Notes From Botany, Photosynthesis

Greg Watson

Staff member
Jan 23, 2005
United States
Photosynthesis Quick Review
1. Light Reactions.

Light is used to make ATP and NADPH (reducing power), and O2 is evolved as a by-product.

Most of the photosynthetic pigments in a leaf, including Chl, form light-harvesting antennae. These capture photons (400-700 nm) and pass them to Reaction Center Chl in Photosystem II (PSII) and Photosystem I (PSI). The investment in antenna, relative to other components, is higher in shade than sun species (why?).

Complementary chromatic adaptation is a term found in earlier aquatic literature (especially red, green and brown algae and depth location) regarding the ability to vary the pigments in relation to the wavelengths filtered out by water. However there is scant evidence that it is a major factor in depth penetration. Shade species do tend to have a lower Chl a / Chl b ratio, but Chl a is always the major pigment in plants.

Photons “excite” Reaction Center Chl and cause it to eject an electron from an outer orbital. This is the photochemistry in photosynthesis. High energy electrons then enter an electron transport chain (redox reactions). Electrons are eventually used to reduce NADP+ to NADPH. During their progress down the electron transport chain they pump H+ into the chloroplast thylakoids and build up a proton gradient. This gradient powers the production of ATP by releasing the protons in a controlled fashion through the ATP synthase enzyme complex (much like water passing through generators in a dam).

The electrons lost from PS II are replaced by splitting water (H+, e-, and O). The O becomes molecular oxygen (O2) and is evolved.

2. “Dark” Reactions (in nature only occur in the light).

ATP and NADPH are used to reduce CO2 to sugar phosphates in the Calvin cycle (or Photosynthetic Carbon Reduction Cycle – PCR cycle). These sugar phosphates are the basic building blocks used to synthesize all the plant’s organic molecules (and for the organic material in all organisms). This cycle is found in all autotrophs (except for a few bacteria),.

A key enzyme in this process is rubisco (ribulose bisphosphate carboxylase-oxygenase). It is the first step in the PCR cycle and is the way by which inorganic enters the biosphere as organic carbon. It is a large, sluggish enzyme (turnover time of 2 s-1), and is the major protein in leaves (the most abundant protein in nature). It occurs in the stroma of the chloroplast and is a major limiting factor in terrestrial photosynthesis (part of mesophyll resistance). It catalyzes the reaction between ribulose bisphosphate (RuBP: a five-carbon sugar bisphosphate) and CO2 to give two molecules of 3-P-glyceric acid (PGA: a three-carbon acid). The PGA then goes on with ATP and NADPH to form sugar-phosphates in the PCR cycle.
RuBP + CO2 ----- 2 x PGA ------ photosynthesis (PCR Cycle).

However, because CO2 and O2 are similar rubisco’s active site has a hard time distinguishing between them, and so O2 can get into it and becomes a competitive inhibitor of rubisco with respect to CO2. So in the presence of atmospheric [O2] and {CO2] the enzyme (and photosynthesis) is inhibited by 30-40%.

In addition, rubisco catalyzes the reaction of O2 with RuBP to form one molecule of PGA and one of P-glycolate (a two-carbon acid). When this happens, no C is added to the organic-C pool of the plant, and even worse the P-glycolate is metabolized in the Photorespiratory Carbon Oxidation (PCO) Cycle and releases previously fixed CO2.

RuBP + O2 -------- PGA + P-glycolate ------- photorespiration (PCO Cycle).

Also, in the PCO cycle organic-N is released as ammonium and has to be refixed into organic-N – an energetically very expensive process (uses lots of ATP).

Plants that just use the PCR cycle, and thus also photorespire, are called C3 plants (C3 photosynthesis), because the first compound formed is PGA (a three-carbon acid). They constitute the majority of autotrophic species on the planet. High [O2], low [CO2], high temperature and irradiance enhance photorespiration, and thus reduce net photosynthesis. (Look at the figure in Van et al for water conditions during the day in a Hydrilla mat).

Some species have a way around the problem of photorespiration. They are called C4 species because the first compound formed is not PGA but a four-carbon acid (OAA: oxaloacetate which is rapidly turned to malate or aspartate). PEPC (phosphoenolpyruvate carboxylase) in the cytosol catalyzes the reaction of PEP with HCO3- to form OAA. Unlike rubisco, this enzyme is not inhibited by O2. OAA (malate) starts the C4 cycle which eventually releases CO2 in the vicinity of rubisco, and acts as a CO2 pump to increase the [CO2] around rubisco and thus outcompete the O2.

In terrestrial C4 species PEPC and rubisco are in separate cellular compartments (mesophyll and bundlesheath cells) to prevent futile cycling of CO2 and competition between the two carboxylases for the same CO2.

CAM species (Crassulacean Acid Metabolism) have similar biochemistry to C4 species, except PEPC operates at night when stomates are open and the malate is stored in the vacuole. During the day the malate is decarboxylated to release CO2 in the leaf (high internal concentration) with the stomates closed. Rubisco fixes it and the PCR cycle can operate in the light using ATP and NADPH. The enzyme activities are thus separated in time (night and day) as opposed to in space (mesophyll and bundlesheath).

How do submersed plants fit into these categories? Are there submersed C4 and CAM species?

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Required reading:
Bachman et al. 2002. Relations between trophic state indicators and plant biomass in Florida lakes. Hydrobiologia 470: 219-234

Background reading:
Bachman et al. 2000. The potential for wave disturbance in shallow Florida lakes. Lake and Reservoir Management 16: 281-291
Canfield et al. 1983. Trophic state classification of lakes with aquatic macrophytes. Canadian Journal of Fisheries and Aquatic Sciences 40: 1713-1718
Wetzel Limnology text
Philips et al. 1978. A mechanism to account for macrophyte decline in progressively eutrophicated freshwaters. Aquatic Botany 4: 103-126

Introduction to Ecology
Ecology defined: (Krebs 1972) “the scientific study of the interactions that determine the distribution and abundance of organisms.”

Key terms: Scientific study; interactions; distribution and abundance
Assumed familiar terms: Environment; Biome; Ecosystem; Community; Habitat; Niche; Species; Population; Biotype/ecotype

Interactions: with biota – mutualism; predation; disease/parasitism; allelopathy; competition
with abiotic environment – list of conditions and resources
Relationship between organism survival and growth and range of a condition – curve with optima and tolerances; ranges and optima for multiple conditions define the species’ niche in n dimensions.
Relationship between organism survival and growth and range of a resource – curve with plateau as another resource becomes limiting.

Overall ecosystem productivity
What are differences between low productivity and high productivity systems?
In aquatic systems in Florida what resources are likely to limit primary productivity (plant productivity)?
Trophic status classification of lakes: Oligotrophic, mesotrophic, eutrophic, and hypereutrophic
Measures in water of trophic status: Total P; Total N; Chlorophyll a; Transparency (Secchi depth)

Bachman et al. 2002 paper
What is the alternative stable states theory?
What are the objectives of this paper?
What is the assumed relationship between macrophyte biomass and trophic status?
What might be the assumed correlation between macrophyte and phytoplankton abundances?

