ECOLOGY

1. Aquatic Food Webs:

Trophic (i.e. feeding) Relationships: Essential for
understanding aquatic ecosystem functions.
 Trophic Pyramid: Producers at the base (largest
level) and successively smaller levels above due to low
energy transfer efficiency (average of 10%).
Food Chains: are simple and linear.
Food webs: are more complex and illustrate omnivorous behaviors and life cycle
changes in consumers (shift levels on the pyramid). Typically begins with
photosynthesis.
 ex: a larval fish initially eats fine particulate material, then switches to grazing on
larger zooplankton and ultimately ends up feeding on fish.
 Food webs may be described in terms of both energy and nutrient (carbon,
nitrogen, or phosphorus) flows. Is influenced by both bottom-up (nutrient
availability) and top-down (predator-prey interactions) forces.
 There is no stable balance between bottom-up and top-down forces, but they
create a dynamic equilibrium that varies based on environmental and
biological factors.

N.B. The number of trophic levels influences

the effects of top-down forces, thus the
biomass distribution:
When the food web has an even number of
trophic levels, the algal biomass
(phytoplankton) is relatively small (their main
predators can thrive as they have less
predation upon them, thus phytoplankton are
eaten at a higher rate)
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The potential biomass at the different trophic levels is mainly determined by productivity (e.g.
amount of nutrients) (bottom-up forces)
The actual biomass is mainly dependent on consumer-
control (top-down forces).

2. Water quality and fish community

Generally, an increase in nutrients boosts fish biomass, but
excessive nutrients can lead to eutrophication, disrupting the
ecosystem and leading to the loss of certain species and
habitats. Highly eutrophicated waters can become extremely
turbid (murky), resembling green "pea-soup."
Eutrophication Effects on Lake Ecosystems
 Eutrophication often leads to a dominance of phytoplankton in shallow lakes, overshadowing
sunlight for macrophytes (water plants) , which consequently die off.
 The loss of vegetation shifts lakes from clear and vegetated to turbid and barren, disrupting
various interactions within the food web.
 The absence of macrophytes homogenizes the water column and removes structures
essential for spawning, hiding, and foraging for many species. This results in decreased species
diversity and complicates hunting for piscivorous fish that rely on vision, such as pike,
leading to their rarity or disappearance.
 With the decline of predators, prey fish populations increase.
Studies show qualitative and quantitative
shifts in fish populations linked to nutrient
levels, notably phosphorus, indicative of
eutrophication.
Different fish families react differently to
various nutrient levels. Ex: nutrient levels
rising can lead to an increase in benthivores
(fish that eat bottom-dwelling organisms -
ex: large bream)
Fish communities found in NL shallow
freshwater bodies have been categorized
based on nutrient levels, vegetation cover,
and water body type, aiding in
understanding ecosystem dynamics.
Such classifications, while somewhat
artificial, serve as useful benchmarks for
discussing fish community status and
ecosystem relationships, acknowledging
that fish communities and conditions are
dynamic and continuously evolving.

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Oligotrophic, mesotrophic, and eutrophic are terms used to describe the nutrient status and
productivity levels of lakes and other bodies of water.
Oligotrophic: Low in nutrients, especially phosphorus and nitrogen. High water clarity due to low
algal production. Low biological productivity; fewer algae and aquatic plants. Typically supports fish
species that thrive in clear, cold, and low-nutrient waters, such as trout and salmon.
Mesotrophic: Moderate level of nutrients. Good to moderate water clarity. Supports a more diverse
array of fish species than oligotrophic lakes, including both species that prefer clear waters and those
that can tolerate more productive waters.
Eutrophic: High in nutrients, which often leads to excessive growth of algae and aquatic plants. Often
low water clarity due to high algal blooms; water can appear green and turbid. Often shallow, murky
waters with soft, muddy bottoms rich in organic material. High biological productivity, which can lead
to oxygen depletion in the water especially after algae die off and decompose. Fish species that can
tolerate lower oxygen levels tend to dominate, such as carp and catfish. The diversity of fish adapted
to clearer waters may decline.
The progression from oligotrophic to eutrophic is ka natural aging process for lakes and ponds, often
accelerated by human activities such as agriculture, urban development, and untreated wastewater
discharge. This process, known as eutrophication, can lead to ecological imbalances and problems like
algal blooms, hypoxia, and the decline of desirable fish species.

