RESOURCES

I. LIGHT

Review:

• Global patterns of incident radiation at the top of the atmosphere
• Solar Radiation Spectra/Photosynthetically Active Radiation (PAR)
• Chlorophyll absorption spectrum

Quantity

• Full Sunlight: 200-500 Wm^-2 or 1000-2000 µmol m^-2 s^-1 (W = J s^-1)
• Cloudy sky: 20-90 Wm^-2 or 100-400 µmol m^-2 s^-1

Seasonality: The highest monthly (i.e., growing season) maximum light levels are at higher latitudes. Crop yields in the tropics (compared to temperate zones) are ultimately limited by:

• incident radiation
• cloudiness-compare wet season and dry season yields

Photosynthesis

Plants convert the radiant energy in light to chemical energy by the process of photosynthesis. Light energy is used to decompose water into oxygen, protons (H+), and electrons. The electrons flow through a complex series of oxidation-reduction reactions, in which energy is used to produce ATP and reduce the carbon captured as CO₂.

The quantum requirement for C3 photosynthesis is 20 photons/mol CO₂. The quantum requirement is the inverse of the physiological RUE for radiation. Some maximum observed RUE for solar radiation are:

• maize: 0.85 g C/mol
• rice: 0.70 g C/mol
• soybean: 0.60 g C/mol

Values of 0.6-1.0 g C/mol represent just 2.0%-3.4% conversion of solar radiation to chemical energy.

Growth and Yield are ultimately related to light interception.

• At the leaf level: There is a minimum amount of light required for a positive net photosynthesis to occur, called the light compensation point. Maximum levels of photosynthesis (measured as amount of carbon per unit leaf area per unit time) occur at the light saturation point, usually much less than full sunlight.
• At the canopy level: Because some leaves in a canopy will be shaded by other leaves, some leaves will be at or above their light saturation points, some below, and perhaps some below the light compensation point. The leaf-area index (LAI) is the ratio of total leaf surface area to ground surface area; rates of canopy photosynthesis are usually proportional to LAI and do not show a plateau or saturation point.
• At the crop level: Crop growth (and yield) is generally a function of leaf-area duration (LAD), the area under a curve of LAI vs. time. LAD is proportional to the total amount of light energy absorbed during the crop's growing season, and thus to yield.

[Sinclair & Sheehy (1999, Science 283: 1456-1457) recently argued that high yield depends on ability of plant to accumulate and store sufficient N. That is, that yield is generally more limited by N than by light. N is stored in leaves, and high LAI is required to provide sufficient N storage capacity. Green Revolution varieties have higher leaf angles to provide higher LAI. Like HI, there is probably an upper limit to LAI].

II. CARBON (CO₂)

Plants obtain carbon by absorbing CO₂ from the atmosphere. Uptake of CO₂ is primarily through the plant's stomata; when the stomates are open CO₂ is absorbed and water vapor is lost.

There are three photosynthetic pathways that differ in their efficiency of uptake of CO₂:

The C3 pathway is most common. The enzyme RUBISCO (ribulose biphosphate carboxylase-oxidase) is the most abundant protein on earth. It has also been called the most inefficient enzyme on earth (but that characterization may be due to a failure to understand all the ecological consequences of RUBISCO function). RUBISCO is capable of reacting with both CO₂ (photosynthesis) and with oxygen (photorespiration), resulting in a loss of CO₂ (lower rates of net photosynthesis). The carboxylase activity of RUBISCO increases with increasing CO₂ concentration, and decreases with increasing temperature. Wheat, rice, barley, cotton, and all legumes are C3 plants.

Plants with the C4 pathway have a second carboxylating enzyme, PEP (phospho-enol pyruvate) carboxylase that does not react with O₂. C4 plants capture CO₂ initially with PEP carboxylase producing 4-carbon organic acids, which are then decarboxylated in the center of the leaf within cells ("bundle-sheath cells") having the C3 pathway. The resulting high concentration of CO₂ in these cells essentially eliminates the oxidase activity of RUBISCO. Photosynthetic rates of C4 plants-especially at higher temperatures-are thus much higher than those of C3 plants. Maize, sorghum, and sugarcane are C4 plants.

