Fundamentals of Aquatic Ecology - GXLIBUNAO - Compressed

Lecture Notes in
AQUATIC RESOURCES AND ECOLOGY

Mentor: GARDEL XYZA LIBUNAO
4 SEPTEMBER 2021
Click to edit Master title style AQUATIC RESOURCES

AND ECOLOGY
FUNDAMENTALS OF AQUATIC
ECOLOGY
GARDEL XYZA LIBUNAO
Lecture 6
04 September 2021
ONLINE MENTORING PROGRAM

Licensure Examination for
1
FISHERIES TECHNOLOGISTS 2021
Click to edit Master title style

Learning points
What is ecology?
Definitions
Biological organizations
Biotic and Abiotic
Species interaction
Ecological succession and adaptation
What is an ecosystem?
Flow of energy and materials
Specialist feeding mechanisms
Population Dynamics in Ecosystem
Biodiversity in Ecosystem
Reproduction and life histories
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Fisheries Development Network

Licensure Exam for Fisheries Technologists
Lecture Notes in
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Ecology
Interaction of organisms and environment
• branch of biology that studies how and why organisms interact with each other and with their environment
(Webster’s Unabridged Dictionary).
• branch of biological science concerned with the distribution, abundance, and productivity of living organisms,
and their interaction with each other and with their physical environment.
• “Ecology” from two Greek roots: oikos, meaning “house or household” or “place to live” and ology, meaning
“study of.”
1. Ecology is the study of the relationship of an organism to both biotic (living) environment and its abiotic
(physical) environment (Ernst Haeckel).
2. Ecology is the study of organisms “at home” and is usually defined as the study of the relation of organisms or
group of organisms to their environment, or the science of the interrelations between living organisms and
their environment (Eugene P. Odum).
3. Ecology as the scientific study of interactions that determine the distribution and abundance of organisms
(Krebs).
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Ecology
Main branches of ecology
1. Autecology deals with the study of the individual organism or individual species. Life histories and behavior as a
means of adaptation to the environment are usually emphasized.
2. Synecology deals with the study of groups of organisms which are associated together as a unit. For example,
the study of the forest.
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Ecology
Biological organization
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Ecology
Biotic and abiotic components
• The nature of life (biotic component) in a particular habitat (a

place where an organism lives) is determined to a large extent
by the non-living, or abiotic, part of the environment (physical
and chemical features such as salinity or bottom type).
• Each environment has different characteristics that present
both challenges and opportunities for the organisms living
there.
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Ecology
Species Interaction
• Organisms are also affected by other organisms—the

living or biotic, environment. Biological populations
interact in complex ways that make the organisms in a
community dependent on each other.
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https://www.researchgate.net/figure/The-interaction-compass-A-two-species-interaction-is-
illustrated-with-the-terms-defining_fig1_309034853

Ecology
Species Interaction
COMPETITION
• interaction that results when a resource is in short supply
and one organism uses the resource at the expense of
another
• When members of the same species compete it is called
intraspecific competition. Competition between species is
known as interspecific competition.
• Competitive exclusion – says that one is certain to become
extinct if two species are competing for the same resource in
a homogenous and constant environment.
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http://pediaa.com/wp-content/uploads/2018/09/Difference-Between-Interspecific-and-Intraspecific-
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https://nanopdf.com/download/ammensalism_pdf

Ecology
Species Interaction
AMENSALISM
• A type of biological interaction where one species causes harm to another organism without any cost or benefits to itself.
• Example: Algal blooms can lead to the death of many species of fish, however the algae do not benefit from the deaths of
these individuals.
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Ecology
Species Interaction
PREDATION
• act of one organism eating another. The organism that does the eating is the
predator, and the organism that gets eaten is the prey. Herbivory is a special
case of predation that occurs when organisms eat algae or plants.
• Prey exhibit a wide variety of anti-predator defenses involving modifications in
behavior, morphology and life history that reduce their vulnerability to
predators:
1. Constitutive defenses – expressed at all times
Example: Surgeonfish have brightly colored, scalpel-sharp spines at the base
of their tail. Boxfishes and seahorses have armored scales.
2. Inducible defenses – expressed only when predators are present
Example: Pufferfish will “puff up” if they are threatened.
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Ecology
Species Interaction
PREDATION
• act of one organism eating another. The organism that does the eating is the
predator, and the organism that gets eaten is the prey. Herbivory is a special
case of predation that occurs when organisms eat algae or plants.
• Prey exhibit a wide variety of anti-predator defenses involving modifications in
behavior, morphology and life history that reduce their vulnerability to
predators:
1. Constitutive defenses – expressed at all times
Example: Surgeonfish have brightly colored, scalpel-sharp spines at the base
of their tail
Boxfishes and seahorses have armored scales.
2. Inducible defenses – expressed only when predators are present
Example: Pufferfish will “puff up” if they are threatened.
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https://www.seriousfacts.com/wp-content/uploads/2017/12/Puffer-fish-do-not-have-scales..jpg
https://www.quora.com/Nature-What-allows-a-puffer-fish-to-inflate

Ecology
Species Interaction
PREDATION
• There is a continual “arms race” between predators and
their prey. The predator keeps getting better at catching
the prey and overcoming its defenses. In response, the
prey becomes more adept at escaping or develops
better defenses. This interplay, with each species
evolving in response to the other, is known as
coevolution.
• Natural selection, therefore, favors the most efficient
predators in the population and at the same time favors
prey that are most successful at getting away.
• Example: Knifefish prey on native fish species in Laguna
de Bay. (Watch:
https://www.youtube.com/watch?v=27FQegUa6B0)
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https://medium.com/@michaelajyramelo
http://www.savethestan.org/predation/