3. Ecological Guilds

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Ecological Guild: A group of fish species that show similar ecological functioning in terms of
resource use (food or habitat).
 Compared to changes in a single species, changes in composition and distribution of guilds can be
more informative about ecological processes and habitat availabilities.
 Fish species can be classified according to their:
a. Flow preference b. Reproduction ecology c. Diet
i. N.B. above is an example, however, there is no common classification system and different
authors adapt the guild classifications according to their own specific ecological questions.

4. Alternative stable states and biomanipulation

Alternative stable states: Multiple stable states may exist for one
ecosystem  over time an ecosystem may transition from one state
to another, through internal or external factors, altering the
structure/function of the ecosystem. The states reach stability and
are reinforced through positive feedback loops
Ex Lake: Oligotrophic  less algae  clear water containing water
plants; Eutrophic  more algae turbid water.
In a large range of intermediate nutrient levels however, both the
vegetated clear and the turbid algae-dominated state can exist. These two states are self-reinforcing
and called ‘alternative stable states’.
ii. Self-reinforcing positive feedback loops ex:
i. Water plants need clarity but also increase the clarity
of the water through nutrient uptake and production
of substances that inhibit algae growth; they also
reduce wave action, which decreases sediment
resuspension.
ii. The absence of water plants increases turbidity and
sediment resuspension, making it difficult for plants to
reestablish.
iii. Zooplanktivorous and benthivorous fish increase
turbidity. Piscivorous fish enhance water clarity and
support vegetation.
Biomanipulation: Manipulating the food web by breaking
one/several of the positive feedback loops. Ex: massive fish
removal and enhancing piscivorous fish populations  used to
shift lakes from turbid to clear states with vegetation.
River Continuum Concept (RCC): There are biological and
physical changes along the length of a river, forming
continuous gradients and abiotic/biotic adjustments.
Upstream areas are often shaded and rely on external organic
material, while downstream areas have higher light and
nutrient levels supporting more photosynthesis and diverse
aquatic life.

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 Fish zones: zones of the river based on the types of fish species typically found there and the
ecological characteristics of those areas.

Issues with the zonation model:

i. Based on undisturbed rivers (rare due to human impact), thus the model is difficult to apply.
ii. Only considered adult fish, neglecting the varying habitats used by young fish/larvae.
iii. Only considered the longitudinal aspects of rivers (length), ignoring width and time.
iv. Tailored for north-western Europe species, limiting its applicability globally.
v. Fish distribution is actually gradual rather than neatly segmented as suggested by the zonation
model.
Flood Pulse Concept (FPC): Considers the
ecological dynamics between rivers and their
floodplains (sideways cut view of river)
It claims that the predictable rise and fall of water on
the floodplain enhances nutrient cycling, biological
productivity, and biodiversity by spreading river
nutrients across the floodplains.
The “moving littoral (nearshore) zone” act as critical
habitats for many species, particularly during floods,
which trigger high primary and secondary production.
Ex: many fish use floodplains as a nursery.
Going from the main river channel sideways across to
the floodplain, the character of the water changes
from colder running waters with relatively high O2
contents, with sand/clay bottoms, to stagnant waters
with silt and organic deposits, undergoing
territorialization and subjected to periodic O2 deficits
and high-water temps. With this ‘transversal gradient’
the associated fish guilds also change.

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Many rivers and floodplains have been significantly altered by human activities (ex: dams), severely
impacting natural dynamics and biodiversity  has led to the decline in guilds of specialized fish
species adapted to riverine environments, while more eurytopic species (able to tolerate a wide range
of ecological conditions) have become dominant.

