PMNQ Deliverable 1 Scientific Principles

A Review of
The scientific principles

underlying impact of
aquaculture on the
environment
Deliverable 1 for PHILMINAQ
Mitigating impact from aquaculture in the Philippines
Project number: FP6-2004-INCO-DEV-SSA- 031640 6th Framework
Programme
Duration: 08/2006 to 02/2008 (18 months) Specific Support Action
The scientific principles underlying impact of aquaculture on the environment
Table of contents
1 Abstract ..................................................................................................................3
2 Environmental impacts from Aquaculture .............................................................3
2.1 Environmental awareness and sustainability .................................................3
2.2 Types of waste and effluent deposition..........................................................4
3 Environmental impacts...........................................................................................5
3.1 Soluble wastes ............................................................................................5
3.2 Solid wastes....................................................................................................9
3.2.1 Organic matter......................................................................................12
3.3 Chemicals and other additives .....................................................................13
3.4 Effects on wild fish populations...................................................................14
3.4.1 Contamination with waste....................................................................14
3.4.2 Parasites and diseases...........................................................................15
3.4.3 Escapees and genetic transfer...............................................................15
3.5 Direct impacts on wildlife............................................................................16
Implications for biodiversity ................................................................................16
4 Scientific rationale behind monitoring methods ..................................................17
4.1 Hydrographic/ water quality analyses and other assessments......................17
4.2 Chemical analyses ........................................................................................18
4.3 Benthic faunal analyses................................................................................18
5 Aquaculture Regulation .......................................................................................19
6 Conclusions ..........................................................................................................23
2
1 Abstract
As aquaculture expands, regulation to prevent environmental damage is an essential
requirement for sustainability. In this review, the scientific principles underlying impact on
the environment, monitoring programmes and aquaculture regulation pertaining to 1)
protection of other resource users, 2) protection of ecosystem structure (conservation) and 3)
protection of ecosystem function (recycling) are discussed. Some of the approaches taken to
regulation of aquaculture in several countries are presented emphasising the need for these to
be based firmly in a good scientific understanding of the ecosystem and the processes by
which it interacts with aquaculture.
2 Environmental impacts from Aquaculture

The aquaculture industry has experienced considerable expansion over the past decades, with
attention being paid subsequently to the environmental effects of its activities. The potential
impacts of aquaculture are wide-ranging, from æsthetic aspects to direct pollution problems.
Marine aquaculture operations and their associated infrastructure can disturb scenic rural
areas. Fish production may generate considerable amounts of effluent (e.g. waste feed and
faeces, together with associated by-products such as medication and pesticides) which can
have unacceptable impacts on the environment. There may also be some unwanted effects on
wild fish populations, such as genetic disturbance and disease transfer by escapees or
ingestion of contaminated waste.
Direct outputs from aquaculture operations to the aquatic environment may be summarised
into three broad categories: aquaculture production (continuous discharges); farm activities
(periodic discharges); and medication (periodic discharges). The behaviour of any type of
waste released into the water column will largely depend on the current conditions and
bottom topography of the area in question. Indeed, the selection of sites with good water
exchange, together with good management practices that minimise food waste, will reduce
the environmental impacts of aquaculture and optimise fish health and growth.
Environmental awareness and sustainability

The aquaculture industries have experienced considerable expansion over past decades, with
attention being paid subsequently to the environmental effects of such activities. It is not
possible to generalise and distinguish between the actual and potential impacts of aquaculture
given that a multitude of approaches is in place. However, in general, the potential impacts
of aquaculture are wide-ranging, from aesthetic aspects to direct pollution problems
(O'Sullivan 1992). Marine aquaculture operations and the associated infrastructure can, for
example, impact on scenic rural areas. Fish production generates considerable amounts of
effluent (e.g. nutrients, waste feed and faeces, together with associated by-products such as
medication and pesticides) which can have undesirable impacts on the environment (Gowen
and Bradbury 1987; Ackefors and Enell 1994; Wu 1995; Axler et al. 1996; Kelly et al.
1996). There may also be unwanted effects on wild populations, such as genetic disturbance
(Crozier 2000; Fleming et al. 2000), and disease transfer by escapees or ingestion of
contaminated waste (Heggberget et al. 1993), and effects on the wider ecosystem. Table 1
summarises current environmental concerns arising from marine aquaculture operations.
Other coastal activities can also have unacceptable impacts on aquaculture operations (e.g.
effluent discharges and physical conflicts with other users) (Anderson 1995; Shereif and
Mancy 1995; Phyne 1996).
3
Table 1. Current environmental concerns arising from marine aquaculture operations

