EVSE 5309 Physical Environment New

EVSE 5309 Physical Environment, p.
EVSE 5309 Environmental Systems

Biological Aspects
Topic 2: The Physical and Chemical Environment
This section of the course focuses on the physical
and chemical environment that organisms experience.
Adaptation
People often speak of organisms adapting to
conditions in their environment.
This use of adapt and adaptation can have two
meanings, one correct and one incorrect.
The correct meaning of adaptation is related to
evolution by natural selection.
An adaptation is a heritable trait that increases
survival or reproduction.
An adaptation increases fitness the ability to
survive and reproduce.
Adaptations are the result of evolution by natural
selection.
They are the traits that the most successful
parents pass on to their offspring.
EVSE 5309 Physical Environment, p. 2
The incorrect uses of the words adapt and

adaptation refer to an individual changing its
characteristics to cope with changes in its
environment.
By definition, adaptation is a population process
that occurs over generations as traits evolve.
Adaptation to the environment does not occur on
the part of an individual organism.
Because an adaptation is a trait, it is part of an
organisms phenotype.
Because an adaptation is heritable, it has a genetic
basis, and so is related also to the organisms
genotype.
Individual organisms that change their characteristics
in response to changes in the environment are
changing their phenotype (without changing their
genotype).
Such changes in individual characteristics are
called phenotypic plasticity.
Coping with environmental variation

There are many responses that individual organisms
can make to cope with changes in their
environment.
Successful change by an individual to cope with
environmental variation is properly called
acclimation or acclimatization (not
adaptation).
The physical environment is highly variable and
may vary outside the limits for sustaining life
or for efficient functioning.
Organisms must be able to maintain their internal
environments within the limits for sustaining
efficient function or even though the
environment may fluctuate beyond those
limits.
The study of the ability of organisms to sustain
function under variable abiotic environmental
conditions is known as Physiological
Ecology.
Organisms can also respond to environmental
changes by migration -- movement to more
favorable conditions.
Homeostasis is a key concept of physiological

ecology.
Organisms have evolved physiological mechanisms
that maintain their internal environments within
the limits for efficient functioning while the
external environment varies outside those limits.
This involves active regulation of the internal
environment (within bodies and cells).
Translation is same place or same state.
Homeostasis is characteristic to some extent of
all living organisms.
Organisms often acclimate to environmental
changes by regulating internal conditions
while external conditions change.
Homeostasis often relies on negative feedback
processes.
These have three components:
receptor
control center
effector
Receptor detects change in internal conditions.
Control Center processes this information,
compares it to a set point or optimal
value, and notifies effector.
Effector Adjusts internal condition in response
to signal from control center.
Example regulation of blood osmolarity in a

mammal:
The hypothalamus (in the brain) acts as both
receptor and control center.
It detects changes in blood ion concentration,
and compares these to a set point.
Thirst and the kidneys act as effectors.
If blood is too concentrated (ions too high), thirst
directs the animal to drink water.
If blood is too dilute, kidneys act to remove and
expel water.
from Mackenzie et al., 2001
Conditions and Resources

For any species, physical and chemical factors in the
environment can often be classified as conditions
or resources.
Condition = an abiotic environmental variable to
which organisms respond.
These responses can consist of changes in
physiological rates, rates of body growth,
rates of reproduction or mortality, etc.
Ultimately, conditions affect the total rate of
change of a species population. Population
persistence thus depends these conditions.
Conditions can be regarded as causes of natural
selection, and organisms typically have
evolutionary adaptations to cope with a
certain range of conditions.
Some of these adaptations involve phenotypic
plasticity, acclimatization, and internal
regulation.
A condition is often something like temperature or
salinity. Organisms do not consume or
deplete such things.
Resource = an environmental variable to which an

organism (or population) responds with increased
growth, and which is consumed by organisms in
the process.
Clearly survival depends on resources, but the
possibility of depletion leads to competition
between individuals.
Such competition is also a cause of natural
selection, and organisms typically have
adaptations to cope with some degree of
resource depletion.
Examples of resources include chemical
nutrients, food items, and space in which to
live.
The Ecological Niche

The range of conditions and resources under which a
species can survive is related to the concept of a
niche.
The meaning of this concept is not fixed among
ecologists, but has evolved historically, and is not
settled yet.
Many modern concepts of the niche include an idea
proposed by Hutchinson: imagine a (high
dimensional) coordinate system in which each
coordinate is one of the conditions or resources
important to a species.
On each axis there will probably be a lower bound
below which the species cannot survive, and
perhaps an upper bound above which it cannot
survive.
Within the high-dimensional space defined by these
coordinates, there will be a high dimensional
hypervolume defining the conditions under which
survival is possible.
Condition 2
A 2-dimensional illustration:
U2
L2
U1
L1
Condition 1
A more concrete example:
Other ideas related to the concept of the niche

include:
The niche describes the habitat and function of a
species: physical location, interactions within
the food web, means of obtaining resources,
adaptations to its lifestyle.
Niches may be subdivided into the fundamental
niche, which is the idealized niche in the
absence of other species, and the realized
niche, which is actually achieved in the
presence of other species that are
competitors.
Resource 2
Fundamental Niche
Realized
Niche
Resource 1
The principle of competitive exclusion says that two

species cannot occupy exactly the same niche.
One will be a superior competitor that drives the
other extinct.
To coexist, two species must therefore have some
differences in their niches. A high degree of niche
overlap may indicate intense competition.
Condition or
Resource 2
Species B
Species A
Condition or
Resource 1
Many of these particular ideas of the niche are
debated among ecologists, and are not
universally accepted.
Nevertheless, the general idea of a niche as a
summary of the conditions and resources
required for survival is still used.
But, contemporary research is moving from abstract

representations to detailed studies of conditions,
resources, and organisms responses.
Two influential ideas summarize how organisms often
respond to the numerous conditions and that
affect survival and reproduction.
1. Liebigs Law of the Minimum (1840)
The total yield or biomass of any organism will be
determined by the nutrient present in the
lowest concentration in relation to the
requirements of that organism.
This idea originated in agriculture: the yield of a crop
is often governed by the soil nutrient in lowest
supply relative to the needs of that crop. This
idea has been generalized to naturally growing
plants.
It has also been generalized to state that the growth
rate of an organism is determined by the nutrient
present in the lowest concentration in relation to
the requirements of that organism.
This idea applies best to plants and many
microorganisms that require distinctly different
nutrient resources e.g. phosphate, nitrate,
This idea sometimes applies to animals, when one
food source, or one dietary component (e.g.
protein, minerals) can be identified as limiting to
biomass or growth.
Note that Liebigs Law applies to what happens when

the level of a nutrient or resource gets too low.
The next law applies to what happens when the level
of an environmental condition gets too high or too
low.
2. Shelfords Law of Tolerance (1913)
For an organism to succeed in an environment,
each of the conditions must remain within the
tolerance range of that organism. If any
condition exceeds the maximum or minimum
tolerance of that organism, the organism will
fail to grow and will be eliminated.
Environmental conditions which tend to follow this law
include examples such as:
Temperature
Moisture and relative humidity
pH (soil and water)
Salinity
Current flow
Soil structure (e.g. grain size)
Pollutants and toxins
Also, some substances that act as nutrients are toxins
at high concentration. For example, many metals
(copper, chromium, selenium, etc.) are required
as nutrients at trace concentrations. Elevated
concentrations are toxic.
Shelfords Law is associated with a generalized

unimodal response of survival or productivity to
an environmental condition:
from Jones, 1997
In the zone of tolerance, performance is high