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Ecology
Species Interaction
SYMBIOSIS
• “living together” – close relationship between two different species.
The smaller partner in the symbiosis is usually called the symbiont
and the larger one the host.
1. Commensalism - one species obtains shelter, food, or some other
benefit without affecting the other species one way or the other.
• OUTSIDE THE BODY: Host species provides a home and/or
transportation for the benefited species. Example: Barnacles
which attached themselves to the back of whales. Remoras are
fish that attach themselves to the belly of sharks by means of a
modified dorsal fin that acts as a suction cup. The remoras
obtain a free ride and also feed on the remains of the shark’s
prey.
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https://www.treehugger.com/remora-fish-suckers-sea-inspiring-new-adhesives-4858201
https://www.sciencenews.org/article/barnacles-track-whale-migration

Ecology
Species Interaction
SYMBIOSIS
1. Commensalism
• INSIDE THE BODY: Inquilism - one species lives within but
does not harm another species. Example: Pearl fish of the
family Carapidae are inquilines, living within holothurians
(live in intestines, enter and exit through anus),
echinoderms (oral cavity), or molluscs (mantle).
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Ecology
Species Interaction
SYMBIOSIS
2. Parasitism - the symbiont benefits at the expense of the host. Usually, the host is
larger than the parasite, and the parasite does not immediately kill the host.
While viruses are the only group of organisms that are obligate parasites (cannot
live outside the host), there are also parasites among bacteria, protista, plants
and animals.
• The smaller parasites tend to be endoparasites that live within the bodies of the
hosts.
• The larger parasites tend to be exoparasites (or ectoparasites) that remain
attached to the exterior of the host by means of specialized organs.
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https://www.parasitol.kr/m/journal/view.php?number=2380
https://zslpublications.onlinelibrary.wiley.com/doi/abs/10.1111/jzo.12674
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Ecology
Species Interaction
SYMBIOSIS
3. Mutualism, both partners benefit from the relationship
• Cleaning Symbiosis is a phenomenon believed to be quite common
among marine organisms. There are species of small fish and shrimp
that specialize in removing parasites from larger fish. The large fish
line up at the “cleaning station” and wait their turn, while small fish
feel so secure they even clean
the mouths of the larger fish. Not everyone plays fair, however, since there are small fish that mimic the cleaners and
take a bite out of the larger fish, and the cleaner fish are sometimes found in the stomachs of the fish they clean.
• Resource partitioning - Species can also avoid excluding each other if they share the limiting resource, with each
species specializing on just part of the resource.
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https://socratic.org/questions/580a7ba3b72cff7dac167dad

Ecology
Ecological succession
• Ecological niche – the role a species play in a community.

• While habitat is the organism’s address (where it lives), ecological niche is its profession (what it does
biologically). This includes the feeding habits, habitat and all other aspects of the species’ lifestyle
• Competitive exclusion – Coexisting species must differ in their niche vs Resource partitioning – Coexisting
species share. What will happen if they compete?
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Ecology
ECOLOGICAL SUCCESSION / DEVELOPMENT

• The process by which organisms occupy a site and gradually change environmental conditions so that
other species can replace the original inhabitants.
1. Primary succession occurs when a community beings to develop on a site previously unoccupied by living
organisms, such as on Island, a sand or silt bed, a body of water or a new volcanic flow
2. Secondary succession occurs when an existing community is disrupted and a new one subsequently develops at
the site. The disruption may be caused by some natural catastrophe, such as fire or flooding, or by a human
activity, such as deforestation, plowing or mining.
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https://upload.wikimedia.org/wikipedia/commons/4/47/Secondary_Succession.png

Ecology
ECOLOGICAL SUCCESSION / DEVELOPMENT

• Both forms of succession usually follow an orderly sequence of stages (called sere) as organisms modify the environment in
ways that allow one species to replace another
• Eventually in either primary or secondary secession a community develops that seemingly resists further change. Ecologists
call this a climax community, because it appears to be the culmination of the succession process.
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Ecology
Models of Succession:
• Facilitation – colonists prepare environment for later
successional species
• Tolerance – modifications that early successional species
impose on environment neither increase nor reduce rates
of recruitment and growth of later successional species;
species sequence is solely a function of life history – any
species can start succession and the competitively superior
species prevail
• Inhibition – once early colonists secure a place and/or
resources, they inhibit subsequent invasion by other
species or suppress the growth of species invading at the
same time
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Ecology
Ecological succession is dictated by how organisms respond and adapt to external environment:
• Organisms respond to the environment in three principal ways:
1. Morphological adaptation - The variety of teeth found in mammals, and lizards, the variation in shape and size of
gills of birds, the different mouth parts of Insets.
2. Physiological adaptation - Structural adaptation for the digestion of food, respiration circulation and excretion
3. Behavioral adaptation - It is the change in behavior of an organism to adapt itself to the conditions of the
environment
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Ecology
Adaptive strategies of animals

1. Bergman’s rule: is connected with heat loss and heat
conservation. It states: As a rule, geographical species
possessing smaller body sizes are good heat dissipaters. On
the other hand geographical species, which have larger body
sizes, are good heat conservers. Because of this those
organisms possessing relatively larger body sizes are found in
the colder regions.
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Ecology

1. Bergman’s rule:
2. Allen’s rule: just like Bergman’s rule this is connected with
heat loss and heat conservation. According to Allen’s rule,
organisms possessing larger body sizes but relatively short
appendage extremities or protruding parts are found in
cooler regions whereas organisms possessing smaller body
sizes with larger appendages extremities or protruding
parts are found in the warmer regions.
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Ecology