Potential Direct Impacts Potential Consequences Management Actions
• Organic enrichment • Impact on wildlife/ • Locational guidelines
• Nutrient enrichment habitats • Biomass maximum
• Chemicals release • Trigger of toxic • Maximum feed limit
• Spread of diseases blooms • Restricted use of
• Demise/quality of wild chemicals
stocks • Management
Guidelines (inc. Codes
of Practice/Conduct)
• Escapees • Genetic dilution • Improved cage design
• Demise of wild stocks • Management
Guidelines
• Interaction with other • visual impacts and • Locational guidelines
coastal activities conflict with e.g. • Derive regional/local
tourism, recreational Coastal Plans and
fishing, maritime integrate with national
transport Coastal Management
Plan
Types of waste and effluent deposition

Discharges from aquaculture to the aquatic environment may be summarised into three broad
categories:
• Aquaculture production (continuous discharges): mainly deposition and spreading of
organic material in the form of faeces, waste food and accidental food spillage. The
various organic compounds include proteins, carbohydrates, vitamins and pigments.
Some inorganic excretory products are also released, mainly ammonium and species-
dependent trace quantities of bicarbonate, phosphate and urea.
• Farm activities (periodic discharges): processing waste and eventual regulated dumping
of mortalities, usually in silage form. Mainly inorganic discharges including detergents,
effluent from net washing (antifoulants, heavy metals), and eventual particle deposition
from, for example, waste incineration. Most of these discharges are usually released
from the non-ongrowing part of the aquaculture farm.
• Chemicals (periodic discharges): various chemical compounds may also be released
from the production sites, mainly antibiotics and pesticides.
The behaviour of any type of waste released into the water column depends on the
hydrographic conditions, bottom topography and geography of the area in question.
Dissolved products include ammonia, phosphorus, dissolved organic carbon (which includes
dissolved organic nitrogen and dissolved organic phosphorus) and lipids released from the
diet, which may form a film on the water surface (Black 2001). The environmental impact of
these dissolved products depends on the rate at which those nutrients are diluted before being
assimilated by the pelagic ecosystem. In restricted exchange environments, there is a risk of
high levels of nutrients accumulating in one area (hypernutrification) and potentially creating
undesirable effects (Midlen and Redding 1998).
In shallow waters, with weak currents, solid waste products from aquaculture installations
will settle to the bottom close to the discharge point. In this case, continued production can
4
give rise to a rapid local accumulation of waste material on the sea floor. On the other hand,
effluent released into deeper waters, or where the bottom is well swept by strong currents,
will be dispersed over a larger area.
The vast majority of the chemicals used by the aquaculture industry are for the treatment or
prevention of disease, although cleaning agents are also used (Costello et al. 2001). The
environmental concerns over the use of chemicals in the aquatic environment relate to the
following (Midlen and Redding 1998): (i) the direct toxicity of the compounds; (ii) the
development of resistance to compounds by pathogenic organisms; (iii) the prophylactic use
of therapeutants; and (iv) the length of time they remain active in the environment.
In addition to selecting sites with good water exchange, management practices that minimise
food waste and chemical usage will also reduce the environmental impacts of aquaculture
and optimise fish health and growth (Cho et al. 1994; Ervik et al. 1994).
3 Environmental impacts
Aquaculture waste released into the water column can be in both dissolved and particulate
forms. In the marine environment the effects of dissolved nutrients from aquaculture waste
are generally rapidly dissipated. However, particularly in brackish areas or where there is
exceptionally poor water exchange, dissolved forms of phosphorus and nitrogen can
stimulate the production of phytoplankton. The resulting algal blooms can harm both farmed
and wild fish. It should also be noted that different water bodies have different limiting
nutrients; the Atlantic is thought to be nitrogen limited whereas the Mediterranean is thought
to be phosphate limited. Neither bicarbonate nor phosphate are considered to be important
factors in marine pollution but the latter can contribute to eutrophication in brackish areas.
Wastes from fish farming are usually considered in 3 overlapping categories:
1. Soluble wastes, being the products of fish excretion and including reactive nitrogen
species such as ammonia
2. Solid wastes, being mainly uneaten feed material and faeces
3. Chemical wastes, being medicines - such as antibiotics and anti-parasitcs, disinfectants,
and antifoulants – such as tin or copper compounds formulated into coatings or paints.
3.1 Soluble wastes