(consistent with survival). Outside of this zone,
performance is low.
The lower incipient lethal level of the environmental
condition marks the lower limit of the zone of
tolerance.
The upper incipient lethal level of the environmental
condition marks the upper limit of the zone of
tolerance.
Many variations in the shapes of these curves can be

found, depending on the species under study, the
condition under study, and the measure of
survival or productivity adopted.
Population
Growth Rate,
For many resources, no upper incipient lethal level

occurs at environmentally realistic
concentrations.
In such cases, a plot of the organisms population
growth rate versus resource level is often an
increasing curve.
max = max. growth rate
K = resource level when

growth is 1/2 of max.
Resource Level
= max R / (K + R)
This equation applies well to the growth of
microorganisms and nutrient resources.
For example, simulation models of the growth of
algae used to study water quality often use this
approach.
It is sometimes also applied to growth of plants in
relation to soil nutrients, or of animals in relation
to supply of particular foods.
Solar Radiation and Climate

Many conditions of the physical environment are
related to climate.
Climate itself is related to solar radiation, which heats
the earths surface.
Winds and ocean currents distribute that heat.
Seasonal variation in solar radiation
The earths surface is heated most strongly when
solar radiation strikes directly (90 angle).
The earths axis of rotation is tilted, so the angle of
solar radiation at any location varies annually.
As a result of this geometry, total solar radiation

received in a day varies with time of year and
latitude.
from Kirk, 1983
Over a day, solar radiation varies with time of day and

meteorological conditions.
from Kirk, 1983
Most sunlight passes through the atmosphere, so little

of its radiant energy is absorbed by air.
High energy wavelengths of sunlight are much
more strongly absorbed by land and water.
Their radiant energy is converted to heat
(molecular motions).
This heat is then transferred to the atmosphere
by conduction and infrared radiation.
As a result, the atmosphere is heated primarily from
the bottom.
Warmed air rises, and expands as pressure
decreases with altitude.
This expansion cools the air, a process called
adiabatic cooling.
Dry air cools 10 C per 1000 m of elevation.
Moist air cools about 6 C per 1000 m of
elevation.
As warmed air in one location rises, it is replaced by

cooler air from another location, where the sun
strikes less directly.
If the earth did not rotate, winds would be
oriented north-south.
The earth rotates, with surface moving at up to
1500 km / h at the equator (slowing to 0 at
poles).
Therefore, the path of the wind with respect to
the ground surface is deflected (Coriolis
effect).
Because of differential solar heating at different
latitudes, air at the earths surface has consistent
high pressure at subtropical latitudes and at the
poles, and consistent low pressure at the equator
and in sub-polar regions.
Winds flow from high pressure regions to low
pressure regions.
The direction is not north-south due to the
Coriolis effect, but is deflected.
Winds tend to blow west to east from about 30
to 60 latitude (westerlies).
Winds tend to blow east to west in tropical
latitudes (trade winds).
At the intertropical convergence zone (ITCZ) near
the equator, the trade winds converge (the
doldrums).
In reality, wind patterns are not symmetric north-south

around the equator.
Land masses alter the wind direction.
There is more land in the northern hemisphere.
The ITCZ is north of the equator as a result.
In the ITCZ air rises from the surface, collecting
moisture if it is over the ocean.
The Caribbean Sea is in the ITCZ, and the
regular presence of moist, warm air makes it
prone to hurricanes.
Ocean currents also distribute heat around the earth.

If idealized wind patterns occurred (no land), then the
corresponding idealized surface ocean currents
would be:
from Press & Siever, 1978
Drifts (consistent currents) would correspond to trade

winds and westerlies.
Gyres would arise in subtropical and subpolar
regions.
Real patterns are much more complex, due to land:
from Press & Siever, 1978
There are also vertical ocean currents.

At the equator, warm ocean water tends to rise.
At the poles, cold ocean water tends to sink.
This sets up a conveyer belt, where warm water
flows on the surface from the equator to the
poles, while cold water returns from the
poles to the equator along the ocean bottom.
Earths is warmer at the equator, and cooler towards

the poles.
But the distribution of climates is not symmetric northto-south, and is altered by the distribution of land
masses.
from Jones, 1997
Further alternation of climate occurs due to elevation

of the land.
As winds rise to pass over mountains, the air
cools (adiabatic cooling).
Cooler air is less able to hold moisture, so rain
becomes likely on the windward side.
Air that descends on the lee side has lost
moisture, and as it heats up it will evaporate
more from the landscape.
Deserts tend to occur on the lee side of mountain
ranges, especially in areas of westerly
winds.
Microclimate
Microclimate is the climate at the scale of an
organism (not the globe).
Most organisms are small (<< 1 m long).
There can be large changes in temperature and
moisture over short distances.
There are also often large changes over the course of
a day.
On land, soil tends to store heat.
Solar radiation is absorbed at the surface. Heat then
passes by thermal conductivity to deeper soils.
At night, deeper soils are often warmer than the
surface.
The surface tends to be warmest in the
afternoon, warmer than deep soil.
Daily amplitude of variation is highest at the
surface, and decreases with depth.
A plant < 1 m tall can experience a large range of

temperature from its apex to its roots.
Temperature profiles in air

Temperature profiles develop in the air above the soil
surface or the top of the vegetation, over a scale
of several meters.
At night, the surface cools.
Air at the surface conducts heat into the cooling
soil.
This cools the air, and so a cold layer develops
just above the surface.
Thus the temperature increases with height
above the surface.
During the day, the surface absorbs sunlight and
heats up.
The surface conducts heat to the air immediately
above.
Warm air rises, but cools as it does.
Thus the temperature decreases with height
above the surface.
These idealized patterns are altered between the top
of the vegetation canopy and the soil surface.
They are also altered by wind.
Properties of Water
Water is the only inorganic liquid that naturally occurs
on the surface of the earth.
Other inorganic liquids have lower boiling points.
Water is essential to life, and about 90% of living
mass is typically water.
Water has many unique properties that result from its

molecular shape and charge distribution.
The two hydrogen atoms are bonded to the oxygen at
an angle of 105.
Two sets of paired electrons lie opposite to the
hydrogen atoms, generating a charge separation.
from Lehninger, 1982
The polar nature of water means that it is a good

solvent for ions and for other polar compounds.
The polar nature of water also permits hydrogen
bonding.
from Lehninger, 1982
Hydrogen bonding holds water molecules together,

and raises freezing and boiling points compared
to other inorganic liquids.
Hydrogen bonding gives water a high surface tension
and high viscosity in comparison to molecular
weight.
Hydrogen bonding also explains the unusual

temperature-density relationships of water
The solid form is less dense than the liquid (ice
floats).
For a certain temperature range, water gets
denser as it heats up.
Ice floats because every water molecule forms 4

hydrogen bonds in the crystalline structure of ice
(maximum possible number of hydrogen bonds).
This holds the water molecules far apart, with lots of
empty space in between, making ice less dense.
As ice melts some of the hydrogen bonds break,
and water molecules move closer.
So water just above freezing is denser than ice.
As water warms from 0 to 4 C, more hydrogen
bonds break, and water continues to get
dense as molecules can move closer.
The maximum density of water is at 4 C.
Above 4 C, further warming gives water
molecules enough kinetic energy to move
apart, and density decreases.
When solar radiation passes through water, it is

absorbed.
Absorption of visible light by pure water is relatively
small.
Absorption of light is also due to dissolved substances
and suspended particles.
Irradiance at a given depth (Iz) tends to decline
exponentially from the surface (Beers law):
Iz = I0e-z
where
I0 = irradiance at the surface (W / m2)

= attenuation coefficient (m-1)
z = depth (m)
The radiant energy absorbed by water heats it up.