3. Gloger’s rule: states that races of warm-blooded animals are more dark-
pigmented in the warm and humid areas whereas organisms living in the
dry and cool areas are less pigmented.
4. The egg rule: the average number of eggs in a set, or clutch, laid by
songbirds and several other kinds of birds increases as one moves north
in latitude
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Ecology
Range and limits – plant and animal species have optimal ranges
that restrict their distribution around the world. This fact is
explained by:
• Liebig’s Law (Law of the minimum) - “The rate of growth of each
organism is limited by whatever essential nutrient is present in a
minimal amount”. The law can also be stated as “the functioning of
an organism is controlled or limited by essential environmental
factor or combination of factors present in the least favorable
amount in the environment”. Example: The yield of crops is often
limited not by nutrient required in large amounts, such as water or
carbon dioxide, but by something needed only in trace amounts such
as nitrate or phosphate.
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Ecology
Range and limits

2. Shelford’s Law (Law of tolerance) - For each species, there
is a range of an environmental factor with in which the
species functions at or near optimum. There are
extremes, both maximum and minimum towards which
the functions of a species are curtailed and then inhibited.
• Upper and lower limits of tolerance are intensity levels of a
factor at which only half of the organisms can survive
(LD50). Terms to express the narrowness and wideness of
tolerance (prefixes):
• Steno: narrow range of tolerance (example: stenothermal-
narrow range of tolerance for heat)
• Eury: wider range of tolerance (example: Eurythermal-wider
range of tolerance for heat)
https://www.researchgate.net/profile/Costamagno-
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Ecology
Speciation – splitting of one set of interbreeding populations constituting a species into two or more sets,
each reproductively isolated. It requires the development of a genetic difference between a group of
individuals and the remainder of the parent species. There has to exist some restriction in gene flow between
the group sharing this genetic feature and the rest of the ancestral stock.
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Ecology
Several ways in which speciation takes place:

Allopatric speciation – existing species are separated by a
physical barrier, so that they occupy a non-overlapping area.
The barrier prevents the migration between populations and
so restricts or eliminates gene flow. Each population then
evolves in response to local selection processes, which are
likely to differ between the two areas or diverges as a result
of chance. In time, the populations will become genetically
distinct
Sympatric speciation – occur without the need for geographic separation of populations. A genetic or behavioural
change affecting a subgroup results in the partial restriction or complete cessation of gene flow, despite the fact that it
continues to occupy part of the range of the ancestral stock
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Ecosystem (Ecological system)

• any unit that includes all the organisms (i.e. the “community) in a given area interacting with the physical
environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity (i.e. the variety of
plants, animals, organisms and all other life forms, including humans) and material cycles (i.e. exchange of
materials between living and non-living parts) within the system.
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Ecosystem
Flow of energy
• Energy flow is the transfer of energy through an ecosystem.

When one organism eats another, both the organic material
and the energy stored in it are passed from one to the other.
Thus, energy and chemical substances flow from the non-
living part of the ecosystem to organisms and from organism
to organism.
• The flow of energy and matter through an ecosystem can be traced
by observing the trophic (feeding) relationship among its organisms:
who makes the food and who eats it. The organisms can be divided
into two broad components: primary producers, the autotrophs that
make the food, and consumers, the heterotrophs that eat it.
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Ecosystem
Flow of energy
• Autotrophic Component (autotrophic = self-nourishing) is a component in which fixation of light

energy, use of inorganic substances, and build-up of complex substances predominate.
• Heterotrophic Component (heterotrophic = other nourishing) is a component in which utilization,

rearrangement and decomposition of complex materials predominate:
1. Biophages are heterotrophic organisms consuming other living organisms
2. Saprophages are heterotrophic organisms feeding on dead organic matter.
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Ecosystem
Flow of energy
The transfer of energy through the system usually

takes place in several steps known as a food chain.
• Food chain is the transfer of food energy from the one
type of organism its consumer. It is characterized by a
series of prey and predator interactions. There are two
types of food chains:
1. Grazing chain: algae à water fleas à catfish à herons
2. Detritus chain: detritus à soil bacteria à worms
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Ecosystem
Trophic structure
Trophic structure is usually a complex,

interwoven food web instead of a simple,
straight-line food chain.
• Trophic cascade - An effect on one species may flow through an ecosystem due to the web of indirect
interactions
• Trophic level - Each of the steps in the food chain.
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Ecosystem
Trophic structure
Food chains and food webs are a little easier to understand if we

consider the number of steps, or trophic levels, through which
the energy passes:
• Example: Diatoms are the main primary producers in the food web.
Consumers that feed directly on the producers are called first-level, or
primary consumers and occupy the next trophic level. At the level
above that are second-level, or secondary consumers, predators that
eat the primary consumers. Feeding on the secondary consumers are
the third-level, or tertiary consumers, and so on. Each trophic level
relies on the level below for sustenance. At the end of the food web
are top predators such as killer whales.
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Ecosystem
Flow of energy in trophic structure
Trophic pyramid - Instead of being passed on to the next higher

level, much of the energy contained in a particular trophic level
is used up by the activities of the organisms. Energy and organic
matter are also lost as waste.
• Transfer efficiency (TE) is a measure of the amount of carbon that is
passed between trophic levels and is used for growth.
• Depending on the ecosystem, only about 5% to 20% of the energy in
one trophic level is passed on to the next; an average is about 10%.
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https://upload.wikimedia.org/wikipedia/commons/d/d4/Ecological_Pyramid.png

Ecosystem
The trophic structure of ecosystems

can be represented by a pyramid of
energy, with less energy contained in
each succeeding level.
• The pyramid of energy is based on the actual of energy that individuals take in, how much they burn up during
metabolism, how much retain in their waste products and how much they store in their bodies.
• The energy inputs and outputs are calculated so that energy flow can be expressed per unit of water (or land) per
unit time. An energy pyramid more accurately reflects the laws of thermodynamics (with energy losses being
depicted at each transfer to another trophic level).
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Ecosystem
In the energy pyramid, each succeeding trophic level is smaller

than the previous level. Less energy is found in each succeeding
trophic level because of the following:
• Of the food available, only a certain amount is captured and eaten
by the next trophic level. After all, prey are adapted in many ways to
escape their predators.
• Some of the food that is eaten cannot be digested and exits the
digestive tract as waste
• Only a portion of the food that is digested becomes part of the
organism’s body. The rest is used as source of energy.
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https://upload.wikimedia.org/wikipedia/commons/d/d4/Ecological_Pyramid.png
https://biologysir.com/wp-content/uploads/2019/12/20191210_122757.jpg