CAM (Crassulacean acid metabolism) plants also have both PEP carboxylase and RUBISCO, but separate the functions of these enzymes temporally rather than spatially. CAM plants open their stomates mostly at night, absorbing CO₂ and losing water when the vapor pressure deficit (see below) is lower. PEP carboxylase is used to fix (capture) CO₂ at night. The 4-carbon organic acids are stored at night and decarboxylated during the day when they they are fixed by RUBISCO into 6 carbon sugar molecules. Instantaneous rates of photosynthesis are lower in CAM plants than in either C3 or C4 plants. Most CAM species are succulent. There are few CAM crops-pineapple, sisal, some cacti.

There is abundant evidence that human activities (fossil fuel combustion and oxidation of carbon stored in forests and soils) are increasing the amount of CO₂ in the atmosphere. The direct (physiological) effects of this increase in atmospheric CO₂ are:

• increased rates of photosynthesis, especially in C3 plants, resulting in higher crop yields.
• increased water-use efficiency.
• higher C:N ratios in plant biomass.

Higher CO₂ concentrations induce partial closing of the stomates, which increases the resistance to the flow of water vapor, reducing transpiration and thus increasing water-use efficiency. [What are some of the other potential effects of reduced transpiration? Review the section on energy budgets in Climate]

Whole-plant and ecosystem effects of [CO₂] are less well understood. Higher leaf temperatures (caused by stomatal closure) associated with increased [CO₂] can lead to increased leaf turnover rate (higher leaf temperatures and more rapid leaf aging) and decreased specific leaf area, reducing the CO₂-fertilization effect.

Natural ecosystems may undergo a change in species composition without increasing NAPP.

It is likely that part of the yield increases of crops during the 20^th Century in fact is due to the increases in CO₂ in the atmosphere. Yield gains are usually attributed to genetics (breeding, green revolution, biotechnology) or agronomy (fertilizer and irrigation).

III. WATER

Soil Water

Soil water content (% by weight) is related to the soil water potential.

• Field capacity is the amount of water held in a saturated soil after all excess water has drained off; the water potential at field capacity is -0.1 to -0.2 MPa.
• Permanent wilting point is the point at which a (particular) plant can no longer absorb water from the soil, for most plants in most soils the water potential at the permanent wilting point is about -1.5 MPa.
• Available water is the amount of water between field capacity and permanent wilting point.

Soil water content is influenced by both soil texture and soil organic matter (SOM). Fine-textured soils have a higher total pore volume, and hence can hold more water. Clay particles hold water more tightly, due both to their charge and to their large surface:volume ratio, therefore soils high in clay have both a higher water storage capacity and a higher permanent wilting point. SOM functions similar to clay particles in affecting soil water-holding capacity and soil water potential.

Crop Growth and Water Use (Sinclair et al., 1984)

Water balance/budget approach:

Yield = HI × (WUE × Tc)

where HI = harvest index, WUE = water-use efficiency, Tc = crop transpiration.

Tc = ET - Es - Tw

where ET = evapotranspiration, Es = evaporation from the soil, and Tw = weed transpiration.

ET = (Ppt + I) - R - D - dS

where Ppt = precipitation, I = irrigation, R = runoff, D = drainage below the root zone, and dS = change in water stored in the soil.

If you consider these three rather simple equations, you can see that are just three general strategies for maximizing yield:

• Maximize WUE
• Maximize Tc (reduce Es & Tw)
• Maximize ET (reduce R, D, & S)

The grower can maximize Tc (the proportion of total ET used by crops) by reducing weed growth and managing the crop so as to increase canopy cover as rapidly as possible. The grower can best maximize ET (the proportion of moisture inputs that go into ET) by decreasing runoff (increasing infiltration) by good soil management, or by increasing the storage of soil water during fallow periods.