If solar radiation were the only thing affecting lake
temperature, we might expect to see:
But instead, temperature is typically constant for

some range of depth near the surface, and
decreases only in deeper waters:
This creates stratification with a warm, less dense

water layer above the colder water layers below.
Stratification in many climates varies seasonally,
because solar radiation varies seasonally.
In a typical lake in a temperate climate, the following
patterns occur.
In spring, the water warms up near the surface due
to heating by sunlight. This warm water forms
a hydrodynamically stable layer over colder
water below.
In summer, this stratified situation can become very
stable, as the warmer epilimnion develops a
large temperature difference from the colder
hypolimnion. Stable stratification is
associated with a thermocline a region
where the temperature drops rapidly. Water
from the epilimnion does not mix with that from
the hypolimnion.
In autumn, the epilimnion cools, and stratification
becomes less stable as its temperature
approaches that of the hypolimnion.
Eventually, stratification breaks down entirely
and the lake mixes through its entire depth.
In winter, the lake mixes through its entire depth,
unless it is cold enough for ice to form at the
surface.
Jones (1997)
During winter there is little or no growth of algae (also
called phytoplankton) because of lack of light.
Such organisms may die and release their
nutrient content to the water. Mixing of the entire
depth of the water transports oxygen from the
surface throughout the entire volume of water.
In spring, light increases and the water heats up. The

combination of high light, warm temperature, and
high nutrient concentration typically stimulates a
spring bloom of algae.
However, these algae consume nutrients so that by
the time summer stratification begins, nutrients
are depleted and algal growth slows down, and
their abundance usually declines. This period is
called summer stagnation.
During summer stagnation, stable stratification
prevents the epilimnion, which is oxygen rich,
from mixing with the hypolimnion. Decomposer
organisms consume oxygen in the hypolimnion,
however, and oxygen can become depleted.
These decomposers also recycle nutrients, so
that they hypolimnion may become nutrient-rich.
In autumn, when stratification breaks down, the
nutrients from the hypolimnion are mixed into the
whole lake, and this can stimulate another bloom
of algae.
The abundance of crustacean animals in the water
(zooplankton) which eat the algae tends to
follow the seasonal peaks of algal abundance,
with a time lag.
There are many variations on these patterns, which

depend on climate. For example, winter
stagnation can occur if the climate is cold enough
to freeze the lake.
In subtropical or tropical climates, lakes may never
stratify, or may do so only for short periods of
time.
Many parts of the ocean are permanently stratified,
with a deep thermocline (100-1000 m). Coastal
waters and estuaries may have stratification
patterns that vary seasonally, like those of lakes.
However, complications arise from tides and
ocean currents.
In some areas of the ocean, regular upwelling
occurs, in which deep, nutrient-rich waters flow
up towards the surface, stimulating the growth of
algae. Such areas support some of the most
productive fisheries in the world.
Plants and water

Most plants obtain water from the soil.
Soil water is held in pores by capillary action;
otherwise it drains downward.
Smaller pores hold water more tightly.
Coarse, sandy soils have large pores, and water
tends to drain out.
Fine, clay soils have small pores that might hold
water too tightly for plants to take up.
For a given soil, the field capacity is the amount of
water the soil can hold against the force of
gravity.
The field capacity depends on the size
distribution of soil pores.
The field capacity is an upper limit to the water
resource available to plants.
The lower limit of the available water resource is the
permanent wilting point.
This is the water content at which the binding
force of capillary action just balances the
suction force that roots generate.
When water content drops to this point, plants
cannot extract more and so they wilt.
In arid environments or near the ocean coast, soils

tend to be saline, which produces osmotic forces
that act in addition to capillary forces.
Plants must generate enough suction force to
balance both capillary and osmotic forces.
This makes it more difficult for plants to extract
water in saline soils.
As plant roots take up water, it becomes harder to

extract.
When a root begins taking up water, the larger
pores are emptied first because capillary
forces are weaker.
This creates a resource depletion zone around
the root.
Water is left in the narrower pores, which hold the
water more strongly.
Replenishment of water in the resource depletion
zone then slows down.
For aquatic plants, water per se is not scarce.
However, regulation of ion content can be a
problem.
In freshwater or brackish habitats, plants are
hypertonic to their environment (higher salt
content within).
Thus water tends to flow into the plant tissues,
and must be expelled at a cost.
In marine habitats many plants are isotonic to the
environment, and have no osmotic problems.
Some marine plants are hypotonic to their
environment (lower salt content within), and
tend to lose water.
They must take it up from the environment like
terrestrial plants.
Plants actually consume little of the water they take

up.
Most water passes through the plant only to keep
its tissues moist.
In order to photosynthesize most plants must
open pores in their leaves, called stomata, to
let in CO2.
While stomata are open, water can evaporate
out.
Most of the water that plants take up is used to
balance this loss.
This process is called evapotranspiration.
More available water means stomata can stay open
and the plant can photosynthesize.
Therefore, production of organic matter by plant
photosynthesis tends to increase with
precipitation.
The potential evapotranspiration rate measures

how much water plants need given the local
climate.
It is the rate water would be lost at a site
assuming soil water is not limiting (soil at
field capacity) and vegetation covered the
site.
Potential evapotranspiration rate depends on
temperature, solar radiation, air humidity,
and wind.
The difference between potential evapotranspiration
rate and precipitation is a water deficit that can
prevent a site from developing full vegetation
cover.
These climatic relationships govern the type of
vegetation that develops on a site, and are
summarized by Holdridges Life Zone
Classification.
from Jones, 1997
The productivity of organic matter by plants in these

different vegetation types generally increases
with temperature and precipitation.
Productivity is best measured as net primary
production, the rate of photosynthesis minus
respiration on the part of plants.
Vegetation Type
Tropical Rainforest
Tropical Seasonal
Forest
Temp. Gymnosperm
Forest
Temp. Angiosperm
Forest
Boreal Forest
Woodland & Shrub
Savannah
Temp. Grassland
Tundra
Desert / Semi-desert
Extreme Desert,
Sand, Rock, Ice
Cultivated Land
ALL TERRESTRIAL
Area
(106 km2)
17.0
7.5
Net Primary
Production (g dry
mass m-2 yr-1)
2200
1600
% of World
Production
22.0%
7.1%
5.0
1300
3.8%
7.0
1200
4.9%
12.0
8.5
15.0
9.0
8.0
18.0
24.0
800
700
900
600
140
90
3
5.6%
3.5%
7.9%
3.2%
0.1%
0.9%
0.04%
14.0
145.0
650
5.4%
65.0%
Animals and water

Animals have to deal with two issues:
keeping their tissues and cell contents hydrated;
and regulating the solute concentration
(osmolarity) of tissues and cells.
These are related because absorbing water dilutes
solutes, and dehydration concentrates solutes.
Osmosis for aquatic organisms:
Water enters an organism from the environment
if the solute concentration is higher in cells
and tissues.
Water leaves an organism if the solute
concentration is higher in the environment
than in cells and tissues.
Environmental solute concentration is often
determined by salinity.
Salinity the total concentration of ionic substances
in water.
Because living things evolved originally in seawater,
the ionic composition of cells and tissue fluids is
similar to that of seawater.
Seawater has a salinity of about 34.5 grams / liter.
In many inland waters, salinity is less than 0.5 g / liter

(fresh water). In some saline lakes, however,
salinity may be 3-4X that of seawater.
Brackish waters are found in estuaries and other
transition zones between inland freshwaters and
oceans. The salinity of brackish water often
shows high variability.
Lagoons and tidal pools with high rates of evaporation
of water may become very saline.
Aquatic organisms usually have specific adaptations
to live in waters of higher or lower salinity than
seawater, or in which salinity fluctuates widely.
When an organism is hypotonic to its environment, it

has a lower salinity in its tissues than the
environment. Water diffuses by osmosis from the
organism to the environment, concentrating salts
within its tissues and disrupting physiological
function.
Organisms that are hypotonic to their environment
must have adaptations such as an ability to
eliminate salts or consume water.
When an organism is hypertonic to its environment,
it has a higher salinity in its tissues than in the
environment. Water diffuses by osmosis from the
environment to the organism, increasing osmotic
pressure within cells and risking rupture of
membranes.
Organisms that are hypertonic to their environment
must have adaptations such as an ability to pump
out excess water, or reinforcement of cell
membranes with cell walls.
Stenohaline organisms are adapted to only a narrow

range of salinity. Examples include marine
organisms that live only in normal seawater, or
freshwater organisms that cannot tolerate salinity
> 500 mg / liter.
Euryhaline organisms are adapted to wider ranges of
salinity. Many inhabitants of brackish waters fall
in this category, because they may regularly
experience salinity < 500 mg / liter or > 34.5 g /
liter.
Such adaptations involve two idealized patterns of
osmoregulatory response:
Perfect osmoregulators maintain a constant salt
concentration in internal tissues, regardless of
the variation in environmental salinity.
Perfect osmoconformers allow their salt
concentration in internal tissues to vary and be
equal to the environmental salinity. They use
physiological adaptations to adjust their
biochemistry to function at different salinities.
The following graphs show these idealized patterns,
and some of the more realistic patterns that
organisms actually achieve.
from Jones, 1997
Water balance in fish