Cage farming results in considerable nutrient release into the water column. For farmed
salmon and trout mass balance models have been developed for nitrogen (Gowen &
Bradbury, 1987; Hall et al., 1992), phosphorus (Holby & Hall, 1991) and silicon (Holby &
Hall, 1994). According to these models 50% of the nitrogen and 28% of the phosphorus
supplied with the food is wasted in dissolved form (mainly NH4 and PO4). Seasonal
variability in food supply determines the seasonal variability in environmental loss of carbon,
nitrogen and phosphorus towards the seabed and the water column. However the resulting
seasonal pattern in nutrient availability in the water column is anticipated to differ from the
“natural” seasonal pattern. In the case of non-impacted marine ecosystems, nutrients are
abundant during winter and early spring and are gradually depleted in the surface waters
during the warm season, whereas in mariculture-impacted ecosystems most of the nutrient
loss during feeding (and consequently most of the nutrient enrichment in the water column)
5
occurs during the warm period (i.e. summer and early autumn). Furthermore, fish farming
wastes provide dissolved nitrogen and phosphorus but not silica and therefore such wastes
could be expected to favour the growth of certain phytoplankton groups such as flagellates or
cyanobacteria (Parsons et al., 1978; Doering et al., 1989), though not the Si-limited diatoms.
This modification of the structure of the phytoplankton community could in turn further
affect zooplankton and subsequent trophic links since the quality of phytoplankton biomass
as a food resource varies greatly among different phytoplankton groups (Bianchi et al.,
1993). There is limited information on such impacts; however investigation into phyto- and
microzooplankton communities in Mediterranean fish farms revealed no significant changes
in terms of species composition or diversity between cages and control sites (Pitta et al.,
1997).
Soluble nutrients from aquaculture may constitute a risk of eutrophication. The EU definition
of eutrophication is:
"the enrichment of water by nutrients especially compounds of nitrogen and phosphorus,

causing an accelerated growth of algae and higher forms of plant life to produce an
undesirable disturbance to the balance of organisms and the quality of the water concerned".
The undesirable consequences of eutrophication include(Black et al., 2002):
• increased abundance of micro-algae, perhaps sufficient to discolour the sea and be

