Some microbes also contribute to nutrient depletion in the rhizosphere, for example by converting usable forms of nitrogen, i.e. nitrate or ammonium, into unusable forms like N2.

Microbial activity also produces plant growth regulators such as auxin, cytokinins and gibberellins, sometimes in amounts sufficient to influence root morphogenesis. Ethylene can also be produced by rhizospheric fungi, potentially influencing root morphological changes such as lateral root initiation. Some bacteria have been found to promote plant growth by reducing ethylene levels around roots through production of an enzyme degrading an ethylene precursor, 1-aminocyclopropane-1-carboxylate (ACC) deaminase.

The rhizosphere community is highly structured and not a random collection of species – it is strongly influenced by plant species and even ecotypes, by the type of the soil, availability of nutrients and the exudation of chemicals from the root (Bakker et al 2013).

pH is another important rhizosphere property. Roots can acidify the rhizosphere by up to two pH units compared to the surrounding bulk soil through release of protons, bicarbonate, organic acids and CO2 (Figure 4.17).

The mucigel between the sloughed root cap and root border cells also acts as a lubricant for reducing penetration resistance of the expanding root tip in soil (McKenzie et al. 2012).

Mutants without root hairs would still have a rhizosphere of sorts since the root would still chemically influence its surrounding soil.

For wheat, at least, the size of the rhizosheath correlates with root hair length. Mutants without root hairs have no rhizosheath. The distinction between the terms rhizosheath and rhizosphere are that the first term refers to the soil that physically adheres, and the second term the volume of soil influenced by the root.

Because the time required (t) for diffusion of ions is a function of the square of distance traversed (l), where t = l2/D a nitrate ion would take four days to travel 2 cm, nine days to travel 3 cm and so on. Similarly, organic carbon diffuses away from roots only slowly, sustaining a microbial population as it is consumed in the rhizosphere.

These microbes are saprophytic, pathogenic or symbiotic bacteria and fungi, including rhizobia forming nodules and arbuscular mycorrhizal fungi (Figure 4.14).

Root hairs are particularly important in taking up mineral nutrients that are not readily soluble and therefore not mobile in the soil solution, like phosphate.

Because many soils are deficient in key nutrients, plants have developed a special relationship with certain fungi called mycorrhizae (Section 4.4). In this symbiosis the fungi obtain fixed carbon from the host plant, and in turn supply the host with poorly mobile nutrients, especially phosphorus.

Likewise when light is limiting, plants will invest more energy in leaf area and less in root development

oots of jarrah are also concentrated near the soil surface (Figure 4.10) to access phosphate and nutrients released by litter decomposition, but some roots penetrate very deeply to tap subsoil moisture.

Adventitious roots: any root that forms from anything other than another root. This includes roots that form on the base of stem cuttings, from leaf explants, from stems in flooded plants and also from nodes of cereal crops (often called crown roots).

Uneven surface enrichment arises from diverse sources such as dead fauna, urine patches

For examples, Marscher and Rengel (2012) show that nitrate by diffusion in a ‘typical’ soil travels 3 mm in a day, potassium about 1 mm in a day, and phosphate moves only about 0.1 mm in a day. This illustrates the importance of root hairs in intercepting and accessing phosphate.

By responding to signals and gradients in the soil, the root system can maximise growth in local nutrient patches while minimising growth in areas of deficiency. This is extremely important for plant survival particularly in deficient or marginal soils.

Salt stress causes dephosphorylation and internalization of PIPs, and drought stress induces ubiquitylation of PIPs, which are then degraded in the proteasome.

A second rationale for the presence of water channnels is to balance water flow and prevent bottlenecks. In the root, water channels are most abundent in the endodermis and inner stele where water flow across membranes is rapid. 

(1) ionic fluxes alter and at the same time are determined by voltage across the membrane; (2) in all solutions bounded by cell membranes, the number of negative charges is balanced by the number of positive charges.

Ions such as potassium and chloride (K+ and Cl–) are major osmotic solutes in plant cells. Deficiency of either of these two nutrients can increase a plant’s susceptibility to wilting.

There are other forces that may influence solute diffusion, including the voltage gradient when considering movement of charged molecules (ions) and the hydrostatic pressure when considering movement of highly concentrated molecules (such as water in solutions).

Ions transported into specialised cells cause hydrostatic (turgor) pressure to develop which is suddenly dissipated following mechanical stimulation

Rapid changes in turgor cause the swelling or shrinking of guard cells in leaves that controls the opening and closing of stomata.