Wallace (2000) provides the following estimates for allocation of water in irrigated and rainfed agriculture:

Wallace (2000) and several other recent papers argue that these estimates suggest opportunities for increased crop production through increases in the amount of water going into transpiration.

Gregory et al. (2000) rewrite the water-use equation as:

WUE(field) = (Y/Tc)/[1+ (Es + Tw + R + D)/Tc]

where Y/Tc is essentially the physiological WUE. This equation again emphasizes the potential gains from decreasing Es, Tw, R, and D.

Tc/ET is the ratio of transpiration to total evapotranspiration; Gregory et al. (2000) provide the following estimates:

• Tc/ET = 0.24 - 0.50 for barley in Syria
• Tc/ET = 0.14 - 0.35 for various crops in Kenya

There are surprisingly few options for improving physiological WUE, as described in detail in the Sinclair et al. (1984) paper. The following is from their paper.

WUE can be defined at different spatial and temporal scales:

• Productivity (the numerator) can be based on assimilation (A), biomass production (B), or grain yield (G)
• Water use (the denominator) can be based on transpiration (T), evapotranspiration (ET), or inputs (I)
• The time frame could be seconds (instantaneous, i), daily (d) or seasonal (s)

Physiological WUE = WUE(A,T,i)_L = (1.6c × Pa)/[e*(leaf) - e]

c = constant, depends on photsynthetic pathway. C ~ 0.3 for C3 species and C ~ 0.7 for C4 species

Pa = partial pressure of CO₂ of the air

[e*(leaf) - e] = vapor pressure deficit; difference between the saturation vapor pressure of the leaf e*(leaf) and the vapor pressure of the atmosphere (e)

Sinclair et al. suggest that there are rather limited options for improving WUE(A,T,i)_L, which is mainly determined by the plant's photosynthetic pathway and the air temperature and humidity, which determine [e*(leaf) - e]; e*(leaf) will be higher when the temperature is higher. Plants can optimize WUE(A,T,i)_L in arid zones by exchanging gas only when [e*(leaf) - e] is low; i.e., close stomata at midday. This inevitably results in a tradeoff-- a reduction in CO₂ assimilation when stomata are closed.

Daily, Canopy WUE = WUE (B,T,d) = k_D/[e*(a) - e]

k_D = Constant which depends on photosynthetic pathway, chemical composition of the crop, and LAI;

[e*(a) - e] = mean daily atmospheric vapor pressure deficit.

One gram of photosynthate will yield (Gutschick, 1997 in Jackson):

• 0.7 g carbohydrate (with 0.3 g respiratory loss);
• 0.55 g protein (with 0.45 g respiratory loss);
• 0.4 g lipid (with 0.6 g respiratory loss).

That is plants producing protein or lipids produce less harvestable biomass per unit of glucose produced by photosynthesis, and thus have lower WUE (B,T,d).

Seasonal WUE is obtained by integrating daily values over the growing season; it does not introduce any new parameters: WUE (B, T, s) = integral{k_DT/[e*(a) - e]}/ integral(T)

Overall the opportunities for improving WUE are few:

• Biochemical - increase c for C3 plants; increases in c often associated with decreases in A
• Stomatal physiology - closing stomata when the vapor pressure deficit is high involves a tradeoff; would have to increase growing season subjecting plants to greater potential losses from pests and other stresses.
• Alteration of crop environment - grow crops when vapor pressure deficit is low.
• Improved harvest index.
• Increased proportion of transpired water.

Suggestions to "identify the genes responsible for drought-tolerance in desert plants" and transfer them using genetic-engineering techniques to crop plants ignore the tradeoffs inherent to water conservation and assimilation. When grown with ample supplies of soil water, desert plants (xerophytes) can have rather low WUE compared to mesophytes.

IV. NUTRIENTS

Nutrient Elements

Macronutrients, those required in rather high amounts by plants, are nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S). Most fertilizers contain N, P, and/or K.