recognised as a bloom or “Red Tide”;
• foaming of seawater;
• killing of free-living or farmed fish, or sea-bed animals;
• poisoning of shellfish;
• changes in marine food chains;
• removal of oxygen from deep water and sediments as a consequence of the sinking
and decay of blooming algae .
A nutrient budget for Atlantic salmon shows that the majority of the nutrients that are input
to the system are subsequently lost either directly as soluble wastes or through losses from
solid particulate wastes (figure 2). One method of determining the risk of elevated nutrient
concentrations is called the Equilibrium Concentration Enhancement (ECE) model. The ECE
model is a box model of dissolved ammoniacal nitrogen arising from farmed fish occurring
within an enclosed body of water of known dimensions that is being exchanged at a steady
rate (Gillibrand and Turrell, 1997).
6
Wild fish
17%
protein, 7-
10% oil,
75% water
Fish Feed
40% Protein
30% oil
9% water
1200g:
2.8 kg N 96g Plus 0.8 –
for P 18g 2.3 kg extra
protein for oil
Harvest
Fish
1 kg
N 26g
Soluble
P 32
wastes
N 46g
Mortalities
and escapes
N 1.9g
Particulate
P 0.4g
wastes C 13g
N 22g
P 9.5g
Figure 2. A budget for the flow of nutrients from oceanic wild caught fish to the coastal
environment for a harvest of 1 kg of farmed salmon assuming no substitution with
vegetable protein or oil and a ratio of fish feed to product of 1.2:1 (Black, 2001)
Model input data include the flushing time and volume of the system, rate of excretion of
ammonia by fish and annual production. Using this model, systems can be ranked in terms
of the potential contribution of aquaculture to raise nutrient levels and assigned a Nutrient
Enhancement Index (NUI). In Scotland this index was proposed in a government document
7
called the Locational Guidelines for Fish Farming (Gillibrand et al., 2002). Table 1 shows the
predicted ECE for Scottish sea loch systems, their NUI and the distribution of lochs by NUI.
Table 1. ECE values for nitrogen for Scottish sea lochs and classification using the Nutrient
Enhancement Index (Gillibrand et al., 2002). For an ECE of 0 (i.e. where no emissions from
aquaculture exist, a value of 0 is assigned).
ECE (µmol l-1) Number of Scottish sea lochs Nutrient Enhancement Index
> 10.0 5 (4.5 %) 5
3.0 – 10.0 15 (13.5 %) 4
1.0 – 3.0 23 (20.7 %) 3
0.3 – 1.0 22 (19.8 %) 2
< 0.3 46 (41.4 %) 1
Total 111
More complex models exist, where the biological response from nutrient additions is
predicted in terms of phytoplankton biomass or chlorophyll. Once such model, currently
being adapted for an aquaculture (Laurent et al., 2006) was initially developed for predictions
of the eutrophication potential of nutrient discharges from sewerage marine outfalls. This
model, originally called the CSST model, has been described by Tett et al. (2003). Such
models are capable of being applied at a range of scales and in non-enclosed water bodies,
provided appropriate boundary conditions are known, can be measured or can be predicted
from larger scale models.
Absolute standards for what constitutes eutrophication are not available. What constitutes a
harmful disturbance to the ecosystem will vary according to the normal seasonal cycle which
may be very different in temperate, sub-tropical and tropical regions. Thus to assess the
acceptable level of phytoplankton biomass will require some knowledge of annual nutrient
cycles and the primary production response for different environments and such
measurements have often not been made. An alternative is to look for a deleterious
ecosystem response such as the hypoxia caused by enhanced carbon inputs to deeper waters
and sediments. Hypoxia may constitute a threat not only to the ecosystem but to the farmed
fish themselves.
Poor water quality, resulting from self effects of the fish farm, tends to be a very localised
problem, mainly affecting the cultured fish and local animal and plant populations that
cannot move away from the affected water body. The main problems are H2S/ methane in
the water, arising from outgassing of severely affected sediments, as well as local oxygen
depletion, generally due to poor water exchange and/or failure to prevent clogging of the nets
by fouling organisms.. These issues need to be considered primarily as a local, management-
related problem but should not be disregarded when considering broader environmental
interests. In addition, dissolved products including ammonia, phosphorus and dissolved
organic carbon may lead to possible hypernutrification and the potential for the development
of eutrophic problems in the vicinity of fish farms (as suggested in MacGarvin (2000)). The
nature of this cause and effect relationship and its theoretical connection with the occurrence
of blooms of undesirable algal species in coastal waters is far from clear and should be
addressed in the context of multiple coastal use. Whilst some research is on-going in this
area (OAERRE 2001) much more attention and finances should be directed into this field.
8
Solid wastes
Particulate material from aquaculture effluent in the water column is generally a relatively
localised problem, although there is a risk of affecting wild fish populations and other aquatic
animals. Both particulate and dissolved waste can be of consequence in areas where the
ecosystem is particularly fragile, such as conservation areas (e.g. coral reefs, seagrass beds),
or where the water is used for other activities, such as bathing beaches.
Perhaps the most conspicuous impact of mariculture is the sedimentation of wasted food and
faecal material under the farm cages. The accumulation of such material on the seabed results
in a loose and flocculent black sediment under fish cages (Hall et al., 1990; Angel et al.,
1995), commonly named “fish farm sediment” (Holmer, 1992). This sediment is
characterized by low values of redox potential (Hargrave et al., 1993), high content of
organic material (Hall et al., 1990; Holmer, 1992) and accumulation of nitrogenous and
phosphorous compounds (Hall et al., 1992; Holby & Hall, 1991; Karakassis et al., 1998).
These changes in the physical and chemical characteristics of the seabed induce conspicuous
changes in the structure of the benthic communities (O’Connor et al., 1989; Weston, 1990;
Pocklington et al., 1994). Kupka-Hansen et al. (1991) have reported a farm sediment
thickness up to 30 cm (with 60-90% SWC) in W. Norway indicating that no fauna larger than
5 mm was found when thickness exceeded 20 cm. An azoic zone has also been reported from
the Mediterranean with farm sediment thickness less than 6 cm (Karakassis et al., 1998). The
succession pattern along the nutrient enrichment gradient is similar to that described by
Pearson & Rosenberg (1978). Although significant impacts have been reported at distances
as far as 100 m from the cages (Weston 1990) in general it seems that this impact is a highly
localized phenomenon not exceeding 20-50 m around the cages (Beveridge, 1996). A partial
recovery process of the sediment quality during the winter (Figure 2) has been reported from
a Mediterranean fish farm (Karakassis et al., 1998).
The major solid wastes from fish farming are from uneaten feed and faecal material. The
quantity of both these components will vary by species, food conversion ratio, food
digestibility and the skill of the operator in matching feed availability to demand.
Benthic macrofaunal communities in sediments receiving normal detrital inputs derived from
planktonic production in the overlying water column are species rich, have a relatively low
total abundance/species richness ratio and include a wide range of higher taxa, body sizes and
functional types, i.e. they are highly diverse communities (Pearson, 1992). The total
productivity of the system is dependent on the availability of food - organic matter, and its
quality. Animals have evolved to maximise the utilisation of the available resource by virtue
of a wide range of feeding modes and some species can vary their mode of feeding
depending on environmental factors. Benthic types include filter feeders that gather detrital
material from the water column above the sediment, surface deposit feeders that feed on
material deposited on the sediment surface, sub-surface deposit feeders that consume buried
organic material by burrowing, and carnivores that prey on other macrofauna. Microbes
degrade organic material and are themselves consumed by macrofauna, mediating the
transfer of nutrients up the food chain.
A variety of terminal electron acceptors are used by different bacterial communities in