Ecosystem
Pyramid of numbers
• The trophic pyramid is pictured in terms of numbers of individuals rather than energy.
• Because there is less energy available at each level, there are also fewer individual organisms. Thus, there are fewer
primary consumers than producers, and fewer secondary than primary consumers. There is a progressive decrease in
abundance until the final stage in the food web, where the carnivores are large and few on number.
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https://www.researchgate.net/figure/Size-range-of-Particulate-Organic-Matter-POM-and-Dissolved-
Organic-Matter-DOM-DOM-is_fig7_278041634
Ecosystem
DETRITUS CHAIN
• Detritus consists of non-living organic matter
that is broken down by decay bacteria, fungi,
and other decomposers into its original
components: carbon dioxide, water, and
nutrients.
Detritus may be in the form of:

1. Dissolved organic matter (DOM) – “live” – released by phytoplankton, macroalgae and aquatic plants to surrounding
water.
• Organic compounds that pass through 0.45 µm. Released during messy feeding (grazers may break or crush algal cells
or tissues, releasing fluids into the water. Simply leaks out of phytoplankton cells. Can aggregate into amorphous
particles such as marine snow.
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https://www.researchgate.net/figure/Size-range-of-Particulate-Organic-Matter-POM-and-Dissolved-
Organic-Matter-DOM-DOM-is_fig7_278041634

Ecosystem
DETRITUS CHAIN
• Detritus consists of non-living organic matter
that is broken down by decay bacteria, fungi,
and other decomposers into its original
components: carbon dioxide, water, and
nutrients.
Detritus may be in the form of:
2. Morphous detritus (POM)– fragments of dead producers, fecal pellets released by zooplankton – poor nutritional
quality
• DOM is better food than POM because:

1. Made up of aggregated smaller molecular weight compounds – more assimilable than the large polymers (that remain
in the cells and tissues)
2. Lower content of detrimental or inhibitory secondary compounds than morphous detrital particles
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https://science.sciencemag.org/content/sci/280/5364/694/F1.medium.gif

Ecosystem
DETRITUS CHAIN
• Detritus consists of non-living organic matter that is broken
down by decay bacteria, fungi, and other decomposers into its
original components: carbon dioxide, water, and nutrients.
Nutrient regeneration – when decomposers break down organic matter, the nutrients incorporated into the organic
matter during primary production are released, making the nutrients available again for the photosynthetic
organisms
• Bacteria and fungi are the principal regenerators of the nutrients that were sequestered in the organic matter
synthesized by primary and secondary producers
• Microbial loop: has a critical function – regenerates the microbial elements in the organic matter. Without this
loop, energy in DOM would go largely unused. As much as half of the primary production in the epipelagic (no
phytoplankton) is channelled through this loop
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Ecosystem
MICROBIAL LOOP
• Nutrient regeneration allows availability of nutrients for photosynthetic organisms.
• In microbial loop, bacteria are directly eaten by ciliates and small fauna. The deeper the water column, the greater
the importance of bacteria, since phytoplankton production would occurs only near the surface. More zooplankton
near the surface, high organic matter reaching the sea floor, higher benthic community which can be supported.
Protozoan grazers play an important role in channelling the production of primary producers in the nanoplankton up
in the food chain.
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Ecosystem
The importance of size in aquatic food webs:

• Small organisms have faster rates of carrying out life activities, high
surface area allows faster transport of substrates across surfaces. They
grow faster and have shorter generation times.
Optimal foraging theory – predators tend to choose to feed on
prey whose yield as food is high in relation to the energy or time
spent by the predator in chasing, subduing and eating prey
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Ecosystem
Optimal foraging theory

• Raptorial feeders – consume prey items singly - chase prey hence it seems reasonable to expect their prey to be large
• Suspension feeders – spend much time removing particles from large volumes of water (not energetically costly as hunting)
so they may subsist on smaller prey – but still need to find highly palatable and nutritive food: solved this by having well-
developed selectivity as to which food they feed on and use chemical cues detected by complex chemosensory organs to
make decisions about food items
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Ecosystem
Suction feeding - method of

ingesting a prey item in
fluids by sucking the prey
into the predator's mouth
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https://www.youtube.com/watch?v=eV4Cj6l-Tjc

Ecosystem
Ram feeding - the predator

moves forward with its
mouth open, engulfing the
prey along with the water
surrounding it
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Ecosystem
Lunge feeding – done by

rorquals. Inverted suction
feeding, during which a whale
takes a huge gulp of water,
which is then filtered through
the baleen.
In filter feeding, the water flow is

primarily generated by the
organism itself, for example by
creating a pressure gradient, by
active swimming, or by ciliary
movements.
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https://www.youtube.com/watch?v=cbxSBDopVyw

Ecosystem
Pivot feeding is a method to

transport the mouth towards
the prey by an upward turning
of the head, which is pivoting
on the neck joint. Pipefish such
as sea horses and sea dragons
are specialized on this feeding
mechanism.
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https://www.youtube.com/watch?v=DJ9T-_lCo-A

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Ecosystem
Protrusion is the extension

of the mouth or premaxilla
towards the prey, via
mechanical linkages.
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https://www.youtube.com/watch?v=qut_RIH5Xy4

