−2.5 mole per litre OH⁻). A pH of 3.5 has one million times more hydrogen ions per litre than a solution with pH of 9.5 (9.5–3.5 = 6 or 10⁶) and is more acidic.[177]

The effect of pH on a soil is to remove from the soil or to make available certain ions. Soils with high acidity tend to have toxic amounts of aluminium and manganese.[178] As a result of a trade-off between toxicity and requirement most nutrients are better available to plants at moderate pH,[179] although most minerals are more soluble in acid soils. Soil organisms are hindered by high acidity, and most agricultural crops do best with mineral soils of pH 6.5 and organic soils of pH 5.5.[180] Given that at low pH toxic metals (e.g. cadmium, zinc, lead) are positively charged as cations and organic pollutants are in non-ionic form, thus both made more available to organisms,[181][182] it has been suggested that plants, animals and microbes commonly living in acid soils are pre-adapted to every kind of pollution, whether of natural or human origin.[183]

In high rainfall areas, soils tend to acidity as the basic cations are forced off the soil colloids by the mass action of hydrogen ions from the rain against those attached to the colloids. High rainfall rates can then wash the nutrients out, leaving the soil inhabited only by those organisms which are particularly efficient to uptake nutrients in very acid conditions, like in tropical rainforests.[184] Once the colloids are saturated with H⁺, the addition of any more hydrogen ions or aluminum hydroxyl cations drives the pH even lower (more acidic) as the soil has been left with no buffering capacity.[185] In areas of extreme rainfall and high temperatures, the clay and humus may be washed out, further reducing the buffering capacity of the soil.[186] In low rainfall areas, unleached calcium pushes pH to 8.5 and with the addition of exchangeable sodium, soils may reach pH 10.[187] Beyond a pH of 9, plant growth is reduced.[188] High pH results in low micro-nutrient mobility, but water-soluble chelates of those nutrients can correct the deficit.[189] Sodium can be reduced by the addition of gypsum (calcium sulphate) as calcium adheres to clay more tightly than does sodium causing sodium to be pushed into the soil water solution where it can be washed out by an abundance of water.[190][191]

Base saturation percentage

There are acid-forming cations (e.g. hydrogen, aluminium, iron) and there are base-forming cations (e.g. calcium, magnesium, sodium). The fraction of the negatively-charged soil colloid exchange sites (CEC) that are occupied by base-forming cations is called base saturation. If a soil has a CEC of 20 meq and 5 meq are aluminium and hydrogen cations (acid-forming), the remainder of positions on the colloids (20-5 = 15 meq) are assumed occupied by base-forming cations, so that the base saturation is 15/20 x 100% = 75% (the compliment 25% is assumed acid-forming cations or protons). Base saturation is almost in direct proportion to pH (it increases with increasing pH).[192] It is of use in calculating the amount of lime needed to neutralise an acid soil (lime requirement). The amount of lime needed to neutralize a soil must take account of the amount of acid forming ions on the colloids (exchangeable acidity), not just those in the soil water solution (free acidity).[193] The addition of enough lime to neutralize the soil water solution will be insufficient to change the pH, as the acid forming cations stored on the soil colloids will tend to restore the original pH condition as they are pushed off those colloids by the calcium of the added lime.[194]

Buffering

The resistance of soil to change in pH, as a result of the addition of acid or basic material, is a measure of the buffering capacity of a soil and (for a particular soil type) increases as the CEC increases. Hence, pure sand has almost no buffering ability, while soils high in colloids (whether mineral or organic) have high buffering capacity.[195] Buffering occurs by cation exchange and neutralisation. However, colloids are not the only regulators of soil pH. The role of carbonates should be underlined, too.[196] More generally, according to pH levels, several buffer systems take precedence over each other, from calcium carbonate buffer range to iron buffer range.[197]

The addition of a small amount of highly basic aqueous ammonia to a soil will cause the ammonium to displace hydrogen ions from the colloids, and the end product is water and colloidally fixed ammonium, but little permanent change overall in soil pH.

The addition of a small amount of lime, Ca(OH)₂, will displace hydrogen ions from the soil colloids, causing the fixation of calcium to colloids and the evolution of CO₂ and water, with little permanent change in soil pH.

The above are examples of the buffering of soil pH. The general principal is that an increase in a particular cation in the soil water solution will cause that cation to be fixed to colloids (buffered) and a decrease in solution of that cation will cause it to be withdrawn from the colloid and moved into solution (buffered). The degree of buffering is often related to the CEC of the soil; the greater the CEC, the greater the buffering capacity of the soil.[198]

Nutrients

Seventeen elements or nutrients are essential for plant growth and reproduction. They are carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), magnesium (Mg), iron (Fe), boron (B), manganese (Mn), copper (Cu), zinc (Zn), molybdenum (Mo), nickel (Ni) and chlorine (Cl).[199][200][201] Nutrients required for plants to complete their life cycle are considered essential nutrients. Nutrients that enhance the growth of plants but are not necessary to complete the plant's life cycle are considered non-essential. With the exception of carbon, hydrogen and oxygen, which are supplied by carbon dioxide and water, and nitrogen, provided through nitrogen fixation,[201] the nutrients derive originally from the mineral component of the soil. The Law of the Minimum expresses that when the available form of a nutrient is not in enough proportion in the soil solution, then other nutrients cannot be taken up at an optimum rate by a plant.[202] A particular nutrient ratio of the soil solution is thus mandatory for optimizing plant growth, a value which might differ from nutrient ratios calculated from plant composition.[203]

Plant uptake of nutrients can only proceed when they are present in a plant-available form. In most situations, nutrients are absorbed in an ionic form from (or together with) soil water. Although minerals are the origin of most nutrients, and the bulk of most nutrient elements in the soil is held in crystalline form within primary and secondary minerals, they weather too slowly to support rapid plant growth. For example, the application of finely ground minerals, feldspar and apatite, to soil seldom provides the necessary amounts of potassium and phosphorus at a rate sufficient for good plant growth, as most of the nutrients remain bound in the crystals of those minerals.[204]

The nutrients adsorbed onto the surfaces of clay colloids and soil organic matter provide a more accessible reservoir of many plant nutrients (e.g. K, Ca, Mg, P, Zn). As plants absorb the nutrients from the soil water, the soluble pool is replenished from the surface-bound pool. The decomposition of soil organic matter by microorganisms is another mechanism whereby the soluble pool of nutrients is replenished – this is important for the supply of plant-available N, S, P, and B from soil.[205]

Gram for gram, the capacity of humus to hold nutrients and water is far greater than that of clay minerals, most of the soil cation exchange capacity arising from charged carboxylic groups on organic matter.[206] However, despite the great capacity of humus to retain water once water-soaked, its high hydrophobicity decreases its wettability.[207] All in all, small amounts of humus may remarkably increase the soil's capacity to promote plant growth.[208][205]