Questions about terms, methods and assumptions? Polymictic?
How was plant abundance measured? What is meant by density? PVI? PAC?
How valid are their distinctions between macrophyte and algae dominated lakes?

Figure 1; what is being measured in water color?
Table 3; is there a difference between statistical significance and ecological significance?
Figure 4; what could account for areas where plants are absent in lakes? Are their assumptions about Potential PAC reasonable? Does this lead to the conclusion that it may only be possible to predict where plants cannot grow, not where they will grow?
Figure 5; significant differences in means but why is great overlap important?
How are periphyton and plankton relationships with variables different from macrophytes?

What evidence supports their conclusion that for a given level of Total P there was no obvious effect of macrophyte or algal dominance in the chlorophyll levels or Secchi disk depths?
What difference is there if Water column P (including all P in biomass as well as water) is used?
Figure 9B; what relationship might have been expected?

What relationship was found between macrophyte abundance and trophic state and how was this explained?
What environmental variables did influence plant biomass and number of plant species?
What explanation is given for the different relationship between periphyton abundance and trophic status?

What is the difference between the application of the alternative stable state theory to individual lakes and aggregations of macrophyte or algal dominated lakes?
The three assumptions for Scheffer’s alternative stable state theory are: turbidity increases with nutrient level; vegetation reduces turbidity; vegetation disappears when a critical turbidity is exceeded. Which of these assumptions are supported in this paper and how?

The mechanisms proposed by which macrophytes reduce TP are: reduced resuspension of P-bearing sediments; settling of phytoplankton due to reduced turbulence in plant beds; nutrient uptake by macrophytes or periphyton; change in fish populations with reduced benthivorous fish in macrophyte dominated lakes. They concluded that macrophytes are not producing substances that inhibit the phytoplankton in these lakes.

How were the authors looking the wrong way at the question of whether plant nutrients measure in lake water determined the abundance of macrophytes (as they do phytoplankton)?
How might the likelihood of an alternative stable state switch from macrophyte to algal domination be different in Florida compared to shallow lakes further north?

Trophic state classification of lakes with aquatic macrophytes
The Bachman et al. 2002 paper distinguishes between “water column P” (WCP) and “total P” in the water. This relates to the findings of Canfield et al. 1983 that significant amounts of P may be locked up in aquatic macrophytes and this may result in biases in trophic status classifications that are based only on water N, P, Chl a and transparency.
Why is it unlikely that WCP will be widely adopted for trophic status classification?
How might WCP be more useful than water P in predicting changes resulting from macrophyte removal?

Wave disturbance in shallow lakes
The influence of wind on a lake is affected by: wind speeds and their frequency; prevailing wind direction in relation to lake fetch; water depth; vegetation. Wind will influence: water currents; wave action and damage to vegetation; sediment disturbance and resuspension.
Many Florida lakes are shallow enough that wind will frequently resuspend the sediments and this will increase with large lake area and reduced water levels (examples?). Can this resuspension of sediments change the amount of nutrients in the water and hence the trophic status of a lake even if nutrient loading from outside does not change?

Could wind be a factor in some lakes switching from macrophyte to algal dominance or do macrophytes (floating, floating leaved and submersed) suppress the impact of wind?

Influence of increasing nutrient loading on the relative abundance of phytoplankton and macrophytes
Rather than looking at many lakes at once or at a single lake switching from macrophytes to phytoplankton dominance within a trophic status, what are the effects on macrophytes of increased nutrient loading?

Accepted relationship: at low water nutrient concentrations, rooted macrophytes will dominate because they can obtain nutrients from the sediment as well as water. As water nutrients increase, phytoplankton increases until they significantly reduce light penetration and shade out macrophytes. As macrophytes start to disappear, wind action is more likely to stir up sediments reducing light and resuspending nutrients in the water.

Alternative hypothesis by Philips et al. 1978: in some circumstances, the increase in phytoplankton is the result of macrophyte decline not the cause.

Norfolk Broads – shallow lakes and canals in SE Britain from peat excavation where recent declines in macrophytes not just due to boat traffic (> turbidity) but also nutrient loading. Using several different approaches:
1. Paleolimnological data of diatoms in sediment cores in lakes with different enrichment histories. Increase in epiphytic species only in low-nutrient lakes, and before phytoplankton in enriched lakes.
2. Najas marina was grown in sediment-sealed pots with low-nutrient lake water and the water in some pots was enriched. Non-enriched Najas had twice the biomass of the enriched plants after 5 weeks, with epiphytes and then filamentous algae in enriched pots not phytoplankton. Statistics? Suspended Chl a explained sufficiently?
3. Measured epiphytes on Myriophyllum spicatum in sites with range of fertilities. More epiphytes on plants in enriched system. Was it appropriate to only measured sediment P? Why were there still macrophytes in the enriched system?
4. Light data collected in a lake where macrophytes have disappeared. Light passing through water column should have been sufficient at the bottom for macrophyte growth. But epiphytes attached to Perspex slides shown to reduce light on macrophyte surface by 2 – 5 times. Light at sediments insufficient if macrophytes are covered in epiphytes.
5. Filamentous algae suppressed growth and PHS of macrophytes in field. Ceratophyllum demersum was placed in mesh bags both in the lake where it was collected and an enriched lake. In the enriched lake there was plant loss and growth suppression due to a smothering of filamentous algae. No site difference at a time of year when filamentous algae were rare. Najas incubated with 14C in the enriched lake both under the filamentous algal mat and outside mat, showed 33% less 14C uptake under mat (but no data presented). What about the recolonization of Najas in this lake the following year?

Evidence that epiphytes may cause macrophyte suppression BUT:
Why not more phytoplankton initially as lake starts to become enriched?
How does reduction in macrophytes result in increase in phytoplankton?

In calcareous systems, nutrients may initially be precipitated out so water nutrient concentrations remain low even as loading initially increases but what about low calcium waters?
Is there “active” suppression of phytoplankton by nutrient chelators or anti-metabolites “secreted” by macrophytes? At that time, organic matter secretion had been investigated by Wetzel in lab but not shown in field. Subsequent evidence that water from macrophyte dominated lakes inhibits algal growth and this effect is lost if water is heated.
Assumes epiphytes are not affected by these “secretions”. As epiphytes grow and reduce light to macrophytes, there is a positive feed-back of less suppressor production which allows phytoplankton to grow. Last macrophytes remaining are canopy forming (M. spicatum) or floating-leaved with rhizomes. But now submersed plants missing, recreational boat use of these lakes increases and causes mechanical damage to lilies.

Quality of research?
Was the hypothesis fully supported?
Why are we looking at this study?

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Adaptations That Make Hydrilla Competitive

Major factor that makes Hydrilla a weed

Placement of its canopy at the water surface where it interferes with human activity. Benthic species are far less likely to be “weedy”, unless they block a shallow stream or irrigation waterway.