Ecosystem
Suspension feeding - the water flow is primarily external and the particles themselves move with respect
to the ambient water flow
• Seston – particles suspended in water
• Bioseston – organic portion of seston that contains the food of suspension feeders.
• Examples: Sponges – larger particles (5 to 50 µm) are engulfed by pinacocytes surrounding the pores (ostia).
Particles of 1 µm or smaller are filtered by choanocytes that line the feeding chambers.
• For brittlestar (Ophiopholis aculeata), food particles adhere to mucus-covered tube feet
5050
https://en.wikipedia.org/wiki/Aquatic_feeding_mechanisms#Suction_feeding
http://what-when-how.com/marine-mammals/feeding-strategies-and-tactics-marine-mammals/

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Suspension feeding - the

water flow is primarily
external and the particles
themselves move with
respect to the ambient
water flow
5151
https://www.youtube.com/watch?v=pTZ211cIjX8
Ecosystem
Symbioses with internal autotrophs

• Reef forming, or hermatypic corals, giant clams (Tridacnidae), sea
anemones (Anthopleura), some nudibranch gastropods - contain
large numbers of unicellular algae (dinoflagellate Symbiodinium sp.).
Symbiotic dinoflagellates are often referred to us zooxanthellae.
• Most of the hosts of algal symbionts retain the ability to feed in the
same way as their non-symbiotic relatives. Example: coelenterates
remain capable of capturing zooplankton using nematocysts, and
sponges and bivalves continue suspension feeding
• Symbionts pass fixed carbon to their hosts (zooxanthellae in corals
and giant clams pass organic carbon to host tissues in the form of
glycerol). They are important in the deposition of calcium carbonate
to form coral skeleton.
http://www.whalematch.org/coral.php
5252
https://www.tfhmagazine.com/-/media/Images/TFH2-
NA/US/articles/670_the_reefer_why_do_tridacnids_look_the_way_they_look.jpg

Lecture Notes in
4 SEPTEMBER 2021
https://www.nature.com/articles/s41396-018-0220-z

Ecosystem
Symbioses with chemoautotrophs

• Common in hydrothermal vents
• Example: Pogonophoran worm (Riftia pachyptila) has free-living, purple, sulfur-oxidizing bacteria
5353

Ecosystem
Primary productivity - amount of carbon fixed under a square meter

of sea surface in a day or in a year
• Gross primary production - total amount of organic carbon manufactured
by primary producers. Primary producers immediately respire some of
the organic matter they make to meet their own energy needs, however,
so it is not available as food to other organisms. It is the organic matter
that is left over, or the net primary production, that forms the base of the
trophic pyramid.
• H2A is an electron donor (water). Bacteria that carry out anoxygenic

photosynthesis make use of other electron donors such as H2S.
5454
https://ib.bioninja.com.au/_Media/productivity_med.jpeg

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Primary productivity - amount of carbon fixed under a

square meter of sea surface in a day or in a year
• Autotrophic activity (Photosynthesis) is summarized as:
• Chemosynthesis – organisms fix CO2. This process is carried

out by bacteria that can use chemical energy contained in
inorganic compounds, instead of light energy.
5555
https://archive.bigelow.org/foodweb/chemosynthesis.jpg

Ecosystem
• Net production = gross gross

primary productivity –
respiration (breaking down
organic compounds synthesized
in photosynthesis to release
energy)
5656
https://ib.bioninja.com.au/_Media/productivity_med.jpeg

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Measuring gross primary productivity:

• Biologists determine either the amount of raw materials used
up in photosynthesis or the amount of end products given off.
Photosynthesis produces oxygen and consumes carbon dioxide,
so photosynthesis can be estimated by measuring how much
oxygen is produced or carbon dioxide used up
• Light and dark bottles. Changes in the oxygen or carbon dioxide
level in the light bottle indicate both photosynthesis and
respiration, whereas changes in the dark bottle reflect only
respiration
• Amount of CO2 used by phytoplankton – uses radioactive C14
5757
https://images.slideplayer.com/35/10364790/slides/slide_27.jpg

Ecosystem
Measuring gross primary productivity:

• Satellite Color Scanning – This technique is based on the fact that the
radiance reflected from the sea surface in the visible spectrum (400-700
nm) is related to the concentration of chlorophyll.
5858
http://site.iugaza.edu.ps/elnabris/files/2014/11/4_Primary-production.pdf

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Regional variations in primary productivity

• Coastal waters are more productive than the central ocean for two
main reasons:
1. Runoff from land often contains a high abundance of nutrients
which get deposited in coastal waters and stimulate production.
2. The shallower bottom along the continental shelf can trap
nutrients and prevent them from sinking to greater depths. It is
easier for these nutrients to be brought back to the surface when
they remain trapped in the shallows.
• The central ocean generally has very low primary production, as
these areas are far removed from any terrestrial sources of
nutrients, and the great depth prevents the deep nutrients from
returning to the surface
5959
http://site.iugaza.edu.ps/elnabris/files/2014/11/4_Primary-production.pdf

Ecosystem
Seasonal variations in primary productivity
• Tropical regions – lots of sunlight, but nutrient-

limited = LOW productivity throughout the year
o Thermocline is present (very warm surface
water), leading to highly stratified water that
prevents the nutrient-rich bottom water from
reaching the surface
6060
https://rwu.pressbooks.pub/webboceanography/chapter/7-4-patterns-of-primary-production/