Micronutrients are elements that are also essential for growth but are required in lower amounts; these include iron (Fe), copper (Cu), zinc (Zn), boron (Bo), molybdenum (Mo), manganese (Mn), cobalt (Co), and chlorine (Cl).

Nutrient Cycling

Plant nutrients occur in different pools which vary in their availability to plants: dissolved inorganic forms, absorbed inorganic forms, organic forms, and precipitated minerals.

Nutrient cycling refers to the processes that transfer nutrients to and from plants and the various soil (and atmospheric) pools.

These pools can be characterized as:

• active, inorganic forms and microbial biomass-very rapid turnover;
• slow, new crop residues and coarse particulate organic matter; and
• passive, fine particulate organic matter and humic substances-very slow turnover.

Nitrogen

A diagram of the nitrogen cycle shows the principle pools and processes. The key processes are:

1. Nitrogen fixation (250-350 M Mg y^-1 global total; ocean BNF is most uncertain):

• Industrial (ca. 90 M Mg y^-1)
• Atmospheric
• Biological (Only procaryotic organisms fix N) BNF requires 6.5 g C g^-1 N fixed (Shantharam & Mattoo, 1997)

Several kinds of microbes-all prokaryotes-are capable of fixing N:

• Free-living cyanobacteria (Anabaena, Nostoc) ca. 15 kg N ha^-1
• Symbiotic cyanobacteria (Anabaena azollae in Azolla; Nostoc in Gunnera) 7-80 kg N ha^-1
• Free-living aerobic bacteria (Azobacter, Azospirillium, Beijerinickia) ca. 36 kg N ha^-1
• Free-living anerobic bacteria (Clostridium, Bacillus, Klebsiella)
• Symbiotic actinomycetes (on Alnus, Casuarina) 2-362 kg N ha^-1
• Symbiotic bacteria [Rhizobium, Bradyrhizobium, Azorhizobium on legumes, Parasponia (Ulmaceae, Malaysia and western Pacific)] 24-584 kg N ha^-1. These are the most important associations for agriculture

Azospirillum also produces auxins and cytokinins stimulating root growth of seedlings, which may be as important as its BNF (Shantharam & Mattoo, 1997).

Environmental constraints on BNF: mineral N, pH, soil temperature, soil moisture, certain minerals (Al, Mn)

Nitrogen fixation is an energy intensive process; 940 kJ/mol required to break bound in N₂.

Estimate for BNF by legumes range from 10-35% of the energy captured by photosynthesis.

BNF rates (from Prasad and Power):

• Forage legumes 57-700 kg N ha^-1 y^-1
• Grain legumes 17-350 kg N ha^-1 y^-1
• Azolla-Anabaena 335-670 kg N ha^-1 y^-1 in lab; field estimates 30-40 kg N ha^-1 y^-1

2. Atmospheric deposition

Globally 40 M Mg/y; up to 40 kg N ha^-1 y^-1 in heavily polluted areas

Smil (1991) estimates average values of 6-10 kg N ha^-1 y^-1 on arable lands.

3. Uptake or Assimilation (of NO₃- or NH₄+)

NO₃- needs to be reduced to be incorporated into proteins; therefore plants in theory should perform best when N is available as NH₄+ rather than as NO₃-. Most experiments show highest yields when crops are grown with a mixture of NH₄+ and NO₃-

Uptake of N as NO₃- should balance uptake of cations.

4. Exudation

Roots exude organic compounds, including amino acids and other compounds containing N. These exudates influence other microbial nutrient cycling processes through their stimulation of microbial growth.

5. Residue Deposition or Litterfall

Nitrogen (and other nutrients) are returned to the soil in litter and residues from aboveground biomass. The C:N ratio of these materials and their lignin and polyphenol contents are important in determining their decomposition rates.

6. Immobilization and 7. Mineralization

These are perhaps the most important processes in the N cycle in controlling the availability of N to growing plants. Immobilization refers to the assimilation (uptake) of mineral N by soil microbes; mineralization refers to the release of mineral N by soil microbes.