This occurs because nutrient uptake is an active process, independent of water uptake from the soil, and continues during the night – the rate of nutrient uptake varies little over 24 h. When nutrients are pumped into the stele, water flows in by osmosis, and the pressure builds up. Positive pressures of 30-300 kPa can be achieved in this way.

Plants that have had shoots removed have very concentrated xylem fluid, which exudes from the cut stumps under positive hydrostatic pressure from the roots (‘root pressure’). Root pressure is also responsible for the droplets of water seen on the margins of guttating leaves early in the morning

Suberin is a hydrophobic polymer, deposited in the secondary cell wall in lamellae. It therefore seals off the plasma membrane from solutes, as water and ion channels are sealed. So the transcellular and apoplastic pathways are curtailed, and water and solutes enter the endodermis only through plasmodesmata from neighbouring cells

The endodermis also functions in structural support for the stele, particularly in drying soil, and minimises shrinkage or swelling of the cells of the stele. Its role in ion selectivity is minor compared to the cells of the cortex and epidermis.

For nutrients, this form of transport is facilitated by carriers that are distributed in a polar fashion, with influx carriers located on the outer walls and efflux carries on the inner walls. Water transport across cell membranes is via aquaporins for which there is no “rectification”, or intrinsic directionality of transport. They are therefore most likely to be distributed evenly along the plasma membrane.

morphological features determine how effective roots are at absorbing and transporting water and nutrients from the soil to the shoot.

They are often sodic, that is, sodium dominates the exchange complexes on soil particles, altering the soil structure so that it sets like concrete when dry, and becomes impermeable to water when wet. Moreover, subsoils can be acutely deficient in some nutrients that are required locally by roots.

In summary, the dense root systems common in topsoils extract water effectively from surface soil layers. Extracting water from subsoil layers is more difficult. Australian subsoils are typically inhospitable to roots. They are dense, have a large resistance to penetration.

It is notable that in the small pots (70 mm tall) often used for growing Arabidopsis, all of the medium is in danger of becoming hypoxic, for the porosity ranges from 0 to only 7%within the pot (Figure 3.40). With a frequent watering regime, say twice daily, the medium could be permanently hypoxic.

Soil at wilting point is not dry. Different soil types hold very different amounts of moisture at their wilting points. As plant remove water and the soil starts to dry, the small pores make it difficult for roots to extract all the water, so clay soils hang onto their water more strongly than sandy or loamy soils, and results in the plant available water being less for clay soils than for loamy soils which have a lower clay content

As the width of a vessel becomes smaller, the forward flow (a function of r4) is reduced much more strongly than the leaks (a function of r). The proportion of water lost to leakage therefore increases as vessels become smaller.

The mestome sheath of these large veins is impermeable to water. There is no apoplastic path for water through the mestome sheath of large veins, except through a connecting transverse vein.

If you look at a grass leaf with your hand lens, parallel veins run the length of the leaf, but they are not all the same size. A few large veins have several small veins lying between them. On closer inspection with a light microscope, all these parallel veins are connected at intervals by very small transverse veins

Most solutes in xylem sap are inorganic ions (e.g. nitrate, potassium, magnesium and calcium), but organic solutes are also present

Living/immature xylem vessels can be recognised by their high K+ concentrations, 100 mM or more.  In contrast, xylem sap that flows through the roots has  K+ concentrations of only 5-10 mM

Xylem conduits (vessels and tracheids) are dead at maturity. They do not mature until sometime after they are fully elongated, and so they remain alive long after they leave the growing zone of the root.

that can be appreciated by revisiting equation (6).

Xylem is not composed merely of pipes: it is made up of partially sealed units (technically vessels, tracheids and fibres, called collectively conduits), which most effectively limit the spread of introduced gases and thus, maintain water flow in some conduits despite very severe disruption from embolisms in others.

Cohesion (due to hydrogen bonding between molecules of water), adhesion to walls of the vessels, and surface tension, are central features. In short, in the absence of microscopic gas bubbles water could withstand quite enormous tensions.

Suction from the shoots was an alternative explanation, but manmade suction pumps cannot do this without inducing formation of air bubbles (embolisms) in the xylem and blocking flow.