marine sediments. The oxygen concentration at any point in the sediment is dependent on
the rate of its uptake, either to fuel aerobic metabolism, or to re-oxidise reduced products
released from deeper in the sediment. When the oxygen demand caused by input of organic
matter exceeds the oxygen diffusion rate from overlying waters, sediments become anoxic
9
and anaerobic processes dominate. As sediments become more reducing with increasing
distance from the water column interface, a range of microbiological processes become
successively dominant in the order:
• aerobic respiration, ammonium oxidation (to nitrite) and nitrite oxidation (to nitrate).
These aerobic nitrifying processes are inhibited by sulphide and are, therefore, of limited
importance in sediments beneath marine fish farms;
• denitrification (producing dinitrogen from nitrate);
• nitrate reduction (producing ammonium from nitrate) and manganese reduction;
• iron reduction;
• sulphate reduction (producing hydrogen sulphide)
• and lastly, under the most reducing conditions, methanogenesis (producing methane).
To some extent, these processes may overlap spatially. Oxygen in sediment porewaters is
rapidly depleted and sulphides are generated by sulphate reduction, which is the dominant
anaerobic process in coastal sediments (Holmer and Kristensen, 1992).
These effects on sediment biogeochemical processes have profound consequences for the
seafloor fauna that becomes dominated by a few small, opportunistic species, often at very
high abundances, and confined to the upper few centimetres of the sediment (Brooks and
Mahnken, 2003a; Brooks et al., 2003a; Brooks et al., 2003b; Hargrave et al., 1997; Heilskov
and Holmer, 2001; Holmer et al., 2005; Karakassis et al., 1999; Pearson and Black, 2001;
Pearson and Rosenberg, 1978; Weston, 1990). Away from the farm, as organic material flux
and oxygen demand decreases, animal communities return to background conditions typified
by high species diversity and functionality (Gowen and Bradbury, 1987; Nickell et al., 2003;
Pereira et al., 2004).
The redox potential (Eh) profile measured down the sediment column to a depth of 10-15 cm
gives a useful guide to the relative degree of carbon enrichment in the sediments (Pearson
and Stanley, 1979). Positive Eh values are indicative of aerobic conditions whereas negative
values are associated with anaerobic microbial processes. Under normal rates of detrital
carbon input to sediments the redox discontinuity level (RDL), i.e. the point at which
anaerobic processes become predominant, lies some centimetres below the surface. As
carbon inputs increase the RDL approaches ever closer to the surface as the BOD (Biological
Oxygen Demand) within the sediments increases. Eventually, under very high detrital inputs,
the RDL coincides with the sediment/water interface, where, under low flow conditions, it
might even rise into the water column.
It is important to emphasise that highly organically enriched sediments can occur naturally
from large marine or terrestrial inputs of detritus. This may be transient and localised or
long-lived and wide scale. Hypoxia/anoxia in sediments and overlying water occurs when the
supply of new oxygenated water is poor as may be the case, for example, in deep silled
fjordic systems. In such systems, benthic communities are modified and specialist
opportunist animals may dominate.
The process of organic particulate material impacting the seabed and causing benthic effects
is amenable to modelling (Cromey and Black, 2005; Cromey et al., 2002a; Cromey et al.,
2002b; Silvert and Cromey, 2001; Silvert and Sowles, 1996). A widely used model is that of
Cromey et al. (2002a) – DEPOMOD. The outputs of this model are in terms of accumulated
carbon per unit area of sea bed per unit time – the word accumulation is used here as
10
resuspension processes are accommodated in the model. The output is visualised as a

contour plot of carbon deposition on a spatial grid (an example is shown in figure 3).
-2 -1
g solids m bed yr
450
400
15000
350
5000
300
Northing (m)
250 Group 3 2500
200
M 500
B3 A3
150
25
100
50
0
0 50 100 150 200 250 300 350 400 450 500
Easting (m)
Figure 3. Example of a DEPOMOD particle tracking model output. Cages are represented
by squares; the contours show the accumulation of organic matter on the seabed
beneath and around the cages.
In Scotland, as in several other countries, the regulator (Scottish Environment Protection

Agency, SEPA) is required to manage the impacts of fish farming to avoid unacceptable
damage of the sea bed and its fauna. SEPA have gone a little further than most regulators in
giving some examples of where they think the boundary between acceptable and
unacceptable seabed conditions lies. They have established Sediment Quality Criteria (SQC,
table 2) as indicators of when they will take action in order to reduce impacts, e.g. by
reducing the maximum allowable biomass or by entirely revoking the discharge consent.
The SQC are not the only criteria used – SEPA will accept and consider all the available
evidence – but as many benthic indicators co-vary, they do offer a meaningful insight into
what SEPA consider to be unacceptable benthic conditions. Discharge consents have
monitoring conditions specified in detail: both their level (i.e. the number of stations, types of
measurement and analysis) and their frequency are matched to the perceived risk of the farm.
For example, a small farm over a hard sediment with strong currents will be monitored less
intensively than a large farm over a soft substrate with weak currents. This process is given
in great detail, together with its underlying philosophy and science, in the regularly-updated
Fish Farm Manual that can be downloaded from the SEPA website (www.sepa.org.uk).
Table 2 Sediment Quality Criteria (SEPA Fish Farm Manual, Annex A)
Determinand Action Level Within Action Level Outside