5. The role of fish in integrated water management

EU Water Framework Directive (WFD): Aims to prevent deterioration and restore aquatic
ecosystems by assessing and classifying water quality into five classes: High, Good, Moderate, Poor,
and Bad.
 The biological elements assessed for quality include phytoplankton, macrophytes,
phytobenthos, benthic invertebrate fauna, and fish fauna.
 For example, with fish fauna, indicators such as species composition, abundance, age structure,
and presence of sensitive species can be used.
These variables give an indication of what should be measured to assess ecological water quality,
but the interpretation of these measurements is much less clear (can be biased or to general
with terms used like ex: ‘totally, or nearly totally undisturbed’,)

Indicators: measures that summarize key elements of a complex ecosystem  evaluation of the
fundamental condition of the ecosystem without having to capture the full complexity of the system.
 In aquatic environments, indicators include physical, chemical, and biological measures, and
are important for monitoring (time) and classification (distinguishing between water bodies).
 Biological measures are preferred as they reflect the overall health of aquatic ecosystems and
are sometimes the only measure practical to take for evaluating impacts that are difficult to
measure directly, e.g. diffuse pollution impacts or habitat degradation.

AMOEBE Method: Variables are chosen to assess the ecosystem. These variables are measured in a
reference situation (undisturbed situation) and are given the value 100%. The ecosystem
measurements for each variable are expressed as a percentage of the reference values.
 All these values are plotted in a radar plot. The black
circle is the reference values, and the plotted
ecosystem values show how far the ecosystem is from
the ideal.
 Reference conditions are reconstructed, either from
historical data or from other parts of the world, due to
the absence of undisturbed ecosystems in Western
Europe, leading to subjectivity in assessments. Since
the reference is usually not realistic to modern day
circumstances, a more realistic target value is often
included.

 Although a great visual tool, it is rather imprecise, and

based on an arbitrary choice of variables and
reference situations and does not give any spatial
information.

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N.B. Many of the above disadvantages are outweighed by the widespread advantages and are also
present in other biological indicators.
Multi-metric fish indexes: use an array of measures/metrics that incorporate information from
individual, population, and community levels into a single, ecologically based index of water quality.
Steps to develop a good fish index:
1. Selection of fish community measures or metrics. In this case, the metrics are usually defined by
biological measures such as species diversity, species dominance etc.
N.B. A measure is a number, while a metrics are measures of quantitative assessment commonly
used for comparing and tracking performance or production.
2. Evaluation of selected metrics. A calibration of the method with field data or relevant ecological
literature is needed to ensure they adequately measure ecological condition.
3. Development of reference conditions. Reference conditions are needed against which the data
collected can be compared. Some methods include using historical records, expert input,
predictive models and selecting least impacted sites.
4. Establishment of metric thresholds. Each metric
is rated high, good, moderate, poor, or bad based
on its deviation from the reference. To adequately
describe the degree of deviation from the
reference, thresholds, usually based on the
evaluation of site-specific sampling data, are used.
5. Index calculation and appraisal. The final Fish
Index can be calculated by adding up all values of
the metrics. Scores are categorized (e.g., 40-44 is
considered 'moderate') based on the cumulative
metric values. Absence of fish leads to an
ecological water quality rating of 'critical'.

N.B. The index should be designed to respond to

environmental stress and reflect the condition of
ecosystems.

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An ideal Fish Index should comply with the following conditions:
i. Reproducible: small sampling variations shouldn’t result in significant differences in the
Fish Index score.
ii. Responsive to environmental stress; sensitive enough to monitor changes in ecosystem
iii. Robust: Can accommodate natural variability i.e. not too sensitive so that the outcome of
assessments of ecological quality does not indicate dramatical changes from year to year.
iv. Reflects structural and functional attributes of fish communities and integrate these.
v. Conceptually simple and has easily measured metrics.
vi. Effective communication tool: Translates ecological data into easily understood
information
Ecological Habitat Potentials for Fish:
When aiming to restore fish populations in specific
water bodies, it is crucial to investigate the potential of
the habitat, including the habitat requirements of the
specific fish species.
A Habitat Suitability Index (HSI): a numerical
index derived from a certain set of habitat variables,
that determines the suitability of a given habitat to a
selected species. Can be simple or complex and may
incorporate variables for different life-stages.
 Output of model is a score between 0 (not suitable for a viable population) and 1 (optimal habitat).
 Quality of model depends on available biological knowledge and status of validation (how well the
models fit reality in reference situations).
 can be used for identification of the bottlenecks in the habitats and life cycles of species.
3 ways of linking multiple habitat variables to calculate the HSI:
Choosing how to combine variables depends on the biological knowledge of the interaction between
the species and its environment.
1. Averaging: Used if different variables can compensate for each other. Ex: if an unfavorable
value for one variable can be compensated for by a favorable value of another variable. If some
variables are considered to be more important than others, weighting can be applied. No
limiting factors.
𝐻𝑆𝐼 = (𝑎 ∗ 𝑉 + 𝑎 ∗ 𝑉 + ⋯ + 𝑎 ∗ 𝑉 )/∑𝑎𝑛
V is a habitat variable and a is a weighting coefficient
2. Geometric mean: This is also used in the case of compensatory relationships, but in this case
the result is zero if one variable has a value zero, thus there is a limiting factor.