Plant nutrients, their chemical symbols, and the ionic forms common in soils and available for plant uptake[209]
Element	Symbol	Ion or molecule
Carbon	C	CO₂ (mostly through leaves)
Hydrogen	H	H⁺, HOH (water)
Oxygen	O	O²⁻, OH⁻, CO₃²⁻, SO₄²⁻, CO₂
Phosphorus	P	H₂PO₄⁻, HPO₄²⁻ (phosphates)
Potassium	K	K⁺
Nitrogen	N	NH₄⁺, NO₃⁻ (ammonium, nitrate)
Sulfur	S	SO₄²⁻
Calcium	Ca	Ca²⁺
Iron	Fe	Fe²⁺, Fe³⁺ (ferrous, ferric)
Magnesium	Mg	Mg²⁺
Boron	B	H₃BO₃, H₂BO₃⁻, B(OH)₄⁻
Manganese	Mn	Mn²⁺
Copper	Cu	Cu²⁺
Zinc	Zn	Zn²⁺
Molybdenum	Mo	MoO₄²⁻ (molybdate)
Chlorine	Cl	Cl⁻ (chloride)

Uptake processes

Nutrients in the soil are taken up by the plant through its roots, and in particular its root hairs. To be taken up by a plant, a nutrient element must be located near the root surface; however, the supply of nutrients in contact with the root is rapidly depleted within a distance of ca. 2 mm.[210] There are three basic mechanisms whereby nutrient ions dissolved in the soil solution are brought into contact with plant roots:

Mass flow of water
Diffusion within water
Interception by root growth

All three mechanisms operate simultaneously, but one mechanism or another may be most important for a particular nutrient.[211] For example, in the case of calcium, which is generally plentiful in the soil solution, except when aluminium over competes calcium on cation exchange sites in very acid soils (pH less than 4),[212] mass flow alone can usually bring sufficient amounts to the root surface. However, in the case of phosphorus, diffusion is needed to supplement mass flow. For the most part, nutrient ions must travel some distance in the soil solution to reach the root surface. This movement can take place by mass flow, as when dissolved nutrients are carried along with the soil water flowing toward a root that is actively drawing water from the soil. In this type of movement, the nutrient ions are somewhat analogous to leaves floating down a stream. In addition, nutrient ions continually move by diffusion from areas of greater concentration toward the nutrient-depleted areas of lower concentration around the root surface. That process is due to random motion, also called Brownian motion, of molecules within a gradient of decreasing concentration.[213] By this means, plants can continue to take up nutrients even at night, when water is only slowly absorbed into the roots as transpiration has almost stopped following stomatal closure. Finally, root interception comes into play as roots continually grow into new, undepleted soil. By this way roots are also able to absorb nanomaterials such as nanoparticulate organic matter.[214]

Estimated relative importance of mass flow, diffusion and root interception as mechanisms in supplying plant nutrients to corn plant roots in soils[215]
Nutrient	Approximate percentage supplied by:
Nutrient	Mass flow	Root interception	Diffusion
Nitrogen	98.8	1.2	0
Phosphorus	6.3	2.8	90.9
Potassium	20.0	2.3	77.7
Calcium	71.4	28.6	0
Sulfur	95.0	5.0	0
Molybdenum	95.2	4.8	0

In the above table, phosphorus and potassium nutrients move more by diffusion than they do by mass flow in the soil water solution, as they are rapidly taken up by the roots creating a concentration of almost zero near the roots (the plants cannot transpire enough water to draw more of those nutrients near the roots). The very steep concentration gradient is of greater influence in the movement of those ions than is the movement of those by mass flow.[216] The movement by mass flow requires the transpiration of water from the plant causing water and solution ions to also move toward the roots.[217] Movement by root interception is slowest as the plants must extend their roots.[218]

Plants move ions out of their roots in an effort to move nutrients in from the soil, an exchange process which occurs in the root apoplast.[219] Hydrogen H⁺ is exchanged for other cations, and carbonate (HCO₃⁻) and hydroxide (OH⁻) anions are exchanged for nutrient anions.[220] As plant roots remove nutrients from the soil water solution, they are replenished as other ions move off of clay and humus (by ion exchange or desorption), are added from the weathering of soil minerals, and are released by the decomposition of soil organic matter. However, the rate at which plant roots remove nutrients may not cope with the rate at which they are replenished in the soil solution, stemming in nutrient limitation to plant growth.[221] Plants derive a large proportion of their anion nutrients from decomposing organic matter, which typically holds about 95 percent of the soil nitrogen, 5 to 60 percent of the soil phosphorus and about 80 percent of the soil sulfur. Where crops are produced, the replenishment of nutrients in the soil must usually be augmented by the addition of fertilizer or organic matter.[215]

Because nutrient uptake is an active metabolic process, conditions that inhibit root metabolism may also inhibit nutrient uptake.[222] Examples of such conditions include waterlogging or soil compaction resulting in poor soil aeration, excessively high or low soil temperatures, and above-ground conditions that result in low translocation of sugars to plant roots.[223]

Carbon

Measuring soil respiration in the field using an SRS2000 system.

Plants obtain their carbon from atmospheric carbon dioxide through photosynthetic carboxylation, to which must be added the uptake of dissolved carbon from the soil solution[224] and carbon transfer through mycorrhizal networks.[225] About 45% of a plant's dry mass is carbon; plant residues typically have a carbon to nitrogen ratio (C/N) of between 13:1 and 100:1. As the soil organic material is digested by micro-organisms and saprophagous soil fauna, the C/N decreases as the carbonaceous material is metabolized and carbon dioxide (CO₂) is released as a byproduct which then finds its way out of the soil and into the atmosphere. Nitrogen turnover (mostly involved in protein turnover) is lesser than that of carbon (mostly involved in respiration) in the living, then dead matter of decomposers, which are always richer in nitrogen than plant litter, and so it builds up in the soil.[226] Normal CO₂ concentration in the atmosphere is 0.03%, this can be the factor limiting plant growth. In a field of maize on a still day during high light conditions in the growing season, the CO₂ concentration drops very low, but under such conditions the crop could use up to 20 times the normal concentration. The respiration of CO₂ by soil micro-organisms decomposing soil organic matter and the CO₂ respired by roots contribute an important amount of CO₂ to the photosynthesising plants, to which must be added the CO₂ respired by aboveground plant tissues.[227] Root-respired CO₂ can be accumulated overnight within hollow stems of plants, to be further used for photosynthesis during the day.[228] Within the soil, CO₂ concentration is 10 to 100 times that of atmospheric levels but may rise to toxic levels if the soil porosity is low or if diffusion is impeded by flooding.[229][199][230]