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
• Polar regions – Nutrient is abundant, but sunlight is during late

spring to summer only = HIGH productivity during spring to
summer only
o No thermocline, little stratification, mixing occurs (water is
uniformly cold at all depths) à nutrients are distributed in
the water column BUT little or no light during the winter.
By late spring the sunlight returns, and combined with the
abundance of nutrients, a spring/summer bloom of
phytoplankton occurs. By late summer, the nutrients have
been depleted and have been grazing on the
phytoplankton, so the bloom begins to decline.
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Ecosystem
• Temperate regions
o Winter = mixing = nutrient-rich water BUT no sun = LOW
winter productivity
o Spring = abundant nutrients in water + abundant light = HIGH
spring bloom productivity
o Summer = plenty of light BUT nutrients have been depleted
during spring + warm surface waters (thermocline formation)
= LOW summer productivity
o Autumn = Cooler temperatures weaken thermocline plus
storms bring nutrients back to the surface BUT less light since
approaching winter already = HIGH autumn bloom but less
than spring bloom.
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Lecture Notes in
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Ecosystem
Photosynthetic rates increase to a certain depth, and then

decrease beyond that.
• Exposure to high light intensities (near water surface) inhibit
photosynthesis. This is because of photo-oxidation (too much
light that cannot be absorbed by the photosynthetic apparatus)
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Ecosystem
Standing stock - or standing crop of phytoplankton

• Related to the primary productivity, but the two are not the same thing.
• Standing crop refers to how much phytoplankton is already in the water. Primary productivity refers to the amount
of new organic material being created.
• Determined by measuring the chlorophyll concentration – under certain kinds of light, chlorophyll emits a glow or
fluorescence; the amount of chlorophyll can be determined measuring this.
Biomass
• Total weight (total numbers × average weight) of all organisms in a given area or volume
• It is possible to count numbers and measure volumes of phytoplankton electronically to provide an estimate of
phytoplankton biomass, although cell volume may not always accurately reflect cell weight.
• Biomass is then expressed as the total volume (total numbers × volumes = mm3 ) of phytoplankton cells per unit
volume of water.
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Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Cycles of essential nutrients
• Once energy that is stored in organic

compounds is used in metabolism or given
off as heat, it is lost to the system forever.
Unlike energy, the materials that make up
organic matter can be used over and over
in a repeating cycle.
• Nitrogen cycle
6565
https://byjus.com/biology/nitrogen-cycle/

Ecosystem
• Nitrogen Cycle is a biogeochemical process

through which nitrogen (inorganic) is
converted into many forms (nitrates,
nitrite), consecutively passing from the
atmosphere to the soil to organism and
back into the atmosphere.
• It involves several processes such as

nitrogen fixation, nitrification,
denitrification, decay and putrefaction.
6666

Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
NITROGEN FIXATION: Atmospheric nitrogen, N2 (inert form) à ammonia, NH3

(usable form)
• The entire process of Nitrogen fixation is completed by symbiotic bacteria
which are known as Diazotrophs. Azotobacter and Rhizobium also have a
major role in this process. These bacteria consist of a nitrogenase enzyme
which has the capability to combine gaseous nitrogen with hydrogen to
form ammonia.
• Nitrogen fixation can occur either by atmospheric fixation- which involves
lightening or industrial fixation by manufacturing ammonia under high
temperature and pressure condition. This can also be fixed through man-
made processes, primarily industrial processes that create ammonia and
nitrogen-rich fertilisers.
6767

Ecosystem
NITRIFICATION
• The ammonia is converted into nitrate by the presence of bacteria in the
soil. Nitrites are formed by the oxidation of Ammonia with the help of
Nitrosomonas bacterium species. Later, the produced nitrites are
converted into nitrates by Nitrobacter. This conversion is very important
as ammonia gas is toxic for plants.
ASSIMILATION
• Primary producers – plants take in the nitrogen compounds from the soil
with the help of their roots, which are available in the form of ammonia,
nitrite ions, nitrate ions or ammonium ions and are used in the
formation of the plant and animal proteins. This way, it enters the food
web when the primary consumers eat the plants.
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Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
AMMONIFICATION
When plants or animals die, the nitrogen present in the organic matter is
released back into the soil. The decomposers, namely bacteria or fungi
present in the soil, convert the organic matter back into ammonium. This
process of decomposition produces ammonia, which is further used for
other biological processes.
DENITRIFICATION
The nitrogen compounds makes their way back into the atmosphere by
converting nitrate (NO3-) into gaseous nitrogen (N). This process of the
nitrogen cycle is the final stage and occurs in the absence of oxygen. It is
carried out by the denitrifying bacterial species- Clostridium and
Pseudomonas, which will process nitrate to gain oxygen and gives out free
nitrogen gas as a byproduct.
6969

Ecosystem
7070
https://www.sciencefacts.net/phosphorus-cycle.html https://scied.ucar.edu/learning-zone/earth-system/biogeochemical-cycles

Lecture Notes in
4 SEPTEMBER 2021
https://sites.google.com/site/resource12ubio/_/rsrc/1301059433716/home/population-
dynamics/Population_Dynamics_2008.jpg

Ecosystem
Population Dynamics
Population dynamics is the study of changes in the number

and composition of individuals in a population, and the
factors that influence those changes.
An understanding of population dynamics is needed to:
• Estimate how many animals can be harvested,
• Understand how environmental changes affect populations,
• Predict when a species or population is threatened or endangered with extinction,

• Understand how one population might affect another (i.e., competition or predation), and
• Use populations as indicators of environmental quality.
• Understanding the structure and function of communities and ecosystems.
7171

Ecosystem
Population Dynamics
Factors affecting population :