Opportunistic and invasive. Easily dispersed by humans, animals (birds) and flowing water.

1. Reproduction.

Axillary turions. Possible produced under “stress” conditions.
Subterranean turions produced in the fall (short photoperiod) – transport of carbohydrate into the rhizomes to produce an overwintering organ.
Fragmentation. Shoot pieces can form roots and shoots from nodes. Need only 2-3 node piece in order to reproduce this way. (Spencer & Bowes 1985).

Without sexual reproduction long-term competitive advantage is reduced (though does appear to have genetic diversity in asexual reproducing populations).

2. Morphology.

Placement of canopy at the water surface. Major amount of biomass in top 0.3 m of water column.

Several factors associated with this morphology.

Tuber starch reserves allow shoot to elongate and reach an irradiance in the water column that allows net photosynthesis (i.e. above the light compensation point).

Light Compensation Point acclimates – reduced when the plant is growing at low irradiance (Bowes et al 1977). Lower in shoots from germinating tubers.

Shade avoidance strategy (phytochrome R/FR response). FR more attenuated in water than R. Thus higher R/FR ratio (near sediment) causes main stem to elongate. Lower R/FR (at surface) causes branching rather than main stem elongation. Stems connecting canopy to roots contain few leaves – less tissue to be “parasitic” on the photosynthetic material in the canopy.

Canopy structure (spread out just below water surface) shades competing species – reduces their growth, especially benthic species.
Also in “mat” Hydrilla causes an unfavorable environment during the day (Van et al 1976): high [O2], temperature, pH, low [CO2] and [HCO3-]. Hydrilla can cope with this “hostile” environment by changing in its biochemistry to C4 photosynthesis (Reiskind et al 1997).

Hydrilla has a thin leaf (two cells thick) that reduces diffusion limitations, and no Kranz (bundlesheath) anatomy – unlike terrestrial C4 plants (Reiskind et al 1989).

Hydrilla is a rooted monocot. This means it can extract nutrients from both the sediment and the water column. Thus it can grow in waters that do not have excessive nutrients.

3. Physiology.

Low light LCP – lower than in some other species including Ceratophyllum, Myriophyllum, Cabomba (Van et al 1976). More effective at net carbon assimilation in low irradiance in morning and evening than competitors.

Leaf pH polarity gives plant access to HCO3- on the abaxial side of the leaf when [DIC] are low - pH 10 on adaxial side, pH 4 on abaxial side. When [DIC] is high HCO3- use is inhibited, which saves energy of H+ pumping (van Ginkel et al 2001).

Wide pH range for growth- pH 5, 7, 9 but best at 9 (Bowes and Salvucci 1989).

Ability to tolerate high temperatures – e.g. 40 C (Van et al 1976).

Ability to tolerate photoinhibitory conditions (White et al 1996). Presence of 2 mm HCO3- protected (increased LSP and photosynthesis rate) against full sun irradiance despite fact that plant is a “shade” species with leaves that saturate at less than one-third full sun (600 micromol photon m-2 s-1). Three-fold increase in SOD activity within 15 min at high irradiance (scavenges .O2- radicals produced under high light and O2). Also, exhibits self-shading by chloroplasts (“solarization” – silver grey leaf).

Ability to fix DIC at night through PEPC, build up a malate pool (somewhat like CAM plants), and reduce loss of respiratory CO2. Enables them to retain some of the fixed carbon and not lose it to competing species in carbon-limiting environments.

4. Biochemistry.

Under low [CO2] conditions in the environment the plant shifts from C3 to C4 photosynthesis, but without any change in anatomy (Reiskind et al 1997). In C3 state, with abundant DIC, fixed carbon is lost via photorespiration and photosynthesis is inhibited by O2, especially at high temperatures. Shift to C4 enables the leaf to concentrate CO2 in the chloroplasts, where rubisco is located, and the high concentration suppresses adverse O2 effects on rubisco. All the C4 cycle enzymes are induced within a few days at low [CO2] and a CCM is put in place. Specific isoforms of C4 cycle enzymes (e.g. PEPC) are induced, which have particular kinetic characteristics that allow the plant to fix carbon through PEPC during the day, and initiate the C4 cycle (Rao et al 2002).

The C4 system allows the plant to withstand the adverse environment in the mat it created, and which appear to limit the growth of competing angiosperms. Only filamentous algae later in the season appear to be able to survive the adverse conditions created by Hydrilla in the mat. Hydrilla mat has C3 shoots at the edge, where CO2 is quite high, but C4 shoots in the center, where [CO2] are negligible after noon on a sunny day - used up by photosynthesis in the morning (Spencer et al 1994).

5. References.

Bowes G, Van TK, Garrard LA, Haller WT. 1977. Adaptation to low light levels by Hydrilla. Journal of Aquatic Plant Management, 15:32-35
Bowes G, Salvucci ME. 1989. Plasticity in the photosynthetic carbon metabo-lism of sub-mersed aquatic macrophytes. Aquatic Botany, 34:232-266
Bowes G, Rao SK, Estavillo GM, Reiskind JB. 2002. C4 mechanisms in aquatic angiosperms: comparisons with terrestrial C4 systems. Functional Plant Biology 29: 379-392 (Invited, refereed review).
Reiskind JB, Berg RH, Salvucci ME, Bowes G. 1989. Immunogold localization of ribulose bisphosphate carboxylase-oxygenase and phosphoenolpyruvate carboxyl-ase in aquatic and C3-C4 intermediate plants. Plant Science, 61:43-52
Reiskind JB, Madsen TV, van Ginkel LC, Bowes G. 1997. Evidence that inducible C4-type photosynthesis is a chloroplastic CO2 concentrating mechanism in Hydrilla, a submersed monocot. Plant, Cell and Environment, 20:211-220
Rao SK, Magnin NC, Reiskind JB, Bowes G. 2002. Photosynthetic and other phosphoenolpyruvate carboxylase isoforms in the single-cell, facultative C4 system of Hydrilla verticillata. Plant Physiology, 130: 876-886.
Spencer WE, Bowes G. 1985. Limnophila and Hygrophila: A review and physio-logical assess-ment of their weed potential in Florida. Journal of Aquatic Plant Manage-ment, 23:7-16
Spencer WE, Bowes G. 1990. Ecophysiology of the world's most troublesome aquatic weeds. In: Pieterse AH, Murphy KJ (eds) Aquatic Weeds. Oxford Univ Press, Oxford, UK, pp 39-73
Spencer WE, Teeri J, Wetzel RG. 1994. Acclimation of photosynthetic phenotype to environmental heterogeneity, Ecology, 75: 301-314
Van TK, Haller WT, Bowes G. 1976. Comparison of the photosynthetic charac-teris-tics of three submersed aquatic plants. Plant Physiology, 58:761-768
White A, Reiskind JB, Bowes G. 1996. Dissolved inorganic carbon influences the photosyn-thetic responses of Hydrilla to photoinhibitory conditions. Aquatic Botany, 53:3-13
van Ginkel LC, Bowes G, Reiskind JB, Prins HBA. 2001. A CO2 flux mechanism operating via pH polarity in Hydrilla verticillata plants with C3 and C4-type photosynthesis. Photosynthesis Research 68: 81-88.