Nitrogen

Generalization of percent soil nitrogen by soil order

Nitrogen is the most critical element obtained by plants from the soil, to the exception of moist tropical forests where phosphorus is the limiting soil nutrient,[231] and nitrogen deficiency often limits plant growth.[232] Plants can use the nitrogen as either the ammonium cation (NH₄⁺) or the anion nitrate (NO₃⁻). Plants are commonly classified as ammonium or nitrate plants according to their preferential nitrogen nutrition.[233] Usually, most of the nitrogen in soil is bound within organic compounds that make up the soil organic matter, and must be mineralized to the ammonium or nitrate form before it can be taken up by most plants. However, symbiosis with mycorrhizal fungi allow plants to get access to the organic nitrogen pool where and when mineral forms of nitrogen are poorly available.[234] The total nitrogen content depends largely on the soil organic matter content, which in turn depends on texture, climate, vegetation, topography, age and soil management.[235] Soil nitrogen typically decreases by 0.2 to 0.3% for every temperature increase by 10 °C. Usually, grassland soils contain more soil nitrogen than forest soils, because of a higher turnover rate of grassland organic matter.[236] Cultivation decreases soil nitrogen by exposing soil organic matter to decomposition by microorganisms,[237] most losses being caused by denitrification,[238] and soils under no-tillage maintain more soil nitrogen than tilled soils.[239]

Some micro-organisms are able to metabolise organic matter and release ammonium in a process called mineralisation. Others, called nitrifiers, take free ammonium or nitrite as an intermediary step in the process of nitrification, and oxidise it to nitrate. Nitrogen-fixing bacteria are capable of metabolising N₂ into the form of ammonia or related nitrogenous compounds in a process called nitrogen fixation. Both ammonium and nitrate can be immobilized by their incorporation into microbial living cells, where it is temporarily sequestered in the form of amino acids and proteins. Nitrate may be lost from the soil to the atmosphere when bacteria metabolise it to the gases NH₃, N₂ and N₂O, a process called denitrification. Nitrogen may also be leached from the vadose zone if in the form of nitrate, acting as a pollutant if it reaches the water table or flows over land, more especially in agricultural soils under high use of nutrient fertilizers.[240] Ammonium may also be sequestered in 2:1 clay minerals.[241] A small amount of nitrogen is added to soil by rainfall, to the exception of wide areas of North America and West Europe where the excess use of nitrogen fertilizers and manure has caused atmospheric pollution by ammonia emission, stemming in soil acidification and eutrophication of soils and aquatic ecosystems.[242][243][205][244][245][246]

Gains

In the process of mineralisation, microbes feed on organic matter, releasing ammonia (NH₃), ammonium (NH₄⁺), nitrate (NO₃⁻) and other nutrients. As long as the carbon to nitrogen ratio (C/N) of fresh residues in the soil is above 30:1, nitrogen will be in short supply for the nitrogen-rich microbal biomass (nitrogen deficiency), and other bacteria will uptake ammonium and to a lesser extent nitrate and incorporate them into their cells in the immobilization process.[247] In that form the nitrogen is said to be immobilised. Later, when such bacteria die, they too are mineralised and some of the nitrogen is released as ammonium and nitrate. Predation of bacteria by soil fauna, in particular protozoa and nematodes, play a decisive role in the return of immobilized nitrogen to mineral forms.[248] If the C/N of fresh residues is less than 15, mineral nitrogen is freed to the soil and directly available to plants.[249] Bacteria may on average add 25 pounds (11 kg) nitrogen per acre, and in an unfertilised field, this is the most important source of usable nitrogen. In a soil with 5% organic matter perhaps 2 to 5% of that is released to the soil by such decomposition. It occurs fastest in warm, moist, well aerated soil.[250] The mineralisation of 3% of the organic material of a soil that is 4% organic matter overall, would release 120 pounds (54 kg) of nitrogen as ammonium per acre.[251]

Carbon/Nitrogen Ratio of Various Organic Materials[252]
Organic Material	C:N Ratio
Alfalfa	13
Bacteria	4
Clover, green sweet	16
Clover, mature sweet	23
Fungi	9
Forest litter	30
Humus in warm cultivated soils	11
Legume-grass hay	25
Legumes (alfalfa or clover), mature	20
Manure, cow	18
Manure, horse	16–45
Manure, human	10
Oat straw	80
Straw, cornstalks	90
Sawdust	250

In nitrogen fixation, rhizobium bacteria convert N₂ to ammonia (NH₃), which is rapidly converted to amino acids, parts of which are used by the rhizobia for the synthesis of their own biomass proteins, while other parts are transported to the xylem of the host plant.[253] Rhizobia share a symbiotic relationship with host plants, since rhizobia supply the host with nitrogen and the host provides rhizobia with other nutrients and a safe environment. It is estimated that such symbiotic bacteria in the root nodules of legumes add 45 to 250 pounds of nitrogen per acre per year, which may be sufficient for the crop. Other, free-living nitrogen-fixing diazotroph bacteria and archaea live independently in the soil and release mineral forms of nitrogen when their dead bodies are converted by way of mineralization.[254]

Some amount of usable nitrogen is fixed by lightning as nitric oxide (NO) and nitrogen dioxide (NO₂⁻).[255] Nitrogen dioxide is soluble in water to form nitric acid (HNO₃) dissociating in H⁺ and NO₃⁻. Ammonia, NH₃, previously emitted from the soil, may fall with precipitation as nitric acid at a rate of about five pounds nitrogen per acre per year.[256]

Sequestration

When bacteria feed on soluble forms of nitrogen (ammonium and nitrate), they temporarily sequester that nitrogen in their bodies in a process called immobilization. At a later time when those bacteria die, their nitrogen may be released as ammonium by the process of mineralization, sped up by predatory fauna.[257]

Protein material is easily broken down, but the rate of its decomposition is slowed by its attachment to the crystalline structure of clay and when trapped between the clay layers[258] or attached to rough clay surfaces.[259] The layers are small enough that bacteria cannot enter.[260] Some organisms can exude extracellular enzymes that can act on the sequestered proteins. However, those enzymes too may be trapped on the clay crystals, resulting in a complex interaction between proteins, microbial enzymes and mineral surfaces.[261]

Ammonium fixation occurs mainly between the layers of 2:1 type clay minerals such as illite, vermiculite or montmorillonite, together with ions of similar ionic radius and low hydration energy such as potassium, but a small proportion of ammonium is also fixed in the silt fraction.[262] Only a small fraction of soil nitrogen is held this way.[263]