/
𝐻𝑆𝐼 = (𝑉 ∗ 𝑉 ∗ … ∗ 𝑉 )
3. Minimum value: Strong limiting factor relationships (‘weakest link’ idea).
N.B. Depending on the method chosen, the outcomes of the HSI may be quite different. To decide
which of the calculation methods is better, detailed knowledge of the biology of the species is needed.

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Habitat Evaluation Procedures (HEP): an extension on
the HSI concept to include an explicit spatial dimension 
HSI is multiplied by habitat quantity (area), resulting in a
value for the amount of ‘suitable habitat’ in the study area.
HEPs are useful for monitoring the quantity and quality of
habitats in an area through time and comparing quantity and
quality of habitats in different study areas.
They also are useful in Scenario studies of future
developments, which may be autonomous / unplanned (e.g.
climate change), or because of human interference (e.g.
water level changes, damming, shoreline developments).
Methodological considerations on HSI and HEP: realize these models are dealing with potential
and not actual habitat suitability. Usually, the models do not explicitly account for competition
between species, predators, available food resources, or the reachability of specific areas, although
these factors could be incorporated.
There are also so many models and it is difficult to choose between them.
Reasons why there are so many models are:
i. There are different data forms (relative abundance, presence-absence etc.) for different species,
different study areas and different time scales.
ii. HSI models are constantly revised and improved
iii. Ecological reality is complex and most of the time there are no easy solutions.

6. Fish, Water and multiple stakeholders:

Stakeholders: anybody, person, group, organization, or government with an interest. There are
frequently conflicting interests between stakeholders in fish and water management, where interests
do not align.

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Multicriteria analysis (MCA): a decision-making tool used to assess and compare different
management scenarios involving multiple stakeholders with diverse interests. It integrates various
criteria simultaneously, making the subjective reasoning and convictions of stakeholders explicit,
helping to analyze conflicts and explore potential solutions.
The main steps in conducting a MCA:
i. Clearly identify different management scenarios to be
evaluated and define the specific aspects of these scenarios
that require assessment.
ii. Develop and define a comprehensive list of criteria for
comparison, ensuring it reflects the diverse perspectives of
all stakeholders involved.
iii. Perform a quantitative estimate or a qualitative description
of the impact each scenario has on each criterion, typically
organized into a multicriteria evaluation matrix.
iv. Determine an overall judgment of the effects of the
scenarios by evaluating the impacts (ex by averaging scores
of different criteria). Criteria can be weighted differently, but
it is also possible that some criteria are considered so
important that they overrule all other criteria
MCA provides a framework in which all stakeholders are included. Criteria are made explicit and
provide structure in a complex reality allowing decisions to be made in a quantitative way.
MCA is that it only works with a good involvement of all stakeholders in an interactive way, because
the interpretation of the impacts of scenarios on criteria may change over time, or the weighting of
criteria may be subject to discussion. If this interactivity is not well-developed MCA may be used in a
too rigid way, thereby losing its support from stakeholders.