When a consumer feeds on an organic substrate (bacteria or fungi consuming residues; protozoans eating bacteria; nematodes eating protozoans, etc.), the carbon is partitioned in 3 ways: (a) growth, (b) respiration (loss as CO2), and (c) indigestible materials. Assimilation efficiency (AE) can be defined as that portion of substrate carbon that goes into growth of the consumer. Values probably range from about 5%-30%; 10%-15% is probably most common for higher organisms.

Net mineralization will occur if the C:N ratio of the residue or substrate is smaller than the C:N ratio of the consumer divided by its AE:

Mineralization occurs if:

C:N (substrate) < [C:N (consumer)]/AE (consumer)]

Immobilization occurs if:

C:N (substrate) > [C:N (consumer)]/AE (consumer)]

In other words, if there is excess nitrogen in the substrate relative to the consumer's needs for growth, then some of that N can be mineralized or excreted.

Representative values for the C:N ratio are:

Bacteria: 4-10

Fungi: 10-20

Insects: 5-8

Plant residues:

• Legume green manure crops: 10-15
• Grass green manures: ~30
• Cereale residues: 40-80
• Wood: 400

Assimilation rates are imperfectly known. Assume that for bacteria and fungi the assimilation rate over the growing season is 0.30, and that C:N (bacteria) = 8 and C:N (fungi) = 15.

For cereal residues with C:N = 50:

bacteria: 50 > 8/.30 = 27; therefore N will be immobilized from the soil

fungi: 50 = 15/.30 = 50; therefore there should be no net mineralization or mobilization

For cereal green manures with C:N = 30:

bacteria: 30 > 8/.30 = 27; therefore some N will still be immobilized from the soil

fungi: 30 < 15/.30 = 50; therefore there should be net mineralization from the green manure

For legume green manures with C:N = 12:

bacteria: 12 < 8/.30 = 27; therefore N will be mineralized from the legume residues

fungi: 12 < 15/.30 = 50; therefore N will be mineralized from the legume residues

However, consider what is expected when protozoans (C:N approximately 6?) consume bacteria or fungi, assimilating perhaps 30 % of the bacterial and the fungal biomass:

Feeding on bacteria: C:N (bacteria) = 8 < 6/.30 = 20, therefore N will be mineralized

Feeding on fungi: C:N (fungi) = 15 < 6/.30 = 20, therefore N will be mineralized

Conclusion: Decomposition of most plant residues results in immobilization of N, at least over the short term. Predation within soil food webs results in mineralization of N.

Processes that contribute to mineralization include herbivory and predation in the soil, and other factors leading to the death soil microbes. Over the growing season mineralization exceeds immobilization, with average net mineralization rates of 15-25 kg N ha^-1 y^-1 (Smil, 1991).

8. Ammonium Fixation/Release from Clays

2:1 expanding silicate clays trap NH₄+ in the lattice Prasad and Power (1997) state that NH₄+ trapped in illite is "largely unavailable for plant uptake".

9. Nitrification

Nitrification is the conversion of ammonium to nitrate; it is a 2 step process:

• Ammonium to nitrite by Nitrosomonas: NH₄+ --> NO₂-
• Nitrite to nitrate by Nitrobacter: NO₂- --> NO₃-

NO produced during nitrification is volatile and can be released (Matson et al.,1998)

Nitrifying bacteria are present in all soils; generally rates of nitrification exceed rates of mineralization, preventing accumulation of NH₄+

Laboratory results show that nitrification is inhibited by low temperature-yet leaching of NO₃- during the winter can be high. Reasons for this apparent contradiction are not well known.

10. Erosion

Erosion can remove soluble forms of N, NH₄+ adsorbed onto clay particles, and N in SOM particles that are washed away. With a soil erosion rate of 15 Mg ha^-1 y^-1, N loses due to erosion would be 10-30 kg N ha^-1 y^-1.