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Responses to Flooding
Three major categories of plants in their responses to flooding

1. Flood-sensitive (e.g. soybean, tomato, pea). Severely damaged by 24-h anoxia.
2. Flood-tolerant (e.g. Arabidopsis, potato, wheat, corn, oat). Withstand few days anoxia.
3. Wetland (rice, wild rice, cattail, barnyard grass etc). Resist anoxia for months to years.

Wetland or tolerant species show morphological, anatomical, physiological and biochemical adaptations and acclimations that enable them to circumvent problems associated with flooding.

Problem is Oxygen

Problem is not excess water but an O2 deficit. Well-drained porous soil has [O2] close to air equilibrium (20.6%) in the gas spaces between soil particles. But when water displaces the gas spaces the underground parts are subjected to 10,000-fold slower O2 diffusion. This potentially decreases gas exchange in below-ground structures (roots, rhizomes etc), and can affect respiration.

Normoxia (aerobic): ATP production from oxidative phosphorylation (O2 is the terminal electron acceptor from cytochome oxidase).

Hypoxia (low O2: Total ATP production decreased. Oxidative phosphorylation reduced, and ATP from glycolysis (fermentation) becomes more important.

Anoxic (anaerobic): ATP produced only from glycolysis, therefore low production rate. Protein synthesis decreases, cell division and elongation slowed, cells may die.

Glycolytic pathway and fermentation produces only about 2 ATP per glucose consumed. Aerobic respiration (including oxidative phosphorylation) produces 38 ATP per glucose. Critical Oxygen Pressure (COP) is the O2 pressure at which respiration rate in a tissue or organ is beginning to be slowed (limited) by O2. In older roots where respiration is low maybe only 2-3% O2 is required, but in a bulky tissue much more is needed (slow diffusion through the tissue). Km(O2) for cytochrome oxidase (terminal oxidase) in oxidative phosphorylation is only around 1 micromolar O2 (less than 1/200th of O2 in air), but the O2 must diffuse through bulky tissues so much more needed to set up an adequate gradient.

All active tissues need some O2

Probably no plant with active metabolism can survive anoxia in the tissues for very long. Wetland and tolerant species may have adaptations to cope with short-term glycolysis and fermentation but in order for long-term survival in an anoxic environment they must find a way to get O2 to the tissues.

Potential problems in O2-deficit conditions

Lack of ATP for metabolism. Can lead to shortage of nutrients in developing shoot (lack of ATP means cannot actively transport nutrients into root).

Acidosis. Roots turn glucose to pyruvate and then ferment it to lactic acid. This lowers cytosolic pH – cytosolic acidosis becomes a problem and leads to cell death (vacuole contents also leak out). Timing and degree of acidosis is primary difference between flood sensitive and flood tolerant species.

Ethanol production. In some plants (maize) lactic acid build-up causes roots to switch to ethanol production from pyruvate (ethanolic fermentation), but eventually build up of ethanol is harmful. Some species show rapid increase in alcohol dehdrogenase to handle the ethanol – at least temporarily.

Ethylene production is accelerated by hypoxia.

In some species ABA production is stimulated – leads to stomatal closure (no transpiration).

Ways around the problem

Essentially the way around the problem in wetland species is to aerate the roots/rhizomes. This involves morphological and anatomical adaptations, not just biochemical. Give some examples of how this may be achieved.

1. Some parts of plants can tolerate anoxia for extended periods by becoming metabolically far less active so that they can survive on the little ATP from glycolysis and fermentation. These include rice embryo and coleoptile, bulrush and cattail rhizomes (e.g. in mud in winter). They can also for a short period expand leaves and shoots while in anaerobic conditions. Likewise some seeds can remain dormant underwater and anoxic. Can germinate but require some O2 for subsequent development.
2. Development of aerenchyma or lacunae. Gas-filled spaces in stems, roots, rhizomes that allow O2 to diffuse in the gas phase (much more quickly than in the aqueous phase). Can also occur to limited extent in flood-tolerant species like maize. Hypoxia stimulates activity of ACC synthase and ACC oxidase (ACC is a precursor of ethylene) which increases ethylene. Ethylene leads to “Programmed Cell Death” i.e. death and lysis of selected cells in the root or rhizome cortex to give gas-filled voids (aerenchyma) instead of water-filled cells. This can result in continuous gas pathways from stem to rhizome to roots through which air diffuses. The continuous formation of aerenchyma just behind the root tip provides a pathway for O2 for growth (mitosis and elongation).
3. In rice and other species, ethylene also leads to elongation of the shoot, which breaks the water surface and thus acts as a “snorkel” for O2 to diffuse down to the roots. Submerged Nymphoides peltoides (water lily) traps ethylene which causes rapid elongation of petiole to the water surface where leaf expands. Pondweed, however, is insensitive to ethylene. It is acidification that stimulates elongation. Some wetland species. also form a suberized layer to reduce O2 loss to the soil. However, in some species the sediment layer around the roots becomes oxidized due to the presence of O2 leaking out.
4. In Nuphar and Typha can actually measure internal winds (convection driven pressure gradients). Enter in leaf and exit through broken stem after passing through the rhizome.
5. In Mikania we have documented that stem rapidly develops stomata close to water surface when it becomes flooded. Also see substantial increase in aerenchyma in stem and root. Some species form lenticels on the stems.
6. Anoxia causes expression of anaerobic stress proteins (e.g. ADH). Ethanolic fermentation and transport (excretion) of lactate out of cell to reduce acidosis. Also capacity to synthesize sucrose may rise - need more carbohydrate to support ATP production by glycolysis as it is far less efficient than aerobic respiration.
7. Some species (mangroves) produces pneumatophores (negative geotropism of root) that are presumed to aerate the roots.

Think about it…

Is anoxia a problem for submersed leaves? How do they cope if they in an aquatic environment that lacks O2?

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Nutrients and Aquatic Plants
Where Does Most of the Dry Weight of a Plant Come From?

van Helmont (17th Century) – willow seedling in pot with 90.9 kg soil. Only watered. After 5 years grew into tree weighing 76.8 kg, but soil only lost 0.06 kg. Said weight came from water not soil as previously thought. Stephen Hales (18th Century) showed air provided weight. Organic materials (mainly C,H,O) make up 95% of plant’s dry weight. Inorganic 5%. After C,H,O next largest component is N.