A freshwater fish is hypertonic relative to its
environment the solute concentration is higher
in cells and tissues.
Therefore a freshwater fish must excrete excess
water.
The kidneys do this. They retain ions and remove
water to be expelled in urine.
Seawater fish are hypotonic relative to their
environment, with lower solute concentration in
cells and tissues, and thus tend to lose water by
osmosis.
Seawater fish drink seawater to replace this loss.
They have kidneys. These remove some of the
ions obtained in seawater, especially Ca+2,
Mg+2 and SO4-2.
Additionally, the gills remove excess Na+, Cl- and
NH4+.
By drinking seawater, removing excess ions, and
excreting little urine seawater fish regulate both
water content and solute concentration.
Water balance in amphibians

Many amphibians spend part of their life in water and
part on land.
They face different water and solute balance
problems in these two habitats.
Amphibians in freshwater are hypertonic and tend to
absorb water by osmosis.
When in water their kidneys produce urine which is
excreted.
Amphibians on land tend to become dehydrated.
The conserve body water by absorbing water back
from urine in the bladder.
Water balance in terrestrial animals

Terrestrial animals also tend to become dehydrated.
Exchange of O2 and CO2 takes place on moist
surfaces of large area (e.g. lungs in vertebrates).
Inevitably, water is lost by evaporation from these
surfaces.
This is replaced primarily by drinking, but also from
water released from digestion of food and
metabolism.
To regulate ion content while conserving water, urine
with high solute concentration must be produced.
Mammals such as humans use the nephrons in the
kidneys to concentrate certain solutes in urine.
Tissue fluid enters the nephron from the blood at
Bowmans capsule, and travels through the
loop of Henle.
The loop passes through tissues that absorb
water and excrete certain solutes (e.g. K+)
while retaining others (Na+).
At the end of this passage, the collecting tubule
has produced a urine with solutes about 4X
as concentrated as in blood.
Mammals that live in deserts (e.g. kangaroo rats)

have very long loops of Henle to produce very
concentrated urine while excreting little water.
Mammals that spend much time in water (e.g.
beavers) have short loops of Henle.
Temperature and metabolism

In common speech, we talk of warm blooded and
cold blooded organisms as those that can and
cannot regulate their internal temperatures,
respectively.
Biologists use more precise terminology to
characterize the relationships between an
organisms internal temperature and the
environmental temperature.
Homeotherms organisms who maintain an
approximately constant internal temperature
while external temperature varies.
Poikilotherms organisms whose internal
temperature varies with external temperature.
Problems with these terms:
For some animals, body temperatures vary but
with regulated levels: e.g. hibernating
mammals reduce body temperature during
hibernation.
Some animals that are poikilothermic exert some
degree of regulation of temperature.
Endotherms organisms who produce heat

metabolically within their own bodies to regulate
temperature.
Ectotherms organisms that cant do this.
By these definitions, only birds and mammals are
endotherms.
Problems with these terms:
Some insects and reptiles can obtain body heat
behaviorally (basking in the sun).
Some colonial insects produce heat within the
colony by vibrating (e.g. bees).
Endotherms typically regulate their temperature at 3540 C.

This is the maximum temperature of air or water
in many climates.
Therefore, endotherms produce heat as needed
when it is cooler.
However, fur and feathers act as insulators, so in hot
weather endotherms must lose heat by panting or
sweating.
Rate of Energy Consumption
Regulation of temperature by endothermy is costly.

Endotherms consume more metabolic energy
than ectotherms.
Within a favorable temperature range called the
thermoneutral zone, endotherms consume
about the same amount of energy at all
temperatures.
For temperatures outside the thermoneutral
zone, metabolic energy consumption is
much higher.
At low temperatures, heat production requires
metabolic energy.
At high temperatures, cooling mechanisms also
require metabolic energy.
Thermoneutral Zone
Endotherm
Ectotherm
Temperature
All organisms (endotherms and ectotherms) are

affected by various heat exchange processes.
Organisms can affect these processes by

fixed structural properties, e.g. surface
characteristics that affect reflection, radiation
exchange, and evaporation.
physiological properties, e.g. methods of gas
exchange, proximity of blood vessels to skin.
behavioral characteristics, e.g. choosing to bask
in direct sunlight or go to the shade.
Both endotherms and ectotherms achieve some

degree of temperature regulation by altering heat
exchange.
But ectotherms generally regulate less effectively and
so their temperature varies more in relation to the
environment.
Ectotherms
have fewer temperature regulation mechanisms
than endotherms.
must rely to some extent on an external source of
heat.
must consume energy to alter heat exchange, so
all regulation is a matter of cost and benefit.
Temperature thresholds set limits to the activity and
even survival of organisms.
High temperatures
can denature enzymes by disrupting protein
structure (this is uncommon in most
environments but can happen in hot springs
and geothermal discharges).
can cause dehydration due to higher evaporation
(this is much more common).
Often, at a threshold temperature, water loss

increases dramatically.
Specialized structures such as seeds can sometimes

withstand dehydration, but many tissues and
structures cannot.
At extreme low temperatures, water freezes within

cells.
Ice crystals expand, which can rupture cells.
As ice forms, remaining cell water has high solute
concentration, which may cause problems of
osmotic regulation.
Organisms adapt to low temperatures by
behavioral changes, such as moving to warmer,
insulated locations (e.g. under the snow at
the ground surface).
producing solutes that prevent formation of ice
crystals (antifreeze).
producing specialized structures that are
dehydrated so ice crystals cannot form (e.g.
seeds).
Responses to temperature
Rates of biological processes have a characteristic
response to temperature.
Rates of enzyme-catalyzed biochemical reactions
follow the same kinetic laws as other chemical
reactions.
Arrhenius equation:
k (Ta ) = Ae
where
E
RTa
k(Ta) = reaction rate at absolute

temperature Ta
A = constant
E = activation energy
R = ideal gas constant
Biologists rarely work with the Arrhenius equation

directly.
Instead they work with the implication that the ratio of
the rate at one temperature Ta2 to the rate at
another temperature Ta1 depends only on the
temperature difference.
k (Ta 2 )
T T
= ( a 2 a1 )
k (Ta1 )
where
= constant derived from the Arrhenius

equation.
This further implies that if you increase the

temperature by a specified difference, the rate
increases by a specified factor.
Biologists measure this increase as Q10:

Q10 = the factor by which rate increase when
temperature increases by 10 C.
For many biochemical reactions, Q10 is about 2 (rate
doubles for every 10 C temperature increase).
For aggregated processes like metabolism,
respiration, development rate, or reproductive
rate Q10 is again roughly 2 (range 1-3).
For organisms whose development rate is a strong

function of temperature (e.g. many ectotherms),
the period of time required for maturity varies with
temperature.
This leads to the concept of physiological time,
measured in degree-days (i.e. a day at 20 C
counts twice as much as one at 10 C).
Biological rates do not increase indefinitely with
temperature.
At sufficiently high temperatures, enzymes are
denatured.
If an organism becomes dehydrated,
physiological rates are often impaired.
Metabolic and genetic regulation is impaired at
high temperature.
Therefore, most biological rates show a unimodal
relationship to temperature.
The following graph shows the rate of population
growth and abundance achieved by populations
of the toxic alga Prymnesium parvum.
from Baker et al., 2001
Temperature and species distribution