11. Denitrification

Reduction of NO₃ to N₂ under anaerobic conditions: NO₃ -> NO₂ -> NO -> N₂0 -> N₂

Carried out by bacteria mostly in genera Pseudomonas and Bacillus; can amount to 3-62% of applied N; losses from arable lands may be 15 kg N ha^-1 y^-1 or more.

Fertilized agriculture accounts for 70% of anthropogenetic N₂0 emissions.

Irrigation produces temporarily waterlogged soils which can lead to high rates of N loss by denitrification:

"The interplay between the timing of fertilization and irrigation was critical to inorganic N transformation and gas losses in this site [wheat in Sonora].... High losses of N₂0 occurred soon after [preplant] irrigation, largely resulting from denitrification under waterlogged conditions. As the soils dried, NO emissions increased, produced during nitrification." (Matson et al., 1998)

"Plowing under a green manure crop can sometimes result in such a flush of microbial activity that soil O₂ supply is temporarily depleted to the extent that denitrification can occur" (Prasad and Power, 1997)

12. Volatilization

Loss of N as ammonia (NH₃); usually occurs in warm areas with more alkaline soils. Losses of fertilizer N up to 50% are possible; average losses from fertilized fields are approximately 15 kg N ha^-1 y^-1.

13. Leaching

Loss of N as nitrate (NO₃-) in water draining beneath the soil root zone. Leaching of nitrate can pollute ground water, and leads to losses of other nutrients (nitrates carrying along positively charged CA, Mg, and K cations).

Most leaching of N in temperate-zone agricultural soils occurs in the autumn; high leaching rates follow growing seasons with low crop yields (Vagstad et al., 1997)

Approximately 15 % of N fertilizer applied to maize is leached; percentages of residual soil N (mostly nitrate) leached are higher (Deng and Tabatabai, 2000).

Nitrogen use efficiency (NUE)

Ultimately the grower is interested in the amount of yield (Y) produced per unit of N supply--fertilizer N applied (F) and/or N fixed (BNF): NUE (G,s) = Y/(F + BNF)

What else can happen to N inputs? Fertilizer N can be lost by leaching, erosion, denitrification, or volatilization, or it can be stored in the soil as either organic N (as part of SOM) or as inorganic N. Ecological resource-use efficiency is largely a function of the proportion of N remaining in the root zone and available for uptake plants over (F + BNF). Thus ecological NUE is increased by decreasing loses of N via leaching, erosion, denitrification, and volatilization.

Phosphorus

Chemical-physical processes in the soil for P are much more important than for the N cycle.

P is highly immobile; most remains at the site of application.

Soluble inorganic P-orthophoshate ions (H₂PO₄- or HPO₄^2-)--are relatively insoluble, occurring in soils at very low concentrations (0.05 to 0.3 mg l^-1).

Losses of P from soils are relatively low, and occur mostly through erosion.

Soil scientists refer to "labile" and "occluded" P. Labile P is phosphate that is in relatively available forms-P in soil organisms, the coarse fraction of SOM, mineral P, and P adsorbed onto the surface of clay particles.

Occluded P is phosphate that is in relatively stable, unavailable forms, much of which forms complexes soil colloids.

Important processes include:

1. Assimilation

Plants assimilate orthophosphate ions, either through their roots or through mycorrhizal hyphae.

2. Mineralization/Immobilization

These have the same meaning as in the N cycle, depending on the C:P ratios of residues, SOM, and consuming organisms

3. Precipitation/dissolution

P precipitates as Ca-phosphate in alkaline soils and as Al- or Fe-phosphates in acid soils. Mineral phosphates complexed with hydroxide clays are highly stable ("occluded").

4. Adsorption/desorption

P bound to the surfaces of clay particles is known as "fixed" P. Fixed P is relatively "labile"

Cations

For the nutrient cations, the principal pools of cations, from most available to least available, are:

• Soluble cations
• Exchangeable cations
• Cations in SOM
• Secondary minerals
• Primary minerals

All cations are subject to leaching with nitrate (NO₃-) and sulfate (SO₄^-2).

URL: http://ag.arizona.edu/~spmcl/lecturenotes/resources.html