Macronutrients Micronutrients

Carbon as CO2 or HCO3- Chlorine as Cl-
Oxygen as O2 Iron as Fe3+ or Fe2+
Hydrogen as H2O or H+ Boron as H2BO3-
Nitrogen as NO3- or NH4+ Manganese as Mn2+
Sulfur as SO42- Zinc as Zn2+
Phosphorus as H2PO4- or H2PO42- Copper as Cu+ or Cu2+
Potassium as K+ Molybdenum as MoO42-
Calcium as Ca2+ Nickel as Ni2+
Magnesium as Mg2+ (Silicon and Sodium)

Positive ions bind to negatively charged clay particles but can be exchanged with H+ (secreted by plant roots) – Cation Exchange. Negative ions are not so tightly bound by soil. The pH affects availability of minerals. Alkaline makes Ca available but not Fe. Acidic favors binding of P to clay. Ions can influence that availability of each other e.g. Fe and major cations like Ca can precipitate P and reduce its availability. Much P is bound up in organic-P. Oxidized rhizosphere also limits P availability (P more soluble under reducing conditions).

Where do Aquatic Plants Get Their Mineral Nutrients From?

Depends on growth habit.

1. Emergent Rooted: sediment (roots) via active transport of ions and mass flow in the transpiration stream.
2. Emergent Floating: water column only (roots) aided by transpiration.
3. Submersed Rooted: sediment (roots) via active transport and diffusion (no transpiration stream). Also water column (shoots).
4. Submersed Floating: water column only (shoots).

Sediment Versus Water Column as a Nutrient Source for Submersed Rooted Plants.
(Barko et al. 1991. Aquat Bot 41:41-65; Carignan. 1982. Can J Fish Aquat Sci 39:243-247).

Sediment is generally the primary source of N, P, Fe, Mn, and micronutrients
Water column is generally the primary source of Ca, Mg, Na, K, S, Cl


Model by Carignan – Sediment P would be over 50% of plant’s uptake if Dissolved Reactive Phosphorus (DRP is essentially available inorganic-P) ratio in sediment interstitial water to that in water column was >4.

Surface water [P] can vary widely but usually not over 10 ?g L-1. At 20 submersed macrophytes may be outcompeted because of excessive algal growth. Consequently, as little as 40 ?g L-1 in the sediment water should give >50% uptake from the sediment. Large variation in sediment [P] from 40 to 9,000 ?g L-1 so can approach 100% from sediment. As rooted submersed take it from sediment they can be a factor in moving P from sediment to water column, which can influence algal growth (important part of P-cycle by seasonal senescence of macrophytes). These effects most pronounced in shallow lakes with large stands of rooted macrophytes (thus fertile lakes). Less importance and slower recycling in oligotrophic systems with low biomass turnover. Coupled with more macrophyte-driven sediment oxidation (see later) which ties up P.

In many cases it is not [P] that limits growth of rooted submersed macrophytes. In several studies adding or depleting [P] had no effect on plant growth. This is not necessarily true for algae. So in same body of water man have algae limited by [P] but plants not limited by [P].

Are exceptions of course where [P] did appear to be a limiting factor. Littorella growth in an oligotrophic sand bottom lake was enhanced by P addition.

Interesting study by Rattray et al (1991, Aquat Bot 40:225-237). Lagarosiphon major and Myriohyllum triphyllum were planted in situ in either oligo or eutrophic sediments in an oligotrophic or eutrophic New Zealand lake. Growth of both plants was 2-fold greater in the oligotrophic lake on the eutrophic sediment, and tissue P was 2-fold more (sediment provided the P which in the natural lake was limiting). In contrast in the eutrophic lake sediment made no difference to growth (plants got enough from the water).


Fewer N studies than with P (because of algal influences). As with P, large amounts of N in water (50%) may exist bound in organic (DON). 15N study showed uptake in submersed macros was proportional to [N] in sediment or water column. But they tended to prefer NH4+ to NO3- (unlike many terrestrial species). As NH4+ in sediment tends to be much higher than in water the predominant source for N is the sediment. Not always true e.g. Potomac River can have NH4+ > 100 ?g L-1 in macrophyte beds. Unlike P, fertilizing with N often increases growth, thus [N] below 140 ?g L-1 in sediment may limit growth. N pools in sediment are more easily depleted than P pools (less exchangeable N than P) if substantial macrophyte growth.

Littoral zone can have a marked effect on N dynamics. Because run-off from agriculture is mainly NO3- the littoral zone around a waterbody can trap N, but only to a limited extent. Eventually decomposition can place the N into the water/sediment. Sedimentation (trapping soluble and insoluble materials) in the littoral zone is an important buffer effect.

Microbial and Fungal Associations

Rhizosphere of Myriophyllum heterophyllum shown to have very large microbial associations: ammonification bacteria, denitrifying, N2 fixation, acid production (liberates metals and P from minerals). Also macrophytes (but not all) have been shown to have mycorrhizal fungal association with roots that would greatly enhance access to N and P, as well as other sediment nutrient (enhances surface area for active uptake).

Sediment Characteristic Effects

Which would allow for better uptake of nutrients – organic or sandy sediment? Barko and Smart (1986, Ecology 67:1328-1340) showed that growth of Hydrilla and Myriophyllum declined almost linearly with increasing organic matter up to 20% in the sediment. This is a function of bulk density and volume. Sand (high) and organic matter (low) have opposite effects on bulk density. Nutrient uptake on low-density organic sediments can be hindered by long distances over which they must diffuse (low [nutrient] per unit volume), and also by chelation with the organic matter, and phytotoxic compounds. On other hand if too sandy (high bulk density) then also get reduced growth because of low [nutrient] in most sands. Best growth on densities of 0.8 to 1.0 kg L-1. Get bell shaped curve if plot growth against density of sediment.

Morphological Acclimation

Root to shoot ratio. As [N] and [P] in sediment declines so R:S biomass ratio increases, and can reach 1.0 in infertile sediments. Thus root growth in Myriophyllum increased linearly with decreasing [N] and [P] in the root zone (Mantai and Newton 1982. Aquat Bot 13:45-55). Why? However, in fertile conditions plants tend to maximize shoot production. The trade-off involves light and carbon acquisition (photosynthesis) versus N and P acquisition.

In general, emergent and floating leaf species have much greater R:S ratios than submersed rooted macrophytes and thus tend to be less affected by unfavorable sediment properties.

Oxidation of Sediments

Submersed macrophytes can alter the oxidation state of the sediment in proximity to the root. This will cause chemical precipitation and can reduced soluble [P] near the root. However, to do this they must have lacunal or aerenchyma that extend into the root. Thus not all submersed macrophytes show this ability. Also, it appears to be mainly seen in oligotrophic sediments, not eutrophic (maybe because of high rates of reductant generation in fertile sediments).

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Productivity of Wetland Plants
What factors influence productivity?

Irradiance, [CO2], nutrients (N and P), architecture (plant and canopy), biochemistry and physiology (e.g. C3 and C4), water status, temperature, growing season, stresses, herbivores and disease.

Submersed versus Emergent Macrophytes.

Water. Usually not limiting, so emergents can keep stomata open all day. Less a factor for submersed (except seasonal pools or lake drawdowns). Can limit emergents in regions where have dry and wet seasons.