7. Practical Ecology
Reasons to look at the shape of fish:
i. Determining phylogeny (development through evolution-
homologous structures), taxonomy (classification) and ecology (adaption to environment).
ii. Identification
iii. Communication
iv. Evolutionary/biodiversity/comparative studies
v. Management of resources.
Quantitative characteristics: can be meristic (counts, eg. scale counts) or metric (measurements,
eg. fin lengths – metric needs measuring thus not always easiest to use)
Presence-absence characteristics: usually signify deeper taxonomic differences (e.g. jawless fish vs
bony fish). Shape and presence-absence characters are easiest to use thus most used in identification.
Systematics: Study of naming/classifying organisms and investigating their evolutionary relationship.
Taxonomy: Study of describing/identifying/classifying taxa (group of phylogenetically related
organisms)
Nomenclature of Linnaeus: Genus name, species name + (name of discoverer + year of
discoverer), the goal is to have one standardized name for an organism.
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Chordata (Phylum)  Vertebrata (Subphylum) -
 Agnatha (superclass): Jaw-less fish, no pelvic fins, chorda present, endodermal gills and gill
arches fused with neurocranium
 Gnathostomata (superclass): Jaws present (first gill arch), ectodermal gills, paired limbs,
moveable head region and otoliths present
 Osteichthyes (Bony fish)
 Actinopterygii (Ray-finned fish)
 Chondrostei: maxillary bone that does not rotate with opening of mouth, a
heterocercal tail, well-ossified skeleton and skin covered with ganoid scales
 Neopterygii: teleostei: complete ossified skeleton (almost), symmetrical tail
and free moving maxillary bone

Mollusks and Crustacean Tree:

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 SHELLFISH
Shellfish = mollusks and crustaceans, found in the phylum Mollusca and Crustacea respectively.
 We focus on Mollusca, specifically the class Bivalvia, which contains the bivalve mollusks
(e.g. mussels, oysters). Under Mollusca are 2 other classes: Gastropoda and Cephalopoda.
Life Cycle and Behavior:
Bivalves are mostly sedentary. After spawning/fertilization in the water column, larvae go through a
series of metamorphoses and drift for 4 weeks, larvae settle on suitable substrate: oysters permanently
attach to hard substrates, while mussels affix themselves with byssus threads and clams burrow into
sediment. Species such as scallops can swim short distances.
Reproduction and Recruitment:
Bivalves undergo broadcast spawning, producing 105-106 larvae 1-2x/year, but face high larval
mortality due to environmental conditions (ex: unstable sediment) and predation of larvae and spat
( juveniles), thus successful recruitment is critical. High numbers of offspring mean bivalves are
adaptive and resilient to dynamic environments like estuaries with large variations in salinity, turbidity,
and habitats.
Feeding and Growth:
Bivalves are herbivores/detritivores, feeding on phytoplankton and detritus by filtering water through
their gills. Food availability and environmental conditions significantly affect their growth rates, which
can be high during times of food abundance, e.g. seasonal high production of algae (spring/autumn).
The gills function as both pump and filter, determining the particle size they can retain (species and
size specific but ranges from 3 – 8 μm). Clearance rate: Volume of water cleared of suspended
particles per unit of time (e.g. l/h) (Adult mussels: 2-3 l/h ; Adult pacific oyster ≥10 llh)
Prior to ingestion, the edible fraction of the particles retained on the gills is selected (usually, water
concentration of particles > gut capacity = edible fraction is small). The max amount that can be
ingested depends on the size of the gut and the time needed to pass the gut.
Digestion occurs in the digestive gland, with unabsorbed material excreted. Metabolic processes
include maintenance (respiration and ammonia excretion) and anabolism (growth and storage).
Two pairs of labial palps assist in selecting the edible fraction and mucus production. Non-digested
material is packed into this mucus and later eliminated through the in low siphon or mantle edge as
pseudofaeces.
Ingested material is transported through the gut to the digestive gland, which contains digestive
enzymes and food is taken up by digestive cells. Non-digested material is excreted as faeces through
the out low siphon.
The amount that can be ingested depends gut size and gut passage time. Gut passage time depends
on animal species/size; gut capacity is a function of body size and gut passage time.
Metabolic faecal loss (endogenous losses): material lost from the body (ex: enzymes, cell
fragments), enriching the feaces with organic material.
Absorbed material is used for metabolic processes. Maintenance costs = C loss through respiration
and N loss through ammonia excreted.

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