Allowable Zone of effects Allowable Zone of effects
11
Number of taxa Less than 2 polychaete taxa present Must be at least 50% of
(replicates bulked) reference station value
Number of taxa Two or more replicates with no taxa
present
Abundance Organic enrichment polychaetes Organic enrichment polychaetes
present in abnormally low densitiesmust not exceed 200% of
reference station value
Shannon -Weiner N/A Must be at least 60 % of
Diversity reference station value
Infaunal Trophic N/A Must be at least 50% of
Index ( ITI ) reference station value
Beggiatoa N/A Mats present
Feed Pellets Accumulations of pellets Pellets present
Teflubenzuron 10.0 mg/kg dry wt/5cm core applied 2.0 ug/kg dry wt/5 cm core
as a average in the AZE
Copper* Probable Effects 270 mg/kg dry 34 mg/kg dry sediment

sediment Possible Effects 108
mg/kg dry sediment
Zinc* Probable Effects 410 mg/kg dry 150 mg/kg dry sediment
sediment Possible Effects 270
mg/kg dry sediment
Free Sulphide 4800 mg kg-1 (dry wt) 3200 mg kg-1 (dry wt)
Organic Carbon 9%
Redox potential Values lower than -150 mV (as a depth average profile)
OR Values lower than -125 mV (in surface sediments 0-3 cm)
Loss on Ignition 27%

*A detailed description of the derivation of these action levels may be obtained from SEPA on request.
The SQC (or Action Levels, Table A1) are levels at which SEPA may take action against the
farmer i.e. reduce or remove the consent to discharge. Implicit within the approach are:
a) that the farmer is required to monitor the sediments around the farm to measure
compliance or otherwise, and
b) the concept of the Allowable Zone of Effects (AZE).
The AZE represents an area around the farm where some deterioration is expected and
permitted. Thus for several determinands, two SQCs are proposed: one within the AZE and
one at any point outside the AZE. The SQC inside the AZE is less demanding than that
outside the AZE. The SQC approach thus constrains the level of ecological change while the
AZE limits the spatial extent of major changes.
3.1.1 Organic matter

A variety of physical, chemical and biological changes occur in sediments exposed to
continual deposition of organic waste from aquaculture. Where the rate of waste deposition,
mainly in the form of faeces and waste food, exceeds the natural rate of breakdown in the
sediments, a layer of this waste will settle on top of the natural sediment at the sea floor.
This fine-grained, and often slimy, material has a very high organic content. In the absence
of breakdown of this organic material, the sediments can become very acidic, and toxic
12
gasses such as H2S and methane may be produced. In extreme cases, these gasses may
bubble out through the sediments to the detriment of the fish in the overlying water mass. In
these cases, there are generally no macrobenthic animals remaining in the sediments. If
conditions are allowed to deteriorate, the sediments may become oxygen depleted or even
fully anoxic. The deposited material on the sea floor may become blackish in colour, with a
noxious smell and a layer of white, chemoautotrophic bacteria (Beggiatoa sp., Achromatium
sp.) usually forms at the surface (Midlen and Redding 1998).
During the deterioration of healthy sediments, the community structure of benthic animals
changes: the less resistant forms die out to be replaced by fewer, more tolerant forms, which
then become more abundant. This predictable response forms the basis of the biological
component of monitoring programmes. The depth to which the sediments are oxygenated
gradually decreases, from often many centimetres deep, to a very shallow or even absent
oxygenated layer. The depth of sedimentary oxygenation can be detected by measuring the
redox (Eh) potential down the sediment profile (for example at 1cm intervals). The point at
which the sediment switches from being well oxygenated to anoxic is seen by a marked
switch in redox potential readings, known as the redox potential discontinuity (RPD) layer.
This is also a useful indicator of the status of the sediments and is widely used in many
monitoring schemes (Black 2001).
Effluent from net-washing machinery can produce significant local sources of dissolved
contaminants in the water column. This can, however, be minimised in areas where there are
centralised facilities for net-washing, which use water treatment or filtering of the effluent.
Chemicals and other additives