• Density-Dependent Factors - Are factors that act on a population as a function of density.
• Density refers to the number of animals per unit area (usually measured in animals/hectare or animals/square
kilometer).
• As the density of a population increases, the amount of resources available to each individual decreases, and the
health of individuals decreases. As health decreases, mortality (death rate) increases and reproduction decreases.
Thus, we may talk about density-dependent mortality or density-dependent reproduction. Density-dependent
forms of mortality include parasites, disease, starvation, and predation.
• Density-Independent factor - Are those factors that act on a population independent of the size of the
population. Typical density-independent causes of mortality are weather, accidents, and environmental
catastrophes like volcanoes, floods, landslides, fire, etc.
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Lecture Notes in
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Ecosystem
Population Dynamics
Population dynamics involves five basic components of interest to which all changes in populations can
be related: birth, death, sex ratio, age structure, and dispersal.
1. Natality - The rate at which animals reproduce is a basic component of population dynamics.
• Rate of natural increase is the difference between birth and death rates. It measures the degree to which a
population is growing. Since birth and death rates are measured as the number of births (or deaths) occurring per
1000 population, the difference is divided by 10 to convert this rate into a percentage.
• Refers to number of young individuals born or hatched per unit of time.
• Birth rates are usually expressed as fecundity, which is the number of young produced per female over a given
time period.
• Usually one year is the time period considered, but for smaller animals, especially those that may breed several
times a year, a shorter time period may be selected. Thus, if a population of 1,000 female grizzly bears produced
200 young in a year, the birth rate, or fecundity, would be 200/1,000 = 0.2
7373

Ecosystem
Population Dynamics
Factors Affecting Birth Rate:

• a. The amount and quality of food available determines if an individual has enough energy to reproduce.
Animals that are in poor nutritional condition have fewer young and/or breed less often.
• b. Age at first reproduction is also an important factor in determining birth rate. Large, long-lived animals
typically do not become sexually mature until they are several years of age.
• c. The birth interval is also important in determining birth rates.
• d. The average number of young produced is of obvious importance in a population's birth rate. Some animals
such as fish or amphibians produce 100's or 1000's of eggs (not all of them hatch of course), while many
wildlife only have one young at a time.
• e. Potential population growth rates are related to fecundity rates. A doubling in the fecundity rate will more
than double the population growth rate.
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Lecture Notes in
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Ecosystem
Population Dynamics
2. Death rate or mortality rate is another important component of population dynamics.

• Mortality is measured as the number of animals that die per unit of time (usually one year) divided by the
number of animals alive at the beginning of the time period. Thus, if 1,000 fawns are born in June, and
400 are alive the next June, then the mortality rate is 600 (the number that died)/1,000 = 0.6 or 60%.
• Survival is the number of animals that live through a time period and is the converse of mortality. Thus, if
the mortality rate was 0.8 or 80% per year, then survival would be 0.2, or 20% per year
• Longevity is the age at death of an animal. Mortality rates are usually age- and often sex-specific, which
means that animals of different ages or sexes die at different rates.
• In many species, the young and old animals die at faster rates than the prime-age animals. Often, males
have higher mortality rates than females because of activities associated with territorial or mating
behavior.
7575

Ecosystem
Population Dynamics
Different species have different survivorship functions related to life-history traits:

• Type I survivorship curve would be typical of animals that have relatively high survivorship until later
in life when they become subject to age-related mortality. Typically, these are animals with a high
degree of parental care. Many larger mammals, such as whales, bears, and elephants, might have
Type I survivorship curves.
• Some animals have fairly constant survivorship (Type II). Some birds and most reptiles and
amphibians probably fit this pattern, although our knowledge of survivorship in birds is not very
complete because they are difficult to study.
• Type III survivorship curve would be typical of animals with little or no parental care and/or
vulnerable young; mortality is high in the young age classes, then low in older animals. Insects and
fish often have Type III survivorship curves.
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Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Population Dynamics
3. Age structure or age composition of a population will influence population growth. The
age structure of a population refers to the number of individuals of each age within the
population.
• Because ages of animals are often difficult to determine, ecologists often place animals in age
categories or age classes. Many birds and reptiles are classified as young of the year or adult. Some
birds and small mammals may be classified as juvenile, sub-adult, or adult.
• Because of age-specific mortality and fecundity rates, the age structure of a population can greatly
influence population growth. For example, differences in age at first breeding can significantly
influence the rate of population growth.
7777

Ecosystem
Population Dynamics
4. The sex ratio of a population has important implications for mating systems and management.
• Sex ratio is the proportion of males to females in a population. Typically, the sex ratio at birth is 50:50, but usually
sex-specific mortality results in departures from this ratio in the adult population. Depending on the mating system
of the species, a departure from a 50:50 sex ratio may influence the population's dynamics.
• In monogamous species (monogamy is a mating system in which each male only mates with one female), a
deviation from a 50:50 sex ratio will cause a decline in population growth
• In polygamous species (polygamy is a mating system in which successful males mate with more than one female),
deviations from a 50:50 ratio can have major effects on population growth. Fecundity within the population of a
polygynous species is a function of the number of breeding-age females and males.
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Lecture Notes in
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Ecosystem
Population Dynamics
5. Dispersal is the movement of an animal from its natal area (place where it was born) to a new area
where it lives and reproduces (if it survives that long).
• Dispersal is important in the persistence of populations and species. Environments or habitats change over time,
and if an animal (species) does not disperse, it has no ability to colonize new areas.
• Dispersal also functions to prevent inbreeding and provides new genetic material for other subpopulations.
Individuals that disperse likely will not breed with their relatives.
7979

Ecosystem
Population Dynamics
Population growth
• The change in population size over time.
• By monitoring population growth in response to other factors such as habitat change or manipulation,
weather patterns, and hunting seasons, biologists and ecologists increase their understanding of the
factors that limit populations and how management affects a population.
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Lecture Notes in
4 SEPTEMBER 2021

Ecosystem
Population Dynamics
Patterns of population growth:

• 1. Exponential Population Growth - This growth type occurs when no
resources limit the population. When resources are unlimited,
populations grow at the maximum rate that is biologically feasible
for the species. That rate is called the intrinsic rate of increase and is
denoted by the symbol r. Although exponential growth is rare, it
does occur under some circumstances. Population growth by exotic
species when they first colonize a new area often resembles
exponential growth. Exponential growth is typical characteristic of
insects with short lifespan and most annual plants.
8181
content/uploads/sites/1223/2017/02/10222207/Figure_45_03_01.jpg