Losses

Usable nitrogen may be lost from soils when it is in the form of nitrate, as it is easily leached, contrary to ammonium which is easily fixed.[264] Further losses of nitrogen occur by denitrification, the process whereby soil bacteria convert nitrate (NO₃⁻) to nitrogen gas, N₂ or N₂O. This occurs when poor soil aeration limits free oxygen, forcing bacteria to use the oxygen in nitrate for their respiratory process. Denitrification increases when oxidisable organic material is available, as in organic farming[264] and when soils are warm and slightly acidic, as currently happening in tropical areas.[265] Denitrification may vary throughout a soil as the aeration varies from place to place.[266] Denitrification may cause the loss of 10 to 20 percent of the available nitrates within a day and when conditions are favourable to that process, losses of up to 60 percent of nitrate applied as fertiliser may occur.[267]

Ammonia volatilisation occurs when ammonium reacts chemically with an alkaline soil, converting NH₄⁺ to NH₃.[268] The application of ammonium fertiliser to such a field can result in volatilisation losses of as much as 30 percent.[269]

All kinds of nitrogen losses, whether by leaching or volatilization, are responsible for a large part of aquifer pollution[270] and air pollution, with concomitant effects on soil acidification and eutrophication,[271] a novel combination of environmental threats (acidity and excess nitrogen) to which extant organisms are badly adapted, causing severe biodiversity losses in natural ecosystems.[272]

Phosphorus

After nitrogen, phosphorus is probably the element most likely to be deficient in soils, although it often turns to be the most deficient in tropical soils where the mineral pool is depleted under intense leaching and mineral weathering while, contrary to nitrogen, phosphorus reserves cannot be replenished from other sources.[273] The soil mineral apatite is the most common mineral source of phosphorus, from which it can be extracted by microbial and root exudates,[274][275] with an important contribution of arbuscular mycorrhizal fungi.[276] The most common form of organic phosphate is phytate, the principal storage form of phosphorus in many plant tissues. While there is on average 1000 lb per acre (1120 kg per hectare) of phosphorus in the soil, it is generally in the form of orthophosphate with low solubility, except when linked to ammonium or calcium, hence the use of diammonium phosphate or monocalcium phosphate as fertilizers.[277] Total phosphorus is about 0.1 percent by weight of the soil, but only one percent of that is directly available to plants. Of the part available, more than half comes from the mineralisation of organic matter. Agricultural fields may need to be fertilised to make up for the phosphorus that has been removed in the crop.[278]

When phosphorus does form solubilised ions of H₂PO₄⁻, if not taken up by plant roots they rapidly form insoluble phosphates of calcium or hydrous oxides of iron and aluminum. Phosphorus is largely immobile in the soil and is not leached but actually builds up in the surface layer if not cropped. The application of soluble fertilisers to soils may result in zinc deficiencies as zinc phosphates form, but soil pH levels, partly depending on the form of phosphorus in the fertiliser, strongly interact with this effect, in some cases resulting in increased zinc availability.[279] Lack of phosphorus may interfere with the normal opening of the plant leaf stomata, decreased stomatal conductance resulting in decreased photosynthesis and respiration rates[280] while decreased transpiration increases plant temperature.[281] Phosphorus is most available when soil pH is 6.5 in mineral soils and 5.5 in organic soils.[269]

Potassium

The amount of potassium in a soil may be as much as 80,000 lb per acre-foot, of which only 150 lb is available for plant growth. Common mineral sources of potassium are the mica biotite and potassium feldspar, KAlSi₃O₈. Rhizosphere bacteria, also called rhizobacteria, contribute through the production of organic acids to its solubilization.[282] When solubilised, half will be held as exchangeable cations on clay while the other half is in the soil water solution. Potassium fixation often occurs when soils dry and the potassium is bonded between layers of 2:1 expansive clay minerals such as illite, vermiculite or montmorillonite.[283] Under certain conditions, dependent on the soil texture, intensity of drying, and initial amount of exchangeable potassium, the fixed percentage may be as much as 90 percent within ten minutes. Potassium may be leached from soils low in clay.[284][285]

Calcium

Calcium is one percent by weight of soils and is generally available but may be low as it is soluble and can be leached. It is thus low in sandy and heavily leached soil or strongly acidic mineral soils, resulting in excessive concentration of free hydrogen ions in the soil solution, and therefore these soils require liming.[286] Calcium is supplied to the plant in the form of exchangeable ions and moderately soluble minerals. There are four forms of calcium in the soil. Soil calcium can be in insoluble forms such as calcite or dolomite, in the soil solution in the form of a divalent cation or retained in exchangeable form at the surface of mineral particles. Another form is when calcium complexes with organic matter, forming covalent bonds between organic compounds which contribute to structural stability.[287] Calcium is more available on the soil colloids than is potassium because the common mineral calcite, CaCO₃, is more soluble than potassium-bearing minerals such as feldspar.[288]

Calcium uptake by roots is essential for plant nutrition, contrary to an old tenet that it was luxury consumption.[289] Calcium is considered as an essential component of plant cell membranes, a counterion for inorganic and organic anions in the vacuole, and an intracellular messenger in the cytosol, playing a role in cellular learning and memory.[290]

Magnesium

Magnesium is one of the dominant exchangeable cations in most soils (after calcium and potassium). Magnesium is an essential element for plants, microbes and animals, being involved in many catalytic reactions and in the synthesis of chlorophyll. Primary minerals that weather to release magnesium include hornblende, biotite and vermiculite. Soil magnesium concentrations are generally sufficient for optimal plant growth, but highly weathered and sandy soils may be magnesium deficient due to leaching by heavy precipitation.[205][291]

Sulfur

Most sulfur is made available to plants, like phosphorus, by its release from decomposing organic matter.[291] Deficiencies may exist in some soils (especially sandy soils) and if cropped, sulfur needs to be added. The application of large quantities of nitrogen to fields that have marginal amounts of sulfur may cause sulfur deficiency by a dilution effect when stimulation of plant growth by nitrogen increases the plant demand for sulfur.[292] A 15-ton crop of onions uses up to 19 lb of sulfur and 4 tons of alfalfa uses 15 lb per acre. Sulfur abundance varies with depth. In a sample of soils in Ohio, United States, the sulfur abundance varied with depths, 0–6 inches, 6–12 inches, 12–18 inches, 18–24 inches in the amounts: 1056, 830, 686, 528 lb per acre respectively.[293]

Micronutrients

The micronutrients essential in plant life, in their order of importance, include iron,[294] manganese,[295] zinc,[296] copper,[297] boron,[298] chlorine[299] and molybdenum.[300] The term refers to plants' needs, not to their abundance in soil. They are required in very small amounts but are essential to plant health in that most are required parts of enzyme systems which are involved in plant metabolism.[301] They are generally available in the mineral component of the soil, but the heavy application of phosphates can cause a deficiency in zinc and iron by the formation of insoluble zinc and iron phosphates.[302] Iron deficiency, stemming in plant chlorosis and rhizosphere acidification, may also result from excessive amounts of heavy metals or calcium minerals (lime) in the soil.[303][304] Excess amounts of soluble boron, molybdenum and chloride are toxic.[305][306]