Because vitamins and other nutritional additives as well as antibiotics and other medication
are usually introduced via feed, some of these compounds will also remain bound to the
organic matter in waste feed and faeces. The effects of these compounds on the aquatic
environment and the food web are not yet well understood and potential deleterious effects
on the benthic system have been suggested (Black et al. 1997; Davies et al. 1998; Grant and
Briggs 1998) and need further research.
Several classes of chemicals are used in fish farming. Three of the most important are
antibiotics, antiparasitics and antifoulants. Since the advent of effective fish vaccines for
several important bacterial diseases, the use of antibiotics in salmon culture has declined
since the early 1990s (Alderman, 2002), but less is known about the use of antibiotics in
other species, particularly those in the developing world (Graslund and Bengtsson, 2001;
Holmstrom et al., 2003; Tacon et al., 1995).
Antibiotics
The main concerns relating to antibiotic use relate to the possibility of the development of
bacterial resistance that can be transferred to human pathogens reducing the efficacy of
antibiotics in human medicine (Cabello, 2004; Cabello, 2006). Prophylactic use of
antibiotics is a particular concern, as is adequate testing of aquaculture products for
antibacterial residues. Where residues persist, low levels of antibiotic intake can stimulate
resistance in human pathogens but another concern is that some of the antibiotics used in
aquaculture may not be approved for human medicine and carry a health risk. For example,
nitrofurans (e.g. furazolidone) are a group of antimicrobials which possess either
carcinogenic or mutagenic properties whose use is banned in many countries but still
13
permitted in some. In general, limits have not been set for the concentrations of antibiotics
permitted in the environment.
It has been estimated that 50-80 tonnes of antibiotics per year were being used by the salmon
industry in western Europe by the end of 1980s (Beveridge et al., 1994). The main impact of
anti-microbial agents is related to the development of resistant strains of aquatic microbes
which could have serious implications not only for farmed fish, but also for the wild
populations or even for human health (IOE, 1992). The overuse or abuse of
chemotherapeutants could also negatively affect the bacterial activity in the sediments
(Beveridge et al., 1994) and therefore it could inhibit the main mechanism for recovery of
heavily polluted areas under farm cages and interfere with the food chain processes both in
the water column and the sediment.
Antiparasitics
Of the anti-parasitics, the best studied are those that treat infestations of sea lice on
salmonids. These are generally highly toxic substances where the use is tightly regulated. In
Scotland, for example, ecological quality criteria have been set both for both sediments and
the water column www.sepa.org.uk/pdf/guidance/fish_farm_manual/annex/A.pdf and access
to these medicines is strictly controlled. Medicines are only available to farmers after a
multi-step regulatory process of authorisation that includes testing for efficacy, food safety
and environmental effects.
Antifoulants
Antifouling agents are also widely used in mariculture. These slow-leaching biocides prevent
the settlement of the juvenile plankton stages of fouling organisms on the cage structures.
Some types of antifouling chemicals (e.g TBT) have been prohibited after having been
proved to be highly toxic to molluscs (Davies et al., 1988) and they could affect farmed fish
(Bruno & Ellis, 1988).
The most infamous antifoulant product, now banned, is tributyl tin (TBT). TBT disrupts the
endocrine system in invertebrates leading to imposex (Miller et al., 1999) and has now been
replaced by products with a high concentration of copper. Copper, however, is also a potent
toxin, hence it’s utility as an antifoulant, and quality criteria have been set for both the water
column and sediments. A recent study at a fish farm in Scotland found copper at higher
concentrations than the sediment quality criteria (Dean et al., 2007) although its toxicity in
anoxic sediments may be limited by its precipitation as the sulphide (Brooks and Mahnken,
2003b).
Effects on wild fish populations

3.1.2 Contamination with waste
The attraction of aquaculture installations to wild fish is widespread, and seems to be a
combination of the artificial reef effect (physical shelter) as well as food availability (the
waste from the farmed fish). What is interesting in an international context is that
aquaculture installations in Mediterranean waters seem to attract far greater populations of
wild fish than is the case in Atlantic waters. Therefore, there is a greater risk of transfer of
contaminants and pathogens via aquaculture waste to wild populations in the Mediterranean,
or other warmer waters, than may be the case in colder Atlantic waters.
14
Wild fish in the Mediterranean also seem to be responsible for removing a greater proportion
of deposited waste from fish farms than is seen at Scottish and Norwegian farms. This is
particularly important to bear in mind when modelling or predicting waste dispersal
scenarios.
3.1.3 Parasites and diseases

Currently, a major area of concern is the potential transfer of parasites (e.g. sea lice) and
pathogens from farmed fish to wild fish stocks. These may be transmitted in two main ways –
either by wild fish coming into contact with caged fish and their waste-products or by contact
between escaped farm fish and wild individuals. Therefore, the frequency and intensity of
parasite infestations in wild and cultured fish should be addressed by monitoring
programmes. Any overlap between parasites and diseases in wild and cultured populations
will help to identify potential vectors of pathogens. Comparing parasite densities and
intensities at farm sites with those in unaffected areas will help to assess the effect of fish
farms on the health of wild fish.
The issue of potential infestation of wild fish populations with parasites of fish farm origin is
a controversial one. Particular conflict may arise in areas where sport-fishing/angling is a
major source of income and where parasite infestation threatens the popularity of a particular
water course. Several national and international applied research programmes are in
progress, which aim to trace the source of parasites on or in wild fish, using genetic and other
methods.
3.1.4 Escapees and genetic transfer

Another concern is that escaped farm fish may interbreed with wild populations, and
contaminate the wild gene pool. The fear is that the resulting progeny will lose their homing
ability and not spawn where expected, or that there will be a reduced ability to survive in the
natural environment. These issues are generally addressed by national nature management
authorities and will not be considered further in this document. Further information can be
found in Youngson et al. (2001).
The effect of accidental or intentional release of cultured fish into the marine environment
causes widespread concern due to the risk of genetic loss, or of significant modification of
important natural traits and adaptive variations of the wild populations (Hinder et al., 1991).
Evidence of such interactions has been presented for the Atlantic salmon in N. Ireland
(Crozzier, 1993).
Exotic species, or varieties, selected for particular traits such as rapid growth or high
fecundity, are commonly moved from one continent to another in an attempt to capitalize on
already developed technologies and markets (Beveridge et al., 1994). Many of these species
successfully colonise natural waters, after escaping from aquaculture systems. Therefore
there is a potential for impact on natural communities, either through competition with
natural populations, or (in the case of varieties) through modification of the gene pools of
natural stocks.
The introduction of exotic parasites or other disease agents along with the introduction of
exotic farmed species, also causes concern for impacts on native populations which have not
previously been exposed to such agents.
15
Direct impacts on wildlife