If water transport required living cells, it could not be supported by discovery of a pump akin to that in animals. Even roots, which sometimes could pump water by root pressure, lacked the necessary positive pressures to push water so far aloft, especially around midday when water was most needed.

Instead, plants suck!

Plasmolysis is a laboratory phenomenon and does not occur in nature. It is an experimental artifact.

When a cell in an intact plant growing in soil loses water, turgor declines and solute concentrations increase. As explained before (3.1.1), at turgor loss point, when turgor becomes zero, the hydrostatic pressure in the cell sap is equal to the atmospheric pressure, meaning that no net force is exerted on the cell wall, and the plant is wilting.

The turgor pressure of a fully turgid cell may even exceed 1 MPa, about five times the pressure in a car tyre, and ten times the pressure in the atmosphere.

One of the challenging aspects of understanding plant water relations is the range of pressures from positive to negative that occur within different tissues and cells.

SAM plants evolved from their C3 progenitors on land,

The selective pressure for nocturnal storage of CO2 in malic acid by CAM in terrestrial plants may well be closure of stomata to conserve water loss in a dry atmosphere in daylight.

In CAM plants such as Agave and Opuntia, essentially all of the aboveground tissues are photosynthetic, and this partially compensates for lower rates of CO2 fixation on an area basis. With the noted exception of pineapple and Agave, few CAM species are domesticated, but others have been proposed as potential low-input biofuel crops on land not arable for C3 and C4 crops (Borland et al. 2011; Yang et al. 2015).

oung photosynthetic tissues of constitutive CAM plants are often C3 but CAM is always present at maturity, when the magnitude of the phases of CAM nevertheless remains responsive to stress, light and temperature.

In pineapple, for example, degradation of starch in the chloroplast may provide the substrate for PEPC despite the large diel turnover of soluble sugars. The complexity of this “conflict of interest” (Borland and Dodd 2002) in carbohydrate metabolism varies between CAM plants with different deacidification pathways.

The four phases of CAM metabolism are: Phase I - acidification in the dark (PEPC active and stomata open) Phase II - a transitional phase with  stomata open and both carboxylases active Phase III - deacidification (PEPC inhibited, Rubisco active and stomata closed) Phase IV - C3 photosynthesis (stomata open, Rubisco active and PEPC inhibited)

Such events would have generated a strong selection pressure for genetic variants with increased carboxylation efficiency and increased photosynthetic rates.

A decline in atmospheric CO2 concentration during past millennia has likely provided the initial impetus for the evolution of C4 photosynthesis. High temperature and low water availability may have constituted additional evolutionary pressures.

Representative light response curves for photosynthesis in C3 cf. C4 plants (Figure 2.7) can be used to demonstrate some of these inherent differences in photosynthetic attributes. At low temperature (10°C in Figure 2.7) a C3 leaf shows a steeper initial slope as well as a higher value for light-saturated photosynthesis. By implication, quantum yield is higher and photosynthetic capacity is greater under cool conditions. In terms of carbon gain and hence competitive ability, C3 plants will thus have an advantage over C4 plants at low temperature and especially under low light. By contrast, under warm conditions (35°C, upper curves in Figure 2.7) C4 photosynthesis in full sun greatly exceeds that of C3, while quantum yield (inferred from initial slopes) remains unaffected by temperature. Significantly, C3 plants show a reduction in quantum yield under warm conditions (compare 10°C and 35°C curves; right side of Figure 2.7). At 35°C C3 plants also show lower rates of light-saturated assimilation compared with C4 plants. Increased photorespiratory losses from C3 leaves at high temperature are responsible (Section 2.3). C4 plants will thus have a competitive advantage over C3 plants under warm conditions at both high and low irradiance.

From the previous section, the C4 pathway is obviously energetically more expensive than the C3 pathway in the absence of photorespiration. However, at higher temperatures the ratio of RuBP oxygenation to carboxylation is increased and the energy requirements of C3 photosynthesis can rise to more than five ATP and three NADPH per CO2 fixed in air (for these calculations see Hatch 1987).

Under ideal conditions, five ATP and two NADPH are required for every CO2 fixed in C4 photosynthesis (two ATP are required to run the CO2 pump, i.e., regenerate PEP).