Non-essential nutrients

Nutrients which enhance the health but whose deficiency does not stop the life cycle of plants include: cobalt, strontium, vanadium, silicon and nickel.[307] As their importance is evaluated they may be added to the list of essential plant nutrients, as is the case for silicon.[308]

Soil organic matter

Soil organic matter is made up of organic compounds and includes plant, animal and microbial material, both living and dead. A typical soil has a biomass composition of 70% microorganisms, 22% macrofauna, and 8% roots. The living component of an acre of soil may include 900 lb of earthworms, 2400 lb of fungi, 1500 lb of bacteria, 133 lb of protozoa and 890 lb of arthropods and algae.[309]

A few percent of the soil organic matter, with small residence time, consists of the microbial biomass and metabolites of bacteria, molds, and actinomycetes that work to break down the dead organic matter.[310][311] Were it not for the action of these micro-organisms, the entire carbon dioxide part of the atmosphere would be sequestered as organic matter in the soil. However, in the same time soil microbes contribute to carbon sequestration in the topsoil through the formation of stable humus.[312] In the aim to sequester more carbon in the soil for alleviating the greenhouse effect it would be more efficient in the long-term to stimulate humification than to decrease litter decomposition.[313]

The main part of soil organic matter is a complex assemblage of small organic molecules, collectively called humus or humic substances. The use of these terms, which do not rely on a clear chemical classification, has been considered as obsolete.[314] Other studies showed that the classical notion of molecule is not convenient for humus, which escaped most attempts done over two centuries to resolve it in unit components, but still is chemically distinct from polysaccharides, lignins and proteins.[315]

Most living things in soils, including plants, animals, bacteria, and fungi, are dependent on organic matter for nutrients and/or energy. Soils have organic compounds in varying degrees of decomposition which rate is dependent on the temperature, soil moisture, and aeration. Bacteria and fungi feed on the raw organic matter, which are fed upon by protozoa, which in turn are fed upon by nematodes, annelids and arthropods, themselves able to consume and transform raw or humified organic matter. This has been called the soil food web, through which all organic matter is processed as in a digestive system.[316] Organic matter holds soils open, allowing the infiltration of air and water, and may hold as much as twice its weight in water. Many soils, including desert and rocky-gravel soils, have little or no organic matter. Soils that are all organic matter, such as peat (histosols), are infertile.[317] In its earliest stage of decomposition, the original organic material is often called raw organic matter. The final stage of decomposition is called humus.

In grassland, much of the organic matter added to the soil is from the deep, fibrous, grass root systems. By contrast, tree leaves falling on the forest floor are the principal source of soil organic matter in the forest. Another difference is the frequent occurrence in the grasslands of fires that destroy large amounts of aboveground material but stimulate even greater contributions from roots. Also, the much greater acidity under any forests inhibits the action of certain soil organisms that otherwise would mix much of the surface litter into the mineral soil. As a result, the soils under grasslands generally develop a thicker A horizon with a deeper distribution of organic matter than in comparable soils under forests, which characteristically store most of their organic matter in the forest floor (O horizon) and thin A horizon.[318]

Humus

Humus refers to organic matter that has been decomposed by soil microflora and fauna to the point where it is resistant to further breakdown. Humus usually constitutes only five percent of the soil or less by volume, but it is an essential source of nutrients and adds important textural qualities crucial to soil health and plant growth.[319] Humus also feeds arthropods, termites and earthworms which further improve the soil.[320] The end product, humus, is suspended in colloidal form in the soil solution and forms a weak acid that can attack silicate minerals.[321] Humus has a high cation and anion exchange capacity that on a dry weight basis is many times greater than that of clay colloids. It also acts as a buffer, like clay, against changes in pH and soil moisture.[322]

Humic acids and fulvic acids, which begin as raw organic matter, are important constituents of humus. After the death of plants, animals, and microbes, microbes begin to feed on the residues through their production of extra-cellular enzymes, resulting finally in the formation of humus.[323] As the residues break down, only molecules made of aliphatic and aromatic hydrocarbons, assembled and stabilized by oxygen and hydrogen bonds, remain in the form of complex molecular assemblages collectively called humus.[315] Humus is never pure in the soil, because it reacts with metals and clays to form complexes which further contribute to its stability and to soil structure.[322] While the structure of humus has in itself few nutrients, to the exception of constitutive metals such as calcium, iron and aluminum, it is able to attract and link by weak bonds cation and anion nutrients that can further be released into the soil solution in response to selective root uptake and changes in soil pH, a process of paramount importance for the maintenance of fertility in tropical soils.[324]

Lignin is resistant to breakdown and accumulates within the soil. It also reacts with proteins,[325] which further increases its resistance to decomposition, including enzymatic decomposition by microbes.[326] Fats and waxes from plant matter have still more resistance to decomposition and persist in soils for thousand years, hence their use as tracers of past vegetation in buried soil layers.[327] Clay soils often have higher organic contents that persist longer than soils without clay as the organic molecules adhere to and are stabilised by the clay.[328] Proteins normally decompose readily, to the exception of scleroproteins, but when bound to clay particles they become more resistant to decomposition.[329] As for other proteins clay particles absorb the enzymes exuded by microbes, decreasing enzyme activity while protecting extracellular enzymes from degradation.[330] The addition of organic matter to clay soils can render that organic matter and any added nutrients inaccessible to plants and microbes for many years, while a study showed increased soil fertility following the addition of mature compost to a clay soil.[331] High soil tannin content can cause nitrogen to be sequestered as resistant tannin-protein complexes.[332][333]

Humus formation is a process dependent on the amount of plant material added each year and the type of base soil. Both are affected by climate and the type of organisms present.[334] Soils with humus can vary in nitrogen content but typically have 3 to 6 percent nitrogen. Raw organic matter, as a reserve of nitrogen and phosphorus, is a vital component affecting soil fertility.[317] Humus also absorbs water, and expands and shrinks between dry and wet states to a higher extent than clay, increasing soil porosity.[335] Humus is less stable than the soil's mineral constituents, as it is reduced by microbial decomposition, and over time its concentration diminishes without the addition of new organic matter. However, humus in its most stable forms may persist over centuries if not millennia.[336] Charcoal is a source of highly stable humus, called black carbon,[337] which had been used traditionally to improve the fertility of nutrient-poor tropical soils. This very ancient practice, as ascertained in the genesis of Amazonian dark earths, has been renewed and became popular under the name of biochar. It has been suggested that biochar could be used to sequester more carbon in the fight against the greenhouse effect.[338]