At any location, several factors influence the
temperature variation that an organism
experiences.
Factor
Latitudinal /
seasonal
Elevation
Continentality
Microclimate
Depth
Diurnal
Description of variation
These two cannot be separated. The tilt of the
earths axis results in generalized temperature
zones. Hottest temperatures occur in middle
latitudes (38 C) not tropics (35 C). Range of
highest to lowest temperatures is reduced in the
tropics.
Temperature drops 1 C for every 100 m increase
in elevation in dry air and about 0.6 C in moist air.
Land surfaces tend to reflect less heat than water
and quickly warm up; they also cool off more
quickly. Large temperature ranges are usually
found in the interior of continents. Proximity to the
sea reduces temperature variation.
Local variations in temperature occur in relation to
time and position, due to factors such as slope,
aspect, and vegetation cover.
Deep in soil or water temperature ranges are
reduced, and temperatures lag behind those on the
surface. These effects increase with depth.
Daily variation in solar radiation causes daily
variation in temperature.
adapted from Mackenzie et al., 2001
In some cases, the distribution of a species is directly

limited by temperature, i.e. the maximum or
minimum likely to occur at a given location is
lethal.
In other cases, there are indirect temperature effects
on a species performance that make it a poor
competitor or otherwise unable to persist.
In other cases, there are indirect temperature effects
because variation in some other factor is related
to temperature.
For example, at higher temperatures oxygen is
less soluble in water.
Many fish species cannot inhabit warm water
because it will not have enough oxygen for
them.
Only fish species tolerant of low oxygen typically
inhabit warm waters.
In many cases, the proximate limit of a species
distribution is uncertain, but there is a correlation
between its range limit and an isotherm.
Isotherm line on a map joining places that have the
same temperature, usually the same annual
mean temperature.
There are also generalized changes in organismal

characteristics in relation to temperature.
Allens rule endothermic animals (birds and
mammals) from cold climates tend to have
short extremities (limbs, ears, etc.).
Short extremities reduce surface to volume ratio
and reduces heat loss relative to production.
Bergmanns rule endothermic animals from
cold climates tend to be larger.
Geometry dictates that larger objects have lower
surface to volume ratios.
Both rules have many exceptions.
Solar radiation and plants

For plants, light is an energy resource.
Photons are absorbed by pigments such as
chlorophyll a. Thus light is consumed by
shading individuals or leaves below.
The energy of the photons is converted to the energy
of reduced organic compounds such as glucose
by the process of photosynthesis.
h + 6CO2 + 6H2O C6H12O6 + 6O2
Plants, algae, and some bacteria carry out
photosynthesis.
Light is not a simple resource. Instead it is a
resource continuum, distributed continuously
over different wavelengths of the electromagnetic
spectrum.
Visible light is typically defined as that with
wavelengths between 400 and 630 nm.
Photosynthetic organisms use the green pigment

chlorophyll to capture light energy by absorbing
photons.
Wavelengths between 400-500 nm (violet) and
between 600-700 nm (red) are the most
effectively used wavelengths for photosynthesis.
Most photosynthetic organisms have a number of
accessory pigments in addition to chlorophyll
which help to absorb more of the light between
400 and 700 nm.
Therefore, most photosynthetic organisms use at
least some light with wavelengths 400-700 nm,
and this waveband is called Photosynthetically
Active Radiation (PAR).
The spectrum of solar radiation striking the earth has
abundant visible light and PAR.
In aquatic habitats, water absorbs light, limiting

photosynthesis to relatively shallow waters.
Water absorbs different wavelengths unequally.
Violet and red wavelengths that are most
effectively used in photosynthesis are
strongly absorbed.
Green and blue wavelengths transmit more
effectively through water.
Algae living at different depths have different
accessory pigments to try to absorb as much
radiant energy as possible, given what they
receive.
from Jones, 1997
In terrestrial ecosystems there are important

interrelationships between the biochemistry of
photosynthesis, the typical irradiance and
temperature of a habitat, and water availability in
a habitat.
Leaves have a surface that is relatively
impermeable to gases.
In order to carry out photosynthesis, plants need
CO2, and must open pores in their leaves
called stomata.
While CO2 diffuses in, water vapor diffuses out, so
that plants inevitably lose water while
photosynthesizing. This water loss must be
made up for by absorption in the roots.
Habitats that have bright light tend often to be
relatively warm and dry. Thus plants tend to lose
water at the times and places when the most
energy for photosynthesis is available.
Many of the plants that live in hot dry habitats have
biochemical adaptations to avoid drying out.
Normal plants have normal photosynthesis in

which CO2 is first incorporated into a 3-carbon
molecule called phosphoglycerate. Sugars and
carbohydrates are formed by subsequent
reactions. This kind of photosynthesis is called C3 photosynthesis.
Plants with C-3 photosynthesis do not perform well in
tropical habitats because the chemical reactions
involved slow down when the temperature is
above about 28 C.
Also, the C-3 process does not operate well when
CO2 concentration is low, so such plants must
keep their stomata fully open during the day, and
risk losing water.
For these reasons, C-3 plants are found
predominantly in moist, non-tropical habitats.
An alternative method of photosynthesis is the C-4

process, in which CO2 is first incorporated into
phosphoenolpyruvate, and then transferred to
form oxaloacetate, a 4-carbon molecule. Sugars
and carbohydrates are formed by subsequent
reactions.
The formation of phosphoenolpyruvate can take place
at very low CO2 concentrations. This allows
plants to shut their stomata for periods of time,
reducing water loss.
C-4 plants are usually very productive under dry
sunny conditions, and tend to be found in such
habitats.
Many crops that produce well in hot climates are C-4
plants (e.g. maize, millet, sugar cane), so are
many weeds.
Some plants use CAM photosynthesis, in which CO2

is taken up only at night, with the stomata open,
and incorporated into organic acids and stored.
During the day, light energy is used to convert the
organic acids to sugars and carbohydrates.
Stomata are kept closed.
With stomata only open at night when it is cooler,
CAM plants reduce their water loss.
Such plants are common in arid regions, e.g. many
species of cactus do this.
Some CAM plants also use C-3 photosynthesis when
conditions permit this.
Plants have evolved suites of adaptations to sunny or
shady conditions.
Sun plants:
more likely to use C-4 or CAM photosynthesis.
have high maximum rates of photosynthesis.
hold leaves at an acute angle to the sun,
spreading incident radiation over a larger
area.
arrange leaves in a multi-layer canopy.
Shade plants:
more likely to have C-3 photosynthesis.
have low maximum rates of photosynthesis.
use low levels of irradiance more efficiently.
Also, individual plants often produce both sun and

shade leaves for different locations within the leaf
canopy.
Sun leaves:
smaller, thicker, denser, more cells, more
chloroplasts, more veins.
Shade leaves:
larger, translucent, less dense, lower rate of
photosynthesis.
The energetic efficiency of photosynthesis can be
calculated theoretically.
To make one molecule of glucose, 24 electrons
must be energized twice, so 48 photons
must be absorbed.
The energy of these photons varies inversely with
wavelength, but is a minimum of 172 kJ per
mole of photons.
Therefore, at least 8256 kJ of radiant energy
must be absorbed per mole of glucose
formed.
Free energy of formation of glucose is 2872 kJ
per mole.
Efficiency = 2872 / 8256 = 35%
In reality, this theoretical efficiency of photosynthesis

is never achieved.
Of the radiant energy arriving at a 1 m2 surface
occupied by vegetation, less than about 3%
is converted to the chemical energy of
organic matter.
Much of the energy is not absorbed by
photosynthetic pigments.
Either it passes through the vegetation or it is
absorbed by other cellular components and
structural materials (e.g. stems).
Rate of photosynthesis by a plant depends on water
and CO2 availability, in addition to light energy.
Plants reduce the rate of photosynthesis if
their energy needs are low.
opening the stomata risks too much water loss.
CO2 is at low concentration (a problem for
aquatic plants and algae in water, at times).
Sources and cycles of nutrients