Rubisco comprises more than 50% of leaf soluble protein in C3 plants.

in regenerating three molecules of RuBP, nine ATP and six NADPH are consumed

Photochemistry and electron transport activity always quench fluorescence to a major extent unless electron flow out of PSII is blocked. Such blockage can be achieved with the herbicide 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU) which binds specifically to the D1 protein of PSII and blocks electron flow to QB. DCMU is a very effective herbicide because it inhibits photosynthesis completely. As a consequence, signal rise to Fm

ATP synthesis in chloroplasts (photophosphorylation) proceeds according to a mechanism that is basically similar to that in mitochondria.

At saturating light, chloroplasts generate a proton gradient of approximately 3.5 pH units across their thylakoid membranes. Protons for this gradient are derived from the oxidation of water molecules occurring towards the inner surface of PSII and from transport of four electrons through the Cyt b/f complex, combined with cotranslocation of eight protons from the stroma into the thylakoid space for each pair of water molecules oxidised.

In PSI, absorption of quantum energy from a photon causes oxidation of P700, the PSI reaction centre equivalent of P680. In contrast to PSII, where electrons are drawn from a water-splitting apparatus, P700 accepts electrons from PC

These oxidation states are made possible by P680+ (a special form of Chl a with an absorption peak at 680 nm). P680+ is a powerful oxidant generated by absorption of energy from a photon. P680 is referred to as a ‘special pair’ because it is a pair of Chl a molecules. Electrons from P680 pass to pheophytin (Pheo in Figure 1.11) and on to a bound quinone molecule, QA.

In linear flow, water molecules are split in PSII, liberating O2 and providing a source of electrons.

Chl a of photosystem II reaction centres shows absorption peaks at 437 and 672 nm (compared with 429 and 659 nm for purified Chl a in ether; Figure 1.8, upper curves).

Chl a and Chl b. Both forms of chlorophyll are involved in light harvesting, whereas special forms of only Chl a are linked into energy-processing centres of photosystems.

Additional chlorophylls have been discovered that exist in cyanobacteria which extends their absorption spectrum into the infrared

The inner membrane of a chloroplast envelope is an effective barrier between stroma and cytoplasm, and houses transporters for phosphate and metabolites (Section 2.1.8) as well as some of the enzymes for lipid synthesis. By comparison, the outer membrane of the chloroplast envelope is less complex and more permeable to both ions and metabolites. 

This envelope encapsulates a soluble (gel-like) stroma which contains all the enzymes necessary for carbon fixation, many enzymes of nitrogen and sulphur metabolism and the chloroplast’s own genetic machinery. 

The biochemical pathway of CO2 fixation was discovered by feeding radioactively labelled CO2 in the light to algae and then extracting the cells and examining which compounds accumulated radioactivity.

Localised in the stroma of chloroplasts, this enzyme enables the primary catalytic step in photosynthetic carbon reduction (or PCR cycle) in all green plants and algae.

Any loss of catalytic effectiveness or reduction in amount translates to slower photosynthesis and reduced growth.

Shade leaves are larger and thinner, but have more chlorophyll per unit leaf dry weight than sun leaves. They can have a greater quantum yield per unit of carbon invested in leaves, but with a relatively greater allocation of nitrogen-based resources to photon capture, shade leaves achieve a lower maximum rate of assimilation.

While these features restrict water loss, they also impose an increased resistance (decreased conductance) to CO2 uptake. 

Consequently, leaves typically absorb about 85% of incident light between 400 and 700 nm; only about 10% is reflected and the remaining 5% is transmitted.

Consequently, plants adapt by developing an effective sunscreen in their cuticular and epidermal layers. 

known to impede movement of small insects, but also contributing to formation of a boundary layer.

The reason for using many frame-works derives from the way that our minds comprehend the complex world around us by dividing it into a hierarchy of conceptual layers, each one nested within the one above like Matruschka dolls (consider, for example: subatomic particles, atoms, molecules, grains, bricks, walls, buildings, cities). Each of these conceptual layers has its own terms, ideas and principles, and much of what we call ‘understanding’ involves translating the terms and ideas of one layer into those of the adjacent layers.

However, there is one species, Stylites andicola, that has taken an alternative route. This plant has no stomata. CO2 is taken up by its roots and is transported to leaves through continuous air passages in its roots and stems. This species grows in the Peruvian desert on an average annual rainfall of 30 mm with an interval between rains that often lasts for years. As might be expected, it grows very slowly, even when conditions are good

Only by articulating connections be-tween all the layers can we hope to have a comprehensive understanding of how plants work.

Plants are wet inside, and with rare exceptions will die if they do not remain so.