Climatological influence

The production, accumulation and degradation of organic matter are greatly dependent on climate. Temperature, soil moisture and topography are the major factors affecting the accumulation of organic matter in soils. Organic matter tends to accumulate under wet or cold conditions where decomposer activity is impeded by low temperature[339] or excess moisture which results in anaerobic conditions.[340] Conversely, excessive rain and high temperatures of tropical climates enables rapid decomposition of organic matter and leaching of plant nutrients. Forest ecosystems on these soils rely on efficient recycling of nutrients and plant matter by the living plant and microbial biomass to maintain their productivity, a process which is disturbed by human activities.[341] Excessive slope, in particular in the presence of cultivation for the sake of agriculture, may encourage the erosion of the top layer of soil which holds most of the raw organic material that would otherwise eventually become humus.[342]

Plant residue

Typical types and percentages of plant residue components

Cellulose (45%)

Lignin (20%)

Hemicellulose (18%)

Protein (8%)

Sugars and starches (5%)

Fats and waxes (2%)

Cellulose and hemicellulose undergo fast decomposition by fungi and bacteria, with a half-life of 12–18 days in a temperate climate.[343] Brown rot fungi can decompose the cellulose and hemicellulose, leaving the lignin and phenolic compounds behind. Starch, which is an energy storage system for plants, undergoes fast decomposition by bacteria and fungi. Lignin consists of polymers composed of 500 to 600 units with a highly branched, amorphous structure, linked to cellulose, hemicellulose and pectin in plant cell walls. Lignin undergoes very slow decomposition, mainly by white rot fungi and actinomycetes; its half-life under temperate conditions is about six months.[343]

Horizons

A horizontal layer of the soil, whose physical features, composition and age are distinct from those above and beneath, is referred to as a soil horizon. The naming of a horizon is based on the type of material of which it is composed. Those materials reflect the duration of specific processes of soil formation. They are labelled using a shorthand notation of letters and numbers which describe the horizon in terms of its colour, size, texture, structure, consistency, root quantity, pH, voids, boundary characteristics and presence of nodules or concretions.[344] No soil profile has all the major horizons. Some, called entisols, may have only one horizon or are currently considered as having no horizon, in particular incipient soils from unreclaimed mining waste deposits,[345] moraines,[346] volcanic cones[347] sand dunes or alluvial terraces.[348] Upper soil horizons may be lacking in truncated soils following wind or water ablation, with concomitant downslope burying of soil horizons, a natural process aggravated by agricultural practices such as tillage.[349] The growth of trees is another source of disturbance, creating a micro-scale heterogeneity which is still visible in soil horizons once trees have died.[350] By passing from a horizon to another, from the top to the bottom of the soil profile, one goes back in time, with past events registered in soil horizons like in sediment layers. Sampling pollen, testate amoebae and plant remains in soil horizons may help to reveal environmental changes (e.g. climate change, land use change) which occurred in the course of soil formation.[351] Soil horizons can be dated by several methods such as radiocarbon, using pieces of charcoal provided they are of enough size to escape pedoturbation by earthworm activity and other mechanical disturbances.[352] Fossil soil horizons from paleosols can be found within sedimentary rock sequences, allowing the study of past environments.[353]

The exposure of parent material to favourable conditions produces mineral soils that are marginally suitable for plant growth, as is the case in eroded soils.[354] The growth of vegetation results in the production of organic residues which fall on the ground as litter for plant aerial parts (leaf litter) or are directly produced belowground for subterranean plant organs (root litter), and then release dissolved organic matter.[355] The remaining surficial organic layer, called the O horizon, produces a more active soil due to the effect of the organisms that live within it. Organisms colonise and break down organic materials, making available nutrients upon which other plants and animals can live.[356] After sufficient time, humus moves downward and is deposited in a distinctive organic-mineral surface layer called the A horizon, in which organic matter is mixed with mineral matter through the activity of burrowing animals, a process called pedoturbation. This natural process does not go to completion in the presence of conditions detrimental to soil life such as strong acidity, cold climate or pollution, stemming in the accumulation of undecomposed organic matter within a single organic horizon overlying the mineral soil[357] and in the juxtaposition of humified organic matter and mineral particles, without intimate mixing, in the underlying mineral horizons.[358]

Classification

Soil is classified into categories in order to understand relationships between different soils and to determine the suitability of a soil in a particular region. One of the first classification systems was developed by the Russian scientist Vasily Dokuchaev around 1880.[359] It was modified a number of times by American and European researchers, and developed into the system commonly used until the 1960s. It was based on the idea that soils have a particular morphology based on the materials and factors that form them. In the 1960s, a different classification system began to emerge which focused on soil morphology instead of parental materials and soil-forming factors. Since then it has undergone further modifications. The World Reference Base for Soil Resources (WRB)[360] aims to establish an international reference base for soil classification.

Uses

Soil is used in agriculture, where it serves as the anchor and primary nutrient base for plants. The types of soil and available moisture determine the species of plants that can be cultivated. Agricultural soil science was the primeval domain of soil knowledge, long time before the advent of pedology in the 19th century. However, as demonstrated by aeroponics, aquaponics and hydroponics, soil material is not an absolute essential for agriculture, and soilless cropping systems have been claimed as the future of agriculture for an endless growing mankind.[361]

Soil material is also a critical component in the mining, construction and landscape development industries.[362] Soil serves as a foundation for most construction projects. The movement of massive volumes of soil can be involved in surface mining, road building and dam construction. Earth sheltering is the architectural practice of using soil for external thermal mass against building walls. Many building materials are soil based. Loss of soil through urbanization is growing at a high rate in many areas and can be critical for the maintenance of subsistence agriculture.[363]

Soil resources are critical to the environment, as well as to food and fibre production, producing 98.8% of food consumed by humans.[364] Soil provides minerals and water to plants according to several processes involved in plant nutrition. Soil absorbs rainwater and releases it later, thus preventing floods and drought, flood regulation being one of the major ecosystem services provided by soil.[365] Soil cleans water as it percolates through it.[366] Soil is the habitat for many organisms: the major part of known and unknown biodiversity is in the soil, in the form of invertebrates (earthworms, woodlice, millipedes, centipedes, snails, slugs, mites, springtails, enchytraeids, nematodes, protists), bacteria, archaea, fungi and algae; and most organisms living above ground have part of them (plants) or spend part of their life cycle (insects) below-ground.[367] Above-ground and below-ground biodiversities are tightly interconnected,[334][368] making soil protection of paramount importance for any restoration or conservation plan.

The biological component of soil is an extremely important carbon sink since about 57% of the biotic content is carbon. Even on desert crusts, cyanobacteria, lichens and mosses capture and sequester a significant amount of carbon by photosynthesis. Poor farming and grazing methods have degraded soils and released much of this sequestered carbon to the atmosphere. Restoring the world's soils could offset the effect of increases in greenhouse gas emissions and slow global warming, while improving crop yields and reducing water needs.[369][370][371]

Waste management often has a soil component. Septic drain fields treat septic tank effluent using aerobic soil processes. Landfills use soil for daily cover. Land application of waste water relies on soil biology to aerobically treat BOD.