A long list of elements is known to be essential to
living matter.
Bulk elements, present in relatively high
proportions: C, H, O, N, P, S.
Elements occurring as ions, present in varying
proportions: Na, K, Mg, Ca, Cl.
Trace elements, typically present in very low
proportions: Fe, Cu, Zn, Mo, Co, I, Mo, V, Ni,
Cr, F, Se, Si, Sn, B, As.
Not all types of organisms require all of the trace
elements, and some of these elements are toxic
in high concentrations.
At regional and global scales, nutrient elements flow
in biogeochemical cycles.
Nutrient elements are absorbed by plants, algae, or
microorganisms. These organisms are consumed
by other organisms.
Death, decomposition, and excretion of wastes return
nutrient elements to the environment.
Nutrient elements also cycle geologically, from rocks
and soil, to water, maybe to air and back again.
Heavy metal contaminants often have cycles
resembling those of chemically similar nutrients.
Considerations involved in studying biogeochemical

cycles of elements include:
Chemical forms (species) involved
The compartments present in the environment
Processes transferring materials between
compartments
Chemical transformations during such processes
Many elements occur in several chemical forms:
Organically bound forms in living things and
detritus.
Inorganic forms can include ionic forms (which
are often dissolved in water), gaseous forms,
and solid crystalline forms.
Chemical forms can change as a result of
precipitation-dissolution reactions, acid-base
reactions, and oxidation-reduction reactions.
Some of these are biochemical reactions carried
out by organisms.
Many compartments occur in the environment.
These are places where an atom of an element
may reside for a greater or lesser length of time.
On a global scale, we can recognize 4 compartments:
The hydrosphere oceans and fresh waters
The atmosphere
The lithosphere -- land
The biosphere all living things
Most of the earths surface is covered with ocean

water, and collectively the oceans hold huge
amounts of biologically important elements.
Inputs of materials from land occur along the coasts,
and exchanges with air take place over the entire
ocean surface.
Output occurs when materials sink to the sediments
and are buried. Once buried, materials may
return to land only over geological time, when
marine sediments are uplifted during mountainbuilding.
The large mass of elements stored in the oceans
implies that they respond only very slowly to
changes in inputs and outputs.
The residence time (average time that an atom
spends in a compartment) for most elements in
the oceans is typically 100s to 1000s of years.
Fresh waters have much lower volume than the
oceans, and much greater surface area in
proportion to volume.
Because inputs and outputs occur along the surfaces,
they respond much more rapidly to changes in
these processes.
Residence times of elements in freshwater aquatic
ecosystems are typically < 100 years, and may
be shorter (a few days or less).
The lithosphere consists of rocks and soils. Soil

consists of weathered bedrock, plus organic
matter that originates from dead material.
The type of soil that develops in an area depends on
the underlying bedrock, climate, topography, and
the living things present.
Soils develop over time, and go through long periods
of change after the creation of bare rock or after
major disturbances.
Movement rates of materials in soil and rock are slow
compared to rates in water or air.
Soil water and groundwater are critical to transfers of
materials.
Water leaches (dissolves) materials out of soil and
rock, and transports materials within the
lithosphere, or to the hydrosphere.
The atmosphere consists of layers of different
temperatures and pressures. Living things are
directly in contact with the troposphere, which is
at the bottom and contains the greatest mass of
materials.
The stratosphere above it is important as the site of
the ozone layer, which shields the biosphere
from solar ultraviolet radiation. Without the ozone
layer, survival of many living things would be in
jeopardy.
Partial degradation of the ozone layer has been

caused by chlorofluorocarbons released from
human activity.
In the 1980s their manufacture was reduced in
accordance with the Montreal protocol. Recently,
recovery in the ozone layer has been
documented.
Movement rates of materials in the atmosphere are
very rapid, and natural substances and
contaminants are widely transported over
continental distances.
The biosphere consists of all living things.
Collectively, living things exert strong influences
over the movements and transformations of
materials on the earths surface.
Some of the processes and transformations involved

in biogeochemical cycling are illustrated in this
figure:
Cycles of particular elements and substances
The water cycle is linked to the cycles of many other

substances, due to the importance transport in
the dissolved phase, especially for ionic chemical
forms.
from Ricklefs, 1979
The Carbon Cycle

In a sense, there are two carbon cycles.
1. Slow geological cycle, involving acid-base
reactions and precipitation-dissolution reactions.
Atmospheric CO2 dissolves into water.
CO2 in water hydrates to H2CO3, carbonic acid.
Carbonic acid can lose two protons successively
to form bicarbonate and carbonate ions.
Carbonate ions can precipitate with calcium ions
to form calcium carbonate, CaCO3.
CaCO3 sinks to sediments and is compressed
into rock.
Uplift raises carbonate rocks, and then
weathering, erosion, and runoff transport
ions to water.
Ca+2, HCO3-, CO3-2
CaCO3
Rocks & Soils
Weathering & Runoff
CO2
Water Surface
CO2
H2CO3
HCO3-
CO3-2
CaCO3
Sedimentation
Rock Formation
Uplift
2. Fast biological cycle, involving oxidation-reduction

reactions.
Photosynthesis by plants, algae, and
photosynthetic bacteria reduces CO2 to
carbohydrates and other organic matter.
h + 6CO2 + 6H2O C6H12O6 + 6O2
This organic matter is oxidized back to CO2 when
organisms use the energy of organic matter.
Many organisms use aerobic respiration:
C6H12O6 + 6O2 6CO2 + 6H2O
In the absence of oxygen, various series of other
reactions are used to oxidize organic matter.
Plants respire some of the organic matter they
produce by photosynthesis.
Herbivores and carnivores also respire some of the
organic matter they consume in food.
Excreted wastes and dead bodies are decomposed,
which also oxidizes organic matter.
Decomposition
Carnivores
Decomposers
(bacteria &
fungi)
Herbivores
CO2
Respiration
Plants &
Algae
Photosynthesis
Over daily time scales, photosynthetic organisms

remove CO2 from air and water and reduce it to
organic matter.
About equally rapidly, much organic matter is oxidized
by respiration to meet the energetic needs of
organisms.
Over longer time scales (years to decades), C is
stored in the tissues of long-lived organisms
(especially trees) and in detritus (dead material)
in soils and aquatic sediments. Eventually most
of this C is oxidized to CO2 by decomposition.
A small fraction of detritus does not completely

decompose and is eventually buried in
sedimentary rocks, and forms oil and coal.
Thus the biological carbon cycle intersects the
geological carbon cycle.
Under pre-industrial circumstances, very small
amounts of petroleum were brought to the
surface (in oil seeps, etc.) and oxidized to release
CO2.
Modern industry releases C from petroleum at
unprecedented rates. CO2 is increasing steadily
in the atmosphere, and is expected to increase
the average temperature of the atmosphere by
0.5-2.
Atmospheric CO2 traps outgoing infrared radiation,
affecting the net radiation balance of the planet
(greenhouse effect).
Another intersection between the biological and

geological carbon cycles involves calcifying
organisms.
Precipitation of carbonate minerals is often initiated by
calcifying organisms (plants, animals and
microorganisms) that form hardened walls or
shells.
Deposition of such biogenic carbonate in productive
aquatic habitats leads to formation of limestone
and related rocks.
The C content of such rocks is a large reservoir of C,
in addition to that in the atmosphere, dissolved in
water, bound in organisms, and in petroleum.
from Ricklefs, 1979
The Nitrogen Cycle

