Ecosystems, niche and distribution

• Habitat — the place where an organism lives.
• Population — all the individuals of one species in a habitat at one time.
• Community — all the populations of all species in a habitat.
• Ecosystem — the community plus the abiotic (non-living) environment, interacting as a unit.

Numbers and distribution are set by abiotic factors (temperature, light, water, pH, mineral ions, oxygen) and biotic factors (competition, predation, disease). The niche concept explains why: each species can only persist where the whole set of conditions it requires is met, and where it is not out-competed.

Core practical 10: investigate the distribution of a species using random quadrats (for abundance in a uniform area — a random number generator gives the coordinates) or a belt transect (to record change along an environmental gradient, e.g. up a shore).

Succession

Succession is the change in a community over time.

• Pioneer species (e.g. lichens on bare rock) colonise a hostile abiotic environment. They are adapted to extreme conditions and reproduce asexually or by wind-blown spores.
• They change the abiotic conditions — weathering the rock, and adding humus when they die — which makes the environment less hostile and suitable for the next species.
• Each new community out-competes and replaces the last. Soil depth, biomass and biodiversity all increase.
• The stable end point is the climax community, determined by the climate.

If grazing, burning or mowing stops the succession early, the result is a plagioclimax (deflected succession) — a heather moor or a chalk grassland, for example. Removing the grazing pressure lets succession resume.

The light-dependent reactions

Overall: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂ — the light energy is used to reduce carbon dioxide.

The light-dependent reactions take place on the thylakoid membranes of the grana:

• Light strikes chlorophyll in a photosystem; two electrons are excited and leave (photoionisation).
• The electrons pass down an electron transport chain of carriers. The energy released is used to pump protons (H⁺) from the stroma into the thylakoid space, creating an electrochemical gradient.
• Chemiosmosis: the protons flow back down the gradient through ATP synthase, and the energy released drives the phosphorylation of ADP → ATP. (Non-cyclic photophosphorylation.)
• Photolysis of water replaces the lost electrons: 2H₂O → 4H⁺ + 4e⁻ + O₂. The oxygen you breathe is the waste product of this step.
• NADP is reduced (accepting the electrons and H⁺) to reduced NADP.

Products passed to the Calvin cycle: ATP and reduced NADP.

The Calvin cycle and the chloroplast

The light-independent reactions take place in the stroma:

• Fixation: CO₂ combines with the 5-carbon ribulose bisphosphate (RuBP), catalysed by rubisco. The unstable 6C intermediate immediately splits into two molecules of glycerate 3-phosphate (GP, 3C).
• Reduction: GP is reduced to triose phosphate (TP, 3C), using reduced NADP and energy from ATP.
• Regeneration: five out of every six TP molecules are used, with more ATP, to regenerate RuBP. Only one in six leaves the cycle to make sugars, amino acids and lipids.

Chloroplast structure fits function: stacked thylakoids give a huge surface area for the photosystems and the ETC; the thylakoid space is small, so a proton gradient builds quickly; the stroma holds the Calvin-cycle enzymes and is where starch grains and lipid droplets accumulate. Core practical 11 uses DCPIP as an artificial electron acceptor to follow dehydrogenase activity in isolated chloroplasts.

Which stage of photosynthesis?

Tap an event, then tap where it happens.

Your turn — turns of the Calvin cycle

Your turn — ATP cost of a hexose

GPP, NPP and energy transfer

Only about 1–3 % of the light falling on a plant is converted into chemical energy at all — the rest is reflected, transmitted, of the wrong wavelength, or misses the chloroplasts.

Why is so much lost? Not all the organism is eaten (roots, bones); not all that is eaten is digested (it is egested); some energy is excreted as urea; and a great deal is released as heat in respiration — especially in endotherms.

Your turn — net primary productivity

Your turn — energy transfer efficiency

Where does the energy go?

Evidence, causes and effects

Evidence for past climates:

• Ice cores — trapped air bubbles give a direct record of past atmospheric CO₂; oxygen isotope ratios in the ice indicate past temperature.
• Dendrochronology — tree ring width reflects growing conditions each year.
• Pollen in peat bogs — the species present indicate the climate of the time.

Anthropogenic causes: combustion of fossil fuels and deforestation raise atmospheric CO₂; agriculture (cattle, rice paddies) and landfill raise methane. These are greenhouse gases — they absorb outgoing long-wave infrared radiation and re-emit it, warming the lower atmosphere.

Effects (5.15): changing rainfall and temperature alter species distribution (organisms shift polewards and to higher altitudes) and life-cycle timing — and if a plant flowers before its pollinator emerges, the mismatch harms both.

Models and their limits (5.14): predictions come from computer models that extrapolate beyond the data. Extrapolation is uncertain: models must simplify feedbacks (clouds, ocean circulation, permafrost methane) and cannot know future human emissions — so a range of scenarios is given, not a single number.

Why temperature matters so much

As temperature rises, molecules have more kinetic energy, so enzyme and substrate collide more often and with more energy: more enzyme–substrate complexes form per second, and the rate rises. Beyond the optimum, the extra vibration breaks the hydrogen and ionic bonds holding the tertiary structure. The active site changes shape, the substrate no longer fits, and the enzyme is denatured — the rate falls sharply and does not recover on cooling.

This is why climate change is a biological problem, not just a physical one: a few degrees changes metabolic rate, development rate, and therefore the distribution of every ectotherm on the planet.

Speciation

Evolution is a change in allele frequency in a population over time, driven by natural selection acting on genetic variation created by mutation.

Speciation requires a barrier to gene flow:

• Allopatric — a geographical barrier (a river, a mountain range, an ocean) separates two populations. Different selection pressures, mutations and genetic drift make their allele frequencies diverge until, even if reunited, they can no longer interbreed to produce fertile offspring.
• Sympatric — reproductive isolation arises without geographical separation, e.g. by a change in flowering time (temporal isolation), a behavioural change in courtship, or polyploidy in plants.

How science works (5.18, 5.20): conclusions about controversial issues such as climate change are trusted because of peer review, publication in scientific journals, presentation at conferences, and independent replication — not because of a single dramatic paper.

Match the ecological term

Tap a description on the left, then the correct term.

Reducing atmospheric CO₂

The big ideas to know

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