DIC. Compare the A/Ci response curves of submersed and emergent. C3 and C4.
Requires around 300 micromolar CO2 (20 mM HCO3-) to saturate submersed macrophyte (Van et al 1976). Far more than in equilibrium with air (10 micromolar). Emergent C3 plant not saturated at air-levels of CO2, 375 ppm or about 10 micromolar, in some cases needs up to 1,000 ppm (30 micromolar). In contrast, emergent C4 is saturated at below atmospheric levels (250 ppm). In dense vegetation [CO2] in water can fall to low day-time values, rarely occurs in terrestrial situation (though can have some draw-down in canopy).

Irradiance. Compare the A/I response curves of submersed and emergent. Submersed saturate around one-third full sun or less (300-600 micromol photons m-2s-1), and are shade species. Emergent vary from 1,000 to full sun (2,000). Potentially more light attenuation for submersed (at very least reflection from water surface).

Nutrients. Submersed can take up nutrients from shoots and roots (emergent restricted to roots), but in many situations the sediment is the major source for N and P for submersed rooted, so little difference from emergent. Emergents have substantial transpiration stream to facilitate transport of nutrients from root to shoot.

Architecture. Plant LAI varies from 1 to >5. In canopy can have 90-98% interception of light. Emergent (if sun plant) probably less subject to photoinhibition in top of canopy leaves.

Temperature. Better buffered in water – but if water temperatures do get high then slower to drop at night (may exacerbate respiration). Likewise, much reduced sensible heat loss (conduction and convection) and no evaporative heat loss in submersed plants – exacerbates photorespiration.

Herbivores and Disease. Probably submersed have an advantage here.

Some Productivity Comparisons.

Raven (1984) text: might expect 38 kg C m-2 (760 tonnes organic dry weight ha-1).
No reported values approach this.

Westlake (1975) review. Submersed have Biomass values of 0.4-0.6 kg organic weight m-2. Cites Myriophyllum spicatum and Chara. Values for Typha 4-10 kg m-2 (10- to 20-fold higher).

Hydrilla 10 tonnes ha-1y-1. Compare with reported waterhyacinth’s 200 (not natural system - may be overly high, but still does not approach Raven’s maximum value). Usual for waterhyacinth (C3) is in 15-40 range.

The net primary production of Spartina marshes in Europe and Georgia can 30-40 tonnes dry matter ha-1y-1 despite the fact that in a temperate climate. Spartina species all appear to have the C4 photosynthetic pathway. Typha (C3) in Minnesota 25.

Among the highest productivity plant is the C4 grass Echlinochloa polystachya growing on the central Amazon floodplain. Exposed to dry and wet (flooded) seasons. Shows annual net primary production of around 100 Mg ha-1 (Piedade, Junk and Long 1991 Ecology 72:1456-1463). Has an energy conversion efficiency close to what is considered maximum for C4 species. 90-98% of light is intercepted in the canopy. Invests most of its high productivity in stem and high growth rate in wet season is just enough to keep pace with the 8 m rise in water level as part of the annual cycle in river discharge. Suggested that this is rationale for C4 in this aquatic system.

What is rationale for Panicum repens and Cyperus papyrus to be C4 when can find C3 emergent grasses growing in the same habitat? Not water use efficiency. Unresolved question.

Summary: emergent species in natural wetlands can be as productive as the best agricultural situations (e.g. rice and Typha can have similar net primary production – not comparing grain yield).

Keys to high productivity: Continuous water supply, C4, air-CO2, eutrophic sediments (N and P not limiting), and the ability to aerate the roots and rhizomes.

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Overview of The Aquatic Environment and a Physiological Perspective
Wetzel: “Limnology” text
Crawford: “Plant Life in Aquatic and Amphibious Habitats” Blackwell Scientific
Raven: “Energetics and Transport in Aquatic Plants” Alan R Liss Inc N.Y.
Kirk: “Light and Photosynthesis in Aquatic Ecosystems” Cambridge Univ Press.
Sand-Jensen: Aquatic Botany 34: 5-25. Environmental variables and their effect on the photosynthesis of aquatic plants.

Overgeneralizations, Misconceptions and Terms
Concept: aquatic habitats more similar than terrestrial (diverse - deserts to tropical rainforests); accounts for ubiquitous nature of some species. But, erroneous assumption is aquatic plants all subject to same environment, with major difference marine and freshwater.

Not so. Great heterogeneity, partly because of the varied nature of aquatic plant habits. Emergent, amphibious, submersed, floating (on or under) or rooted. Tendency to think too generally in terms of aquatic vs terrestrial habit e.g. aquatic plants exposed to less light than terrestrial- what's wrong with that generalization? Need define habit of aquatic plant: emersed, submersed, surface, benthic, rooted, in order to describe habitat.

Terms. Submersed (adj); Submerged (adj); Emersed (adj); Emergent adj (not emerged vi); Amphibious; Microphytes and Macrophytes -gradation e.g. Chara and Nitella and even the cyanobacterium Lyngbya (filamentous large-celled, almost a macrophyte). A microphyte may be in same water as macrophyte but its microenvironment may differ greatly. Conditions limiting macrophytes may not limit microphytes. Also rooted vs floating, submersed vs emersed.

If list advantages and disadvantages of existence in an aquatic versus a terrestrial habitat, come out with far more advantages to submersed. So why are most higher plant species terrestrial? If aquatic habitat that great, why the massive migration of species to land?

Aquatic environment is more homogeneous and benign than terrestrial in water availability, temp buffer, nutrient bathing. But, some very heterogenous and limiting aspects to aquatic environment. Can be more extreme to a plant than a terrestrial habitat. In this course identify adaptations that enable plants deal with aquatic disadvantages.

Dense, polar solvent. Dense, thus dissolved gases diffuse 104 slower in water than air. Diffusion resistance a major factor for physiology of submersed plants, many adaptations to ameliorate effects of this one factor.
Substantial boundary (unstirred) water layer 50-500 micro meters around submersed leaf or unicellular alga. Reduced by stirring but never eliminated even in turbulent conditions. Unlike aerial leaf where air boundary layer eliminated by wind shearing forces. Aquatic plant canopy boundary.

Note: All organisms operate under water from a physiological/biochemical viewpoint. O2 dissolves in mucus lining of lungs and diffuses to hemoglobin. In aerial leaf, CO2 moves in gas phase across boundary layer, through stomates and intercellular air spaces. But then dissolves in wet cell wall and diffuses in aqueous phase to site of fixation (rubisco in chloroplast). This is mesophyll resistance. Despite short absolute path-length it becomes major resistance because 104 slower than rest of path.

In aquatic macrophytes the boundary layer is a major limitation to CO2 availability. Low CO2 diffusion resistance in terrestrial raison d’ être for the move from aquatic to aerial habitat?

Mechanical damage. Why no equivalent plant to wa-terhyacinth in marine habitats? Hydrostatic pressure (0.1 atmos m-1) may limit depth penetration - crush lacunal air spaces and deprive roots of O2. But light usual factor in depth penetration: angiosperms in surface10 m.