Organic soils, especially peat, serve as a significant fuel resource; but wide areas of peat production, such as sphagnum bogs, are now protected because of patrimonial interest.

Geophagy is the practice of eating soil-like substances. Both animals and human cultures occasionally consume soil for medicinal, recreational, or religious purposes. It has been shown that some monkeys consume soil, together with their preferred food (tree foliage and fruits), in order to alleviate tannin toxicity.[372]

Soils filter and purify water and affect its chemistry. Rain water and pooled water from ponds, lakes and rivers percolate through the soil horizons and the upper rock strata, thus becoming groundwater. Pests (viruses) and pollutants, such as persistent organic pollutants (chlorinated pesticides, polychlorinated biphenyls), oils (hydrocarbons), heavy metals (lead, zinc, cadmium), and excess nutrients (nitrates, sulfates, phosphates) are filtered out by the soil.[373] Soil organisms metabolise them or immobilise them in their biomass and necromass,[374] thereby incorporating them into stable humus.[375] The physical integrity of soil is also a prerequisite for avoiding landslides in rugged landscapes.[376]

Degradation

Land degradation[377] refers to a human-induced or natural process which impairs the capacity of land to function. Soils degradation involves the acidification, contamination, desertification, erosion or salination.

Soil acidification is beneficial in the case of alkaline soils, but it degrades land when it lowers crop productivity and increases soil vulnerability to contamination and erosion. Soils are often initially acid because their parent materials were acid and initially low in the basic cations (calcium, magnesium, potassium and sodium). Acidification occurs when these elements are leached from the soil profile by rainfall or by the harvesting of forest or agricultural crops. Soil acidification is accelerated by the use of acid-forming nitrogenous fertilizers and by the effects of acid precipitation.

Soil contamination at low levels is often within a soil's capacity to treat and assimilate waste material. Soil biota can treat waste by transforming it; soil colloids can adsorb the waste material. Many waste treatment processes rely on this treatment capacity. Exceeding treatment capacity can damage soil biota and limit soil function. Derelict soils occur where industrial contamination or other development activity damages the soil to such a degree that the land cannot be used safely or productively. Remediation of derelict soil uses principles of geology, physics, chemistry and biology to degrade, attenuate, isolate or remove soil contaminants to restore soil functions and values. Techniques include leaching, air sparging, chemical amendments, phytoremediation, bioremediation and natural degradation. An example of diffuse pollution with contaminants is the copper distribution in agricultural soils mainly due to fungicide applications in vineyards and other permanent crops.[378]

Desertification

Desertification is an environmental process of ecosystem degradation in arid and semi-arid regions, often caused by human activity. It is a common misconception that droughts cause desertification. Droughts are common in arid and semiarid lands. Well-managed lands can recover from drought when the rains return. Soil management tools include maintaining soil nutrient and organic matter levels, reduced tillage and increased cover. These practices help to control erosion and maintain productivity during periods when moisture is available. Continued land abuse during droughts, however, increases land degradation. Increased population and livestock pressure on marginal lands accelerates desertification.

Erosion control

Erosion of soil is caused by water, wind, ice, and movement in response to gravity. More than one kind of erosion can occur simultaneously. Erosion is distinguished from weathering, since erosion also transports eroded soil away from its place of origin (soil in transit may be described as sediment). Erosion is an intrinsic natural process, but in many places it is greatly increased by human activity, especially poor land use practices. These include agricultural activities which leave the soil bare during times of heavy rain or strong winds, overgrazing, deforestation, and improper construction activity. Improved management can limit erosion. Soil conservation techniques which are employed include changes of land use (such as replacing erosion-prone crops with grass or other soil-binding plants), changes to the timing or type of agricultural operations, terrace building, use of erosion-suppressing cover materials (including cover crops and other plants), limiting disturbance during construction, and avoiding construction during erosion-prone periods.

A serious and long-running water erosion problem occurs in China, on the middle reaches of the Yellow River and the upper reaches of the Yangtze River. From the Yellow River, over 1.6 billion tons of sediment flow each year into the ocean. The sediment originates primarily from water erosion (gully erosion) in the Loess Plateau region of northwest China.

Soil piping is a particular form of soil erosion that occurs below the soil surface. It causes levee and dam failure, as well as sink hole formation. Turbulent flow removes soil starting at the mouth of the seep flow and the subsoil erosion advances up-gradient.[379] The term sand boil is used to describe the appearance of the discharging end of an active soil pipe.[380]

Soil salination is the accumulation of free salts to such an extent that it leads to degradation of the agricultural value of soils and vegetation. Consequences include corrosion damage, reduced plant growth, erosion due to loss of plant cover and soil structure, and water quality problems due to sedimentation. Salination occurs due to a combination of natural and human-caused processes. Arid conditions favour salt accumulation. This is especially apparent when soil parent material is saline. Irrigation of arid lands is especially problematic.[381] All irrigation water has some level of salinity. Irrigation, especially when it involves leakage from canals and overirrigation in the field, often raises the underlying water table. Rapid salination occurs when the land surface is within the capillary fringe of saline groundwater. Soil salinity control involves watertable control and flushing with higher levels of applied water in combination with tile drainage or another form of subsurface drainage.[382][383]

Reclamation

Soils which contain high levels of particular clays, such as smectites, are often very fertile. For example, the smectite-rich clays of Thailand's Central Plains are among the most productive in the world.

Many farmers in tropical areas, however, struggle to retain organic matter in the soils they work. In recent years, for example, productivity has declined in the low-clay soils of northern Thailand. Farmers initially responded by adding organic matter from termite mounds, but this was unsustainable in the long-term. Scientists experimented with adding bentonite, one of the smectite family of clays, to the soil. In field trials, conducted by scientists from the International Water Management Institute in cooperation with Khon Kaen University and local farmers, this had the effect of helping retain water and nutrients. Supplementing the farmer's usual practice with a single application of 200 kg bentonite per rai (6.26 rai = 1 hectare) resulted in an average yield increase of 73%. More work showed that applying bentonite to degraded sandy soils reduced the risk of crop failure during drought years.