This cycle is notable for the large number of chemical
transformations that take place, the roles of
specialized bacteria that perform these
transformations, and the great importance of the
atmospheric reservoir of N2.
N2 composes about 80% of the atmosphere, and the
atmosphere holds most of the earths nitrogen.
Most of this N is unavailable to almost all types of
living organisms. Most plants and
microorganisms must obtain N in the form nitrate
(NO3-) or ammonium (NH4+) dissolved in water.
Many animals and microorganisms obtain N
primarily in the form of amino acids (R-NH2) in
their food.
In living things, N occurs mainly as proteins
(composed of amino acids) and as nucleic acids,
such as DNA, which make up the genes.
Blue-green algae (cyanobacteria) and some other

types of bacteria can reduce atmospheric N2 to
NH3. The NH3 is incorporated into amino acids.
This reaction is called nitrogen fixation.
Cyanobacteria are the most important N-fixing
organisms in aquatic habitats. When consumers
eat them, N is cycled into the biosphere.
On land, bacteria are the most important N-fixing
organisms. They often live symbiotically with
plants, in root nodules or other structures. They
receive carbohydrates from plants and supply
fixed N in return. Plants with this relationship,
such as legumes, are often found in soils poor in
N, where this relationship is a competitive
advantage.
When animals consume organic matter with excess
amino acids, or when bacteria decompose such
matter, NH3 (or a waste product at the same level
of oxidation) is often released (ammonification).
An example reaction is
C2H5NO2 + 1 O2 2CO2 + H2O +NH3
Specialized bacteria oxidize ammonia, eventually to
nitrate, in the nitrification reactions:
NH3 + 1 O2 HNO2 + H2O
KNO2 + O2 KNO3
Nitrate (a dissolved form) is converted to gaseous

forms in the denitrification reactions, which
certain bacteria carry out under anaerobic
conditions. This is an important means of
decomposition (oxidation) of organic matter
without oxygen, as nitrate is used as an electron
acceptor.
C6H12O6 + 6KNO3 6CO2 + 3H2O + 6KOH + 3N2O
5C6H12O6+24KNO3 30CO2 + 18H2O + 24KOH +
12N2
Nitrogen moves among the various compartments of
the environment, with these chemical
transformations occurring at critical steps.
Graphical summary of the nitrogen cycle
from Schlesinger, 1997
The Phosphorus Cycle

Phosphorus in the environment occurs almost
exclusively as the non-volatile phosphate ion
(PO4-3).
Oxidation/reduction reactions are not directly
important, nor is the atmosphere.
Living things incorporate PO4 groups in a wide variety
of biochemicals: nucleic acids, phospholipids
(which compose cell membranes), bones, the
energy carrier molecule ATP, and many others.
Phosphate weathers out of rocks and soils. It is taken
up by plant roots, and by aquatic algae and
microorganisms.
When these organisms are consumed, phosphate is
often released in excreted wastes, and
phosphate is released by decomposition. It is
then available for uptake again.
Such cycles may take place rapidly and repeatedly.
Small fractions of phosphate are buried in
sediments, form rock, and only weather out again
after millions of years.
The phosphorus atoms do not generally participate in

redox reactions in the environment. However,
redox reactions of other constituents in soils and
sediments do strongly affect the availability of
phosphate to plant roots and microorganisms.
For example, reducing conditions prevail below the
sediment-water interface in aquatic systems.
Under these conditions, iron and manganese are
soluble, and dissolved phosphate is often present
at high concentrations.
When the sediment-water interface is oxidized, iron
and manganese form solid oxyhydroxides that
sorb phosphate, and keep its dissolved
concentration low.
If the sediment-water interface is reduced due to
anaerobic conditions, iron, manganese, and
phosphate are released to the overlying water.
These substances then become available for
uptake by aquatic microorganisms.
Graphical summary of the phosphorus cycle:
Eutrophication
The N and P cycles are greatly altered by human
activities.
Fertilizer production is now massive compared to
natural N fixation and weathering of P. Large
amounts of fertilizer spread on land eventually
wash into lakes, rivers, and coastal oceans.
Burning of fossil fuels releases nitrogen oxides, which
enter rainwater, form nitrate, and are deposited
on the earths surface.
Intensive animal husbandry produces ammonia
vapors that also dissolve in rainwater and are
deposited.
Availability of N and/or P often limits the productivity
of autotrophs in ecosystems.
Excessive fertilization resulting from human activity
has many adverse consequences.
In terrestrial ecosystems, it causes plant species
replacements and changes in vegetation
composition.
The effects in aquatic ecosystems are better known,

however. Excessive nutrients stimulate the
proliferation of undesirable algae.
In freshwaters, cyanobacteria are often stimulated.
These algae can form unsightly scum, and are
poor food for aquatic herbivores, compared to
other types of algae.
In coastal marine systems, blooms of toxic algae (red
tides and brown tides) can occur. They poison
marine animals, and can be deadly to humans
who consume tainted seafood.
The Sulfur Cycle
Sulfur is a relatively common element on the earths
surface. Sulfate (SO4-2) is a major ionic
constituent of ocean water and of most inland
waters.
Sulfur in living things is mostly in a reduced chemical
state. The organic sulfhydryl group (-SH) is an
important constituent of many proteins.
Plants and many microorganisms take up SO4-2 and
reduce it as it is incorporated into organic matter
(reductive sulfate assimilation).
Animals typically consume sulfur in their foods.
Many decomposers release excess sulfur as SO4-2, in
a dissimilatory oxidation process.
When organic matter is decomposed anaerobically,

some bacteria can use SO4-2 as an electron
acceptor. Such sulfate-reducing bacteria often
release hydrogen sulfide (H2S) as an endproduct.
Chemosynthetic bacteria can do the reverse. H2S
serves as an electron donor, to reduce CO2 in the
production of organic matter, releasing SO4-2.
Some chemosynthetic bacteria can also oxidize
sulfide or elemental sulfur in minerals, releasing
SO4-2. This release may acidify streams draining
regions rich in sulfide minerals. Such acid
drainage may also occur where sulfide rich
tailings (wastes) from mining have been
dumped.
In addition to H2S, organisms produce other biogenic

sulfur gases. Dimethylsulfide (DMS) is produced
in cells of some marine algae.
When released to the water, DMS volatilizes, and is
eventually oxidized to sulfate.
Sulfate in the atmosphere can nucleate the
condensation of water vapor. It has been
suggested that the activities of marine algae have
a strong influence on cloudiness over the oceans
by this mechanism. If so, the resulting changes in
the earths albedo could affect climate, and
perhaps influence the greenhouse effect.
Currently, too little is known about rates of DMS
volatilization and oxidation over the ocean to
evaluate this suggestion.
Human alteration of the sulfur cycle is extensive, due
to combustion of fossil fuels, which releases
sulfate. This generates acidity in rain and in dry
deposition (dust and ash).
Combustion of fossil fuels also releases nitrogen
oxides that oxidize to nitrate, which also
generates acidity.
Acid rain can
acidify some aquatic systems, killing some
organisms directly.
solubilize toxic metal ions from soils and
sediments, killing more organisms (esp. fish).
corrode concrete and limestone structures.
Graphical summary of the sulfur cycle:
Plants and consumers

Plants, algae, and some bacteria are autotrophic.
They produce organic matter from CO2 by
reducing it. This requires an input of energy, and
a source of electrons.
Photosynthesis is the most important autotrophic
process. Sunlight is used a source of energy, and
water is used as a source of electrons. Oxygen is
an end product. Photosynthesis often produces
carbohydrates such as glucose:
h + 6CO2 + 6H2O C6H12O6 + 6O2
In nearly all such organisms, light energy is trapped
by the pigment chlorophyll a and other accessory
pigments, used to remove electrons from water,
energize them, and then reduce CO2.
Chemosynthesis is carried out by some specialized
types of bacteria, by using a highly reduced
chemical compound as a source of energy and
electrons. In environments where sulfide is
available, a chemosynthetic reaction is
6CO2 + 6H2O + 6H2S + 6O2 C6H12O6 + 6H2SO4
Autotrophs are also called primary producers.