Dense medium has advantages. Less support tissue needed. Submersed plants have high FW to DW ratios. Soybean leaf (not whole plant) DW = 22% of FW (FW:DW = 4:1); Hydrilla sprig DW only 10% (FW:DW = 9: 1). Cover large areas with less productivity, especially if place biomass at surface. Less photosynthate in support tissue. Plant looks productive, but in fact it is not. This does not apply to emersed plants that need to support emersed parts.

Polar solution. Plants exposed to [H+] and [OH-] that can vary widely. Aerial plant with thin layer of water around cell controls pH of bathing medium (usually acid in cell wall solution). Submersed plants also control external pH (micro and macro level). Measurement bulk pH of a water body may not reflect pH of water bathing the leaf, as macrophytes may modify pH of leaf boundary layer (e.g. Hydrilla pH 4 abaxial surface, pH 10 adaxial).

Solvent properties. Macrophyte leaves can act like roots, bathed by a dilute nutrient solution. Roots or shoots absorb nutrients? Microphytes (unicellular) have to be generalists.

Quantity and Quality. Measurement difficulties. Photons (particles), energy, wavelength. Physical, psychophysical, and phytophysical methods. Also, source, sink, reflectance. Total energy, rate of energy delivery, brightness, measurement in photochemical terms.

Quantity. Measure light intercepted. Termed irradiance (energy per time per area) or photon irradiance (# of photons or quanta per time per area). Full sun photon (quantum) irradiance is about 2,000 micromol photons m-2 s-1 (400-700 nm or PAR or old microE); equivalent in energy to about 400 Wm-2 (Watt is a power term combining energy and time: 107 erg s-l or 0.24 cal s-l); equivalent to about 100,000 lux, or 10,000 ft.c. Problem: lux and ftc tailored to eye not to plant and probe peaks in green region (where does plant “peak”?). Any photons absorbed 400-700 nm will drive photosynthesis – but Chl peaks in blue and red (440 and 660 nm).

Secchi disc. Relative measure of water transparency. 20 cm diameter white disk lowered over shaded side until no longer see, then raise until can see. Do not use at dawn or dusk. Great variation in waters as value of 10% surface irradiance ranges from few cm to 40 m in clear lake.

If all full-sun photons were absorbed and used at highest efficiency (1 mol C per 10 mol photons, 12 h day, 365 days) = 38 kg C m-2 or 760 tonnes organic dry wt per hectare. This is ten-fold higher than gross productivity in emersed communities, and 50-100 times for submersed. Several factors cause less than theoretical (eg. 50% of photons outside 400-700 nm, respiration etc).

Assimilation versus Irradiance (A/I) Curves.

Generally 10-2 of full sun is euphototic zone for submersed macrophytes, but 10-3 for some microphytes (1-2 ?mol photons m-2 s-1). Thus Hydrilla can increase in dry weight (not just increase in length) at about 10-12 micromol photons m-2 s-1, but many other species of macrophytes are in 20-30 range. Tubers lost DW as germinated, by 3rd week LCP = 50 micromol m-2 s-1, but dropped to 20. Light Compensation Point (LCP) for growth and photosynthesis differ. What is LCP? How measure it? Leaf and canopy photosynthesis.

Irradiance is decreased by several factors; but at surface plants can be exposed to irradiance equivalent to that in terrestrial environment (aquatic not always lower).

Reflectance and scattering: 6-7% loss, but >20% when wave action and sun at low angle; snow on top of ice 75-95 % reflected; ice has same transmittance as water. Absorption: plants, algae, cyanobacteria, bacteria, color in water from organic material (yellow substance of organics absorbing blue light), suspended materials (organic/ inorganic) all attenuate. Water itself absorbs.

Quality. It changes in aquatic environment, but depends on composition of water. Pure water attenuates R and FR with peak transmission from sunlight around 500 nm (FR >750 nm = 90% absorption; R 680 = 40%; Y 570 = 8%; G 520 = 4%; B 460 = 2 %). In colored or suspensions then broad peak around 550-650 nm. But always attenuate more FR relative to R; important in phytochrome responses, especially morphology of plants and growth to the surface.

Submersed autotrophs exposed to temperatures ranging from 4 to 40°C (cyanobacteria in hot springs 100°C). Less diel (diurnal/nocturnal) fluctuation than in average terrestrial environment, but can substantial fluctuations in heavily vegetated conditions that prevent mixing. OVERHEAD. Deeper temperate lakes show stratification. Considerable consequence on mixing and nutrient availability.

Plants may be metabolically active under ice. Danish stream 9°C Callitriche/Elodea active. Contrast: Florida temps 30-40°C in Lyngbya mat. Photosynthesis still increasing at 40°C. So temp regimes almost like Death Valley CA (49°C).

Air 20.9% by volume. Wetzel once wrote: "Submersed macrophytes are exposed to lower concentrations of ambient oxygen. . . than are terrestrial and emergent aquatic plants." Although volume of O2 in water less than in same amount of air, concentration in aerial plant in equilibrium with air same as in aquatic if surrounding water air-equilibrated (0.24 mM at 25°C). We cannot breathe under water due to inability to move large volumes of dense solution to extract enough O2.

Dissolved O2 affected by temp: 0° C = 14.6 mg L-1; 25°C = 8.2; 40°C = 6.4. 8 mg L-1 »0.24 mM. Also salinity (decrease) and pressure (increase). "Saturated" considered relative to surface pressure of lake - equilibrium with air at that temp/pressure. But, not always in equilibrium because of diffusion resistance of water. Sub- or super-saturated (0-200% saturation; 200 » 40% in air!). Diel fluctuations.

Stratification in summer affects O2. Oligotrophic lake: O2 in epiliminion decreases as warms, but metalimnion and hypolimnion increased relative to epilimnion (remain saturated at that temp). Eutrophic: hypolimnion depleted by oxidative processes. Anaerobic much of summer.

Polar solvent. Natural water pH 2-12. Less than 4 usually due to volcanic regions - strong acid (H2SO4) input or acid rain deposition in poorly buffered waters. Also organic (tannic acid) e.g. bog and bog lakes (Sphagnum bogs) (Bog men!). High pH in areas of high [Na2CO3]. "Typical" range 6-9 of bicarbonate type regulated by DIC buffer system.

Direct and indirect pH effects. Japan study: of 20 macrophytes only 2 present below pH 5 (bryophytes e.g. Sphagnum). Reason acid rain is detrimental - titrates lake below 5. Contrast: many plants survive pH 9-10.

Direct. H+ essential nutrient for NO3- or HCO3- use; OH- for NH4+. Transport mechanisms move essential nutrients into cell. Include active (ATP-consuming) process that co-transports H+ e.g. uniport H+ /HCO3-. Pump against concentration gradient. Cannot operate at pH extremes. Thus external pH can affect nutrient uptake.

Tolerance varies. However, all must compensate for external pH if greatly different from internal pH. Limnophila and Hygrophila grew best at pH 5-7, poorly at pH 9; Hydrilla well at 5-7, better at 9. Wide pH tolerance maybe factor in distribution. Short-term photosynthesis can occur across wide range. At sub-saturating DIC, photosynthesis greatest in Hydrilla and Ceratophyllum from pH 3-6, declines above 6 along with free [CO2] – needs more DIC to sustain rate at high pH.