In 2008, three years after the initial trials, IWMI scientists conducted a survey among 250 farmers in northeast Thailand, half of whom had applied bentonite to their fields. The average improvement for those using the clay addition was 18% higher than for non-clay users. Using the clay had enabled some farmers to switch to growing vegetables, which need more fertile soil. This helped to increase their income. The researchers estimated that 200 farmers in northeast Thailand and 400 in Cambodia had adopted the use of clays, and that a further 20,000 farmers were introduced to the new technique.[384]

If the soil is too high in clay, adding gypsum, washed river sand and organic matter will balance the composition. Adding organic matter (like ramial chipped wood for instance) to soil which is depleted in nutrients and too high in sand will boost its quality.[385]

History of studies and research

The history of the study of soil is intimately tied to humans' urgent need to provide food for themselves and forage for their animals. Throughout history, civilizations have prospered or declined as a function of the availability and productivity of their soils.[386]

Studies of soil fertility

The Greek historian Xenophon (450–355 BCE) is credited with being the first to expound upon the merits of green-manuring crops: "But then whatever weeds are upon the ground, being turned into earth, enrich the soil as much as dung."[387]

Columella's "Husbandry," circa 60 CE, advocated the use of lime and that clover and alfalfa (green manure) should be turned under, and was used by 15 generations (450 years) under the Roman Empire until its collapse.[387][388] From the fall of Rome to the French Revolution, knowledge of soil and agriculture was passed on from parent to child and as a result, crop yields were low. During the European Middle Ages, Yahya Ibn al-'Awwam's handbook,[389] with its emphasis on irrigation, guided the people of North Africa, Spain and the Middle East; a translation of this work was finally carried to the southwest of the United States when under Spanish influence.[390] Olivier de Serres, considered as the father of French agronomy, was the first to suggest the abandonment of fallowing and its replacement by hay meadows within crop rotations, and he highlighted the importance of soil (the French terroir) in the management of vineyards. His famous book Le Théâtre d'Agriculture et mesnage des champs[391] contributed to the rise of modern, sustainable agriculture and to the collapse of old agricultural practices such as soil improvement (amendment) for crops by the lifting of forest litter and assarting, which ruined the soils of western Europe during Middle Ages and even later on according to regions.[392]

Experiments into what made plants grow first led to the idea that the ash left behind when plant matter was burned was the essential element but overlooked the role of nitrogen, which is not left on the ground after combustion, a belief which prevailed until the 19th century.[393] In about 1635, the Flemish chemist Jan Baptist van Helmont thought he had proved water to be the essential element from his famous five years' experiment with a willow tree grown with only the addition of rainwater. His conclusion came from the fact that the increase in the plant's weight had apparently been produced only by the addition of water, with no reduction in the soil's weight.[394][395] John Woodward (d. 1728) experimented with various types of water ranging from clean to muddy and found muddy water the best, and so he concluded that earthy matter was the essential element. Others concluded it was humus in the soil that passed some essence to the growing plant. Still others held that the vital growth principal was something passed from dead plants or animals to the new plants. At the start of the 18th century, Jethro Tull demonstrated that it was beneficial to cultivate (stir) the soil, but his opinion that the stirring made the fine parts of soil available for plant absorption was erroneous.[394][396]

As chemistry developed, it was applied to the investigation of soil fertility. The French chemist Antoine Lavoisier showed in about 1778 that plants and animals must [combust] oxygen internally to live and was able to deduce that most of the 165-pound weight of van Helmont's willow tree derived from air.[397] It was the French agriculturalist Jean-Baptiste Boussingault who by means of experimentation obtained evidence showing that the main sources of carbon, hydrogen and oxygen for plants were air and water, while nitrogen was taken from soil.[398] Justus von Liebig in his book Organic chemistry in its applications to agriculture and physiology (published 1840), asserted that the chemicals in plants must have come from the soil and air and that to maintain soil fertility, the used minerals must be replaced.[399] Liebig nevertheless believed the nitrogen was supplied from the air. The enrichment of soil with guano by the Incas was rediscovered in 1802, by Alexander von Humboldt. This led to its mining and that of Chilean nitrate and to its application to soil in the United States and Europe after 1840.[400]

The work of Liebig was a revolution for agriculture, and so other investigators started experimentation based on it. In England John Bennet Lawes and Joseph Henry Gilbert worked in the Rothamsted Experimental Station, founded by the former, and (re)discovered that plants took nitrogen from the soil, and that salts needed to be in an available state to be absorbed by plants. Their investigations also produced the "superphosphate", consisting in the acid treatment of phosphate rock.[401] This led to the invention and use of salts of potassium (K) and nitrogen (N) as fertilizers. Ammonia generated by the production of coke was recovered and used as fertiliser.[402] Finally, the chemical basis of nutrients delivered to the soil in manure was understood and in the mid-19th century chemical fertilisers were applied. However, the dynamic interaction of soil and its life forms still awaited discovery.

In 1856 J. Thomas Way discovered that ammonia contained in fertilisers was transformed into nitrates,[403] and twenty years later Robert Warington proved that this transformation was done by living organisms.[404] In 1890 Sergei Winogradsky announced he had found the bacteria responsible for this transformation.[405]

It was known that certain legumes could take up nitrogen from the air and fix it to the soil but it took the development of bacteriology towards the end of the 19th century to lead to an understanding of the role played in nitrogen fixation by bacteria. The symbiosis of bacteria and leguminous roots, and the fixation of nitrogen by the bacteria, were simultaneously discovered by the German agronomist Hermann Hellriegel and the Dutch microbiologist Martinus Beijerinck.[401]

Crop rotation, mechanisation, chemical and natural fertilisers led to a doubling of wheat yields in western Europe between 1800 and 1900.[406]

Studies of soil formation

The scientists who studied the soil in connection with agricultural practices had considered it mainly as a static substrate. However, soil is the result of evolution from more ancient geological materials, under the action of biotic and abiotic (not associated with life) processes. After studies of the improvement of the soil commenced, other researchers began to study soil genesis and as a result also soil types and classifications.

In 1860, in Mississippi, Eugene W. Hilgard (1833-1916) studied the relationship between rock material, climate, vegetation, and the type of soils that were developed. He realised that the soils were dynamic, and considered the classification of soil types.[407] Unfortunately his work was not continued. At about the same time, Friedrich Albert Fallou was describing soil profiles and relating soil characteristics to their formation as part of his professional work evaluating forest and farm land for the principality of Saxony. His 1857 book, Anfangsgründe der Bodenkunde (First principles of soil science) established modern soil science.[408] Contemporary with Fallou's work, and driven by the same need to accurately assess land for equitable taxation, Vasily Dokuchaev led a team of soil scientists in Russia who conducted an extensive survey of soils, observing that similar basic rocks, climate and vegetation types lead to similar soil layering and types, and established the concepts for soil classifications. Due to language barriers, the work of this team was not communicated to western Europe until 1914 through a publication in German by Konstantin Glinka, a member of the Russian team.[409]

Curtis F. Marbut, influenced by the work of the Russian team, translated Glinka's publication into English,[410] and as he was placed in charge of the U.S. National Cooperative Soil Survey, applied it to a national soil classification system.[394]

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External links

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