The total amount of energy produced by autotrophs is
called gross primary production (GPP).
Some of this energy is used by the autotrophs
themselves for their own maintenance, and the
balance is called net primary production (NPP).
All heterotrophs in an ecosystem ultimately rely on
NPP. They consume it and oxidize some of it to
obtain energy, while repackaging some of it as
the organic compounds of their own cells and
bodies.
The amount of repackaged organic matter produced
by heterotrophs is called secondary production.
Some heterotrophs are herbivores, or primary
consumers, obtaining organic matter by directly
ingesting autotrophs.
Heterotrophs that consume herbivores are called
secondary consumers, those that consume
secondary consumers are called tertiary
consumers, and so on.
All organisms produce non-living matter called
detritus, in the form of dead bodies, tissues that
are shed while alive, and feces and liquid wastes.
Animals that consume detritus are called
detritivores. Microorganisms that consume
detritus are sometimes called saprotrophs.
Collectively, organisms that rely on detritus are
often called decomposers.
All organisms also produce waste heat, which is

essentially an energy loss from the ecosystem.
This picture summarizes these energy flows (each
box is called a trophic level):
Energy input (E)
Primary Producers
Heat
Detritus
Energy transfer
Primary Consumers
Heat
Heat
Detritus
Secondary
Consumers
Detritus
Tertiary
Consumers
Detritus
Decomposers
Heat
Heat
The flow of energy here is paralleled by the flow of

carbon.
Primary producers take CO2 and convert it to energyrich organic compounds.
These compounds pass to consumers and to
decomposers.
Production of heat during metabolism is accompanied
by release of CO2, completing the biological
carbon cycle.
Flows of other elements (e.g. N, P, S) also run

parallel to those of energy and carbon.
In most ecosystems, much of the energy and
materials reside in detritus and in decomposers
consuming the detritus.
The release of elements from detritus by
decomposers is essential to the biological cycling
of nutrients, and makes them available for
autotrophs to use.
In aquatic habitats, some of the detritus is in the
form of dissolved organic matter, and some
of the decomposers are microorganisms
suspended in the water.
But more detritus and more decomposers are
typically found in the sediments.
In terrestrial habitats detritus and decomposers
accumulate on the ground and contribute to
soil formation.
Soil formation, properties, and classification

The physical properties of soil or sediment particles
are important conditions for many organisms that
attach or burrow.
Chemical properties may also be important, and
influence such things as adhesion properties, and
availability of nutrients.
Some organisms are adapted to living on or among
large rocks, and cannot tolerate the abrasion
caused by the shifting grains of sediments.
Particle size is an important characteristic of soils and
sediments. The basic classification of soils
begins with particle size:
from Jones, 1997
Soil particle size covaries with soil organic matter

content. Coarse soils and sediments tend to have
low organic content
Large particle size and low organic content leads
to soils and sediments that are unstable and
move around. The resulting abrasion may
prevent some organisms from surviving.
Soils with small particle size and high organic
content bind together and are more stable.
Soils with large particle size and low organic
content dry out quickly and often have low
water content.
Soils with small particle size and high organic
content retain water by capillary action and
tend to be moister.
However, movement of water in soils of small particle
size is restricted, and aeration may be poor.
Many animals that live in mud or silt (with small
particle sizes) must dig tunnels or burrows to
circulate water to obtain oxygen.
Soils consist of weathered bedrock minerals, and

organic matter that derives largely from
vegetation. The weathered minerals in soils are
often various types of clay, but composition
varies widely and depends on bedrock materials.
Weathering also depends on rainfall, temperature,
and vegetation type (i.e. whether a lot of organic
acids are produced by plants and microbes).
In many types of soils, more or less distinct layers
called horizons occur.
A horizon has much organic matter, including
undecomposed plant litter and partially
decomposed humus; also contains mineral
particles; contains shallow plant roots; highly
soluble substances are somewhat depleted by
leaching.
B horizon contains more mineral matter, including
clay minerals formed reactions with bedrock
minerals; substances from above often deposited
here; contains some humus and plant roots.
C horizon contains primarily weathered bedrock
minerals, formed by oxidation or by deposition of
evaporites in dry climates; has fewer plant roots.
R horizon parent material, or bedrock.
References:
Baker, J.W., J.P. Grover, B.W. Brooks, F. UreaBoeck, D.L. Roelke, R. Errera, and R.L. Kiesling.
2007. Growth and toxicity of Prymnesium parvum
(Haptophyta) as a function of salinity, light and
temperature. Journal of Phycology 43: 219-227.
Jones, A.M. 1997. Environmental Biology. Routledge
Press, London & New York.
Kirk, J.T.O. 1983. Light and Photosynthesis in Aquatic
Ecosystems. Cambridge University Press,
Cambridge.
Lehninger, A.L. 1982. Principles of Biochemistry.
Worth Publishers Inc.
MacKenzie, A., A.S. Ball, & S.R. Virdee. 2001. Instant
Notes in Ecology, 2nd ed. BIOS Scientific
Publishers, Oxford.
Press, F., & R. Siever. 1978. Earth, 2nd ed. W.H.
Freeman & Co., San Francisco.
Ricklefs, R.E. 1979. Ecology, 2nd ed. Chiron Press,
N.Y.
Schlesinger, W.H. 1997. Biogeochemistry. Academic
Press, San Diego.

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EVSE 5309 Physical Environment, p.

EVSE 5309 Environmental Systems

EVSE 5309 Physical Environment, p. 2

The incorrect uses of the words adapt and

EVSE 5309 Physical Environment, p. 3

Coping with environmental variation

EVSE 5309 Physical Environment, p. 4

Homeostasis is a key concept of physiological

EVSE 5309 Physical Environment, p. 5

Example regulation of blood osmolarity in a

from Mackenzie et al., 2001

EVSE 5309 Physical Environment, p. 6

Conditions and Resources

EVSE 5309 Physical Environment, p. 7

Resource = an environmental variable to which an

EVSE 5309 Physical Environment, p. 8

The Ecological Niche

EVSE 5309 Physical Environment, p. 9

from Mackenzie et al., 2001

EVSE 5309 Physical Environment, p. 10

Other ideas related to the concept of the niche

EVSE 5309 Physical Environment, p. 11

The principle of competitive exclusion says that two

EVSE 5309 Physical Environment, p. 12

But, contemporary research is moving from abstract

EVSE 5309 Physical Environment, p. 13

Note that Liebigs Law applies to what happens when

EVSE 5309 Physical Environment, p. 14

Shelfords Law is associated with a generalized

from Jones, 1997

In the zone of tolerance, performance is high

EVSE 5309 Physical Environment, p. 15

Many variations in the shapes of these curves can be

For many resources, no upper incipient lethal level

K = resource level when

EVSE 5309 Physical Environment, p. 16

Solar Radiation and Climate

from Mackenzie et al., 2001

EVSE 5309 Physical Environment, p. 17

As a result of this geometry, total solar radiation

from Kirk, 1983

EVSE 5309 Physical Environment, p. 18

Over a day, solar radiation varies with time of day and

from Kirk, 1983

EVSE 5309 Physical Environment, p. 19

Most sunlight passes through the atmosphere, so little

EVSE 5309 Physical Environment, p. 20

As warmed air in one location rises, it is replaced by

EVSE 5309 Physical Environment, p. 21

from Mackenzie et al., 2001

In reality, wind patterns are not symmetric north-south

EVSE 5309 Physical Environment, p. 22

Ocean currents also distribute heat around the earth.

from Press & Siever, 1978

EVSE 5309 Physical Environment, p. 23

Drifts (consistent currents) would correspond to trade

from Press & Siever, 1978

EVSE 5309 Physical Environment, p. 24

There are also vertical ocean currents.

EVSE 5309 Physical Environment, p. 25

Earths is warmer at the equator, and cooler towards

from Jones, 1997

EVSE 5309 Physical Environment, p. 26