Indirect. Influences complexing/chelation of PO42- anions with metal cations, thus affects P availability. Ferric-P low solubility below pH 6, thus access difficult in acidic water. At very alkaline pH hydroxylapatite Ca5(OH)(PO4)3 precipitates. At acid: NH4+ nitrification to NO3- curtailed, thus nitrate less available.

Very important indirect effect. pH drives equilibrium among DIC forms. Low pH: free CO2 and H2CO3; high pH: HCO3- and CO32-. Aquatic unique in plants have access to HCO3- as C source for photosynthesis and growth. Estimated 50% of submersed plant can use HCO3-. Note CO32- not used directly by plants as DIC source. Likewise, pH of natural waters governed partially by H+ and OH- ions from dissociation of carbonic acid and hydrolysis of HCO3-, respectively.

Carbonic acid solubilizes limestone, gives soluble Ca(HCO3)2 which increases [Ca2+] and [HCO3-], and thus increases pH due to OH- release. Ca(HCO3)2 dissociates to CaCO3 (which precipitates), H2O and CO2. Thus in hardwater lakes with DIC input can have [CO2] much higher than atmospheric-equilibrium – source of CO2 to the atmosphere. Danish stream (Dollerup Baek) 200 to 400 microM CO2. Florida springs (Fanning) 460 microM and HCO3- 3.7 mM.

In oligotrophic lake thermal stratification little effect on pH and DIC. In eutrophic lake DIC in hypolimnion increases with stratification (release of CO2 from sedimentary processes) and pH declines, but not much change in epilimnion. Can have stratification of pH and diel changes due to high-density vegetation.

Alkalinity. Measure of quantity and type of compounds producing alkaline pH (HCO3-, CO32-, hydroxides, to lesser extent less borates and phosphates). Determined usually as milliequivalents of acid needed to neutralize those ions = total alkalinity. Often given meq L-1. Acidity - measure of CO2, tannic, humic, uronic, mineral acids in meq L-1.

Dissolved Inorganic Carbon (DIC)
Already discussed at some length under pH, as two almost inseparable.

Approximately 10-15 microM (depending on temp) IF free CO2 in water in equilibrium with air. In freshwater DIC ranges from near 0 to 0.5 M in some African lakes. Usually 0.5 to 1.0 mM DIC. At pH 7 and 1 mM total DIC have 0.8 mM HCO3- and 0.2 mM CO2 (200 ?M), therefore out of equilibrium with air. At pH 8: 0.975 mM HCO3- and 25 microM CO2 - closer to air-equivalent.

Assimilation versus inorganic carbon (A/Ci) curves.

In dense vegetation, dramatic diel fluctuations due to photosynthesis (day) and respiration (night).

Unlike fresh waters, seawater quite constant in pH (8 to 8.2) and DIC (2 to 2.2 mM) except in rock pools. CO2 of seawater close to air-equilibrium in surface waters due to wave action. Ocean is overall sink for rising atmospheric CO2, except in few places where source.

Acquisition can be regarded as two-step process. Initial steps usually have high affinity for solutes and concentrate them in cell.

In all cases initial step concentrates from dilute environment e.g.:
Energy enters as photons. Trapped in PSI and PSII. Chl becomes “excited” (oxidized) and loses electron).
Carbon enters as CO2 (passive diffusion) or HCO3- (active transport). CO2 fixed by Rubisco (PGA), HCO3- by PEP carboxylase (OAA).
Nitrogen enters as NH4+ or NO3-. Active transport.
Phosphorus enters as PO4- or PO42-. Active transport.
Sulfur enters as SO42-. Active transport.

Second series of steps lower affinity and involve interconversions.
Energy. Electrons pass down e transport chain and reduce NADP+ to NADPH. Electron energy also used generate a H+ gradient (chemiosmosis) that drives ATP synthesis.
PGA or OAA eventually converted to sugar-phosphates (energetic process – ATP and NADPH).
NO3- converted to NH4+ by nitrate reductase, and NH4+ reacts with oxoglutarate to produce glutamate (amino acid).
Phosphate - ATP synthetase.
Sulfate - ATP sulphurylase. Incorporated into amino acids methionine and cysteine.

Not all organisms have same nutrient requirements. Two major trends: Lower N and P relative to C in macrophytes than in microphytes (unicellular organisms). Very approx values:
1000 C : 125 N : 10 P unicellular algae
1000 C: 50 N: 2 P macrophytes

Wetzel gives overall values of 1000 C : 175 N : 25 P (l P : 7 N : 40 C). May include emersed plants. Consequently, for two organisms in same environment, one may be limited by specific nutrient, the other not. Also, relative ability of the two organisms to capture (concentrate) the "limiting" resource is a factor. Aquatics do not all have similar resource requirements. Macrophytes have more support tissue, therefore need more C relative to N and P. They have lower growth rates and different abilities to transport materials into cells. Macrophytes have much lower surface area to volume ratio than unicells. Surface area increases as square while volume as cube when size increases. SA : V limits exchange capacity with environment. Macrophyte morphology often so as to increase SA: V ratio (thin/dissected leaves) to enhance exchange of materials.

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis


Tom Barr


Junior Poster
Jan 24, 2005
Re: Notes From Botany, Photosynthesis

I can follow some of it, but the reader needs a few years background to get all of it. The vocabulary of science makes it easy for one scientist to communicate with another (or teacher to student, in this case).

I enjoy it, though, as I can easily look up words in another browser window. Now I know what an autotroph is. :).

I can appreciate the years of work each Botanist does to contribute to the general body of knowledge, giving us this incredibly detailed look at how things work. Really amazing.

So all this research on freshwater lakes can provide me with insights on what goes on in my 30 gallon.

Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

You are not suppose to understand an entire semester's worth of notes from a grad course right away.

I did not put them all up either. Just the main ones.

But they will help see some insight to what is being done and has been done concerning aquatic plants.

If you walk away learning something new, then that is good.

Tom Barr


Junior Poster
Jan 24, 2005
Re: Notes From Botany, Photosynthesis

Tom Barr said:
You are not suppose to understand an entire semester's worth of notes from a grad course right away.
Yeah, I kinda knew that.

Tom Barr said:
I did not put them all up either. Just the main ones.
That's an entire semester? I thought it was just one lecture. Grad students have it too easy.

Tom Barr said:
But they will help see some insight to what is being done and has been done concerning aquatic plants.
Yes, exactly. Just amazing stuff. Why is Hydrilla popular among researchers?

Tom Barr said:
If you walk away learning something new, then that is good.
You have no idea how much I value the things I'm learning here. Absolutely fascinating stuff. God is in the details.


Tom Barr

Staff member
Jan 23, 2005
Re: Notes From Botany, Photosynthesis

Hydrilla is popular because it's the worst submersed weed in the USA and many countries.

It's has odd attributes and grows like mad making the wait times less.
I would not want to work with a slow grower for a model!

Tom Barr