Ecosystem
Population Dynamics
Patterns of population growth:

• 2. Sigmoid or S-Shaped Population growth - Limitations on resources
and/or space cause population growth to change. Populations rarely
grow in environments with unlimited resources. Eventually, some
resource becomes limited. It may be nest holes for cavity-nesting
birds, or food for many species, or space for territorial species.
The carrying capacity (K) of a habitat is the number of
individuals that the area can support.
• It is the natural limit of the population set by the resources available.
As a population approaches K, then density- dependent mechanisms
(increased mortality, decreased reproduction) function to slow
population growth.
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content/uploads/sites/1223/2017/02/10222207/Figure_45_03_01.jpg

Lecture Notes in
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Ecosystem
Population Dynamics
Biotic potential is the maximum growth rate, which a population

could achieve in an unlimited environment.
• In reality however, no organism ever reaches its biotic potential
because of one or more factors which limit growth long before
population size attains its theoretical maximum, such limiting factors
include: food shortages, overcrowding, disease, perdition, and
accumulation of toxic wastes.
Environmental resistance – environmental pressures which limit
a population’s inherent capacity for growth rate.
• Measured as the difference between the potential of a population
and the actual rate of increase as observed under laboratory or field
conditions.
8383
https://ars.els-cdn.com/content/image/3-s2.0-B9780128053720000080-f08-05-9780128053720.jpg

Ecosystem
Biodiversity
Biodiversity encompasses the variety of life, at all levels of organization, classified both by
evolutionary (phylogenetic) and ecological (functional) criteria.
• Genetic variation among individual organisms and among lineages contributes to biodiversity as both
the signature of evolutionary and ecological history and the basis of future adaptive evolution.
• Species that lack substantial genetic variation are thought to be more vulnerable to extinction from
natural or human-caused changes in their environment.
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Lecture Notes in
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Ecosystem
Biodiversity
Components of biodiversity:
1. Species richness – number of species present
2. Dominance or evenness – relative abundances - One species might be represented by 1000 individuals, and
another by 200, and a third by a single individual.
8585
https://ib.bioninja.com.au/_Media/biodiversity_med.jpeg

Ecosystem
Biodiversity
There are 3 types of species diversity:

1. Alpha diversity (ά) – Also ‘local diversity’ - refers to
the diversity within a particular area, or habitat
2. Beta diversity (β) - refers to the difference in
diversity between habitats.
3. Gamma diversity (γ) – Also ‘regional diversity’ –
this refers to the diversity of species observed in
all habitats within a region, or ecosystem.
8686
https://i.ytimg.com/vi/oWmt6NPuquQ/maxresdefault.jpg

Lecture Notes in
4 SEPTEMBER 2021
Ecosystem
Strategies to obtain food, avoid predators and dispersal:

1. Modular colonies
• Form by a process of repeated budding . In modular organisms,
the division products remain partly attached to each other.
• Fragments may also detach from a colony and be dispersed to
give rise to new colonies elsewhere.
• Grow by repeated branching. Branching pattern can be:
a. Runners – stolon-like systems that spread out in a diffuse,
open network across a surface
b. Sheets – two dimensional encrustations forming a complete
cover of closely packed modules over the substratum
8787

Ecosystem

1. Modular colonies
• Grow by repeated branching. Branching pattern can be:
c. Mounds – three dimensional encrustations, grows over previous
generations of modules
d. Plates – sheets of modules growing perpendicularly away from
substratum like a fence
e. Vines – linear, or sparsely branching, cylindrical forms extending
away from a limited number of attachment points
f. Trees – erect, densely branching systems of modules growing from
a single anchorage point
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Lecture Notes in
4 SEPTEMBER 2021

Ecosystem

2. Larval forms
• Two major functional significance for presence of larval stages
in the life history:
a. Food acquisition – “nursery ground” – allows rapid growth
of young
b. Dispersal – away from parents and areas of high population
density and to avoid intraspecific competition for food
and/or space
• Done by non-feeding (lecithothrophic) larvae with a food store
in the form of yolk
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https://ars.els-cdn.com/content/image/1-s2.0-S0960982212003958-gr2.jpg

Ecosystem
Strategies to obtain food, avoid predators and

dispersal:
3. Vertical migration
• Animals move actively over maximum distances of
10-50,000 times their own body length up and down
in the water, each day
• During daylight hours, organisms are relatively deep
in the water column but at dusk they ascend to near
the surface.
• They disperse through the surface water mass
during the night, before re-aggregating near the
surface at dawn and descending again to the
daytime depth as light intensity increases.
9090
https://onlinelibrary.wiley.com/cms/asset/098efebb-5db3-4374-8a1d-bc20b9fbbee1/brv12715-fig-0001-m.jpg


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Lecture Notes in

AQUATIC RESOURCES AND ECOLOGY

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ONLINE MENTORING PROGRAM

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Fisheries Development Network

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Fisheries Development Network

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• The nature of life (biotic component) in a particular habitat (a

Fisheries Development Network

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• Organisms are also affected by other organisms—the

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Fisheries Development Network

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Fisheries Development Network

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Fisheries Development Network

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Fisheries Development Network

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Fisheries Development Network

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• Ecological niche – the role a species play in a community.

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ECOLOGICAL SUCCESSION / DEVELOPMENT

Fisheries Development Network

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ECOLOGICAL SUCCESSION / DEVELOPMENT

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Fisheries Development Network

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Adaptive strategies of animals

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Adaptive strategies of animals

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Adaptive strategies of animals

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Range and limits

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Several ways in which speciation takes place:

Fisheries Development Network

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Ecosystem (Ecological system)

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• Energy flow is the transfer of energy through an ecosystem.