Disturbance of feeding and breeding of wildlife is also a potential consequence of
mariculture since aquaculture activity involves increased human activity, noise, road and boat
traffic and building of floating and land-based structures (Beveridge et al., 1994). Other
potential impacts involve the attraction of predators and scavengers, due to increased
densities of food resources, which could displace local species or increase the conflicts
between human and wildlife resulting in increased (intentional or unintentional) mortality of
natural populations. Some evidence of such risks was presented in respect of double-crested
cormorants (Phalacrocorax auritus) which is perceived to be a significant pest of aquaculture
(Glahn & Stickley, 1995; Nisbet, 1995). Anti-predator nets and shooting of potential predator
species has been resorted to by fish farmers. However there is no evidence that such practices
have had a significant effect on local bird population size, while even less is known with
regard to the effects on mammal populations (Munday et al., 1992). Gowen (1992) noted that
there is a lack of reliable data on this issue since the available information comes mainly
from surveys using answers from questionnaires sent to the farmers.
Implications for biodiversity

Almost all the above-mentioned types of impacts could result in decreasing diversity at
various levels. However not all of them would induce such serious ecological changes as to
affect biodiversity at a significant spatial scale, or to produce irreversible environmental
changes.
The effects on benthic communities are similar to those produced by several other sources of
organic enrichment. The local decrease in diversity could be acceptable unless the following
situations obtain:
(i) the damaged ecosystem constitutes the habitat of an endangered species
(ii) the damaged ecosystem is a nursery ground for species affecting the ecology of a
broad marine area
(iii) the damaged ecosystem is a rare and region-specific habitat
(iv) the damaged ecosystem is impaired, to that an extent that its loss is irreversible on a
human time scale
Marine systems harbour the highest number of phyla (Ray & Grassle, 1991) and the majority
of marine phyla occur in the coastal zone, so it could be argued that the marine coastal zone
is the most biologically diverse realm on the planet (Ray, 1991). Although deep-sea benthic
biodiversity, in terms of species, has been estimated as extremely high (Grassle & Macioleck,
1992), it has been shown that biodiversity per unit area is higher in the coastal environment
than in the deep sea (Gray et al., 1997; Karakassis & Eleftheriou, 1997). Furthermore coastal
ecosystems contribute to the global carbon fixation, to an extent disproportional to the area
they occupy. Estimations of productivity for the worlds' aquatic ecosystems, based on Walsh
& Dieterle (1988), give a productivity 5 times higher in shelf ecosystems than that of the
Ocean. Therefore it could be expected that large scale ecological impacts on the coastal zone
would result in severe impairment of the environmental conditions beyond the limits of the
impacted area. The destruction of seaweed communities for instance could be significant for
biodiversity since they are essential habitats for various life cycles, while they also protect
against shoreline erosion. However no such large scale impacts have been reported in
relation to mariculture with the exception of mangrove habitats in the tropics used for the
culture of milkfish and shrimp (Iwama, 1991; Beveridge et al., 1994).
16
Hypernutrification and change of the trophy status of a particular area could be important
only in highly enclosed areas while exposed areas with adequate water renewal are not
expected to present eutrophication symptoms. Although significant increase in nutrient
concentrations has been reported in the vicinity of fish farms by many authors (references in
Beveridge, 1996) any significant increase in phytoplankton biomass has been rather
exceptional (Wallin & Hakanson, 1991) and no large scale eutrophication has been reported
in relation to aquaculture. However, such impacts may not be excluded in respect of the
large-scale expansion of Aquaculture in combination with unsuitable siting and specific
hydrographic conditions.
Loss of biodiversity as a result of genetic interactions also depends on the state and the size
of wild populations, the number of farmed individuals released into the marine environment
and their ability to survive there in direct competition with native species (Munday et al.,
1992). For instance the use of triploids, which are reproductively sterile, eliminates the risk
of hybridization. However, in some cases, sterile fish live longer and are more robust and
therefore it has been suggested that if competition or predation problems arise between
stocked triploids and native species, then halting stocking would eliminate these interactions
within one life cycle (Habicht et al., 1994). However in the case of large numbers of
triploids, within this period of one life cycle, the natural populations could undergo a
considerable decrease, resulting in "bottle neck effect" and considerable loss in genetic
variability.
4 Scientific rationale behind monitoring methods

Hydrographic/ water quality analyses and other assessments
The dispersal of aquaculture discharges is dependent on the hydrographic conditions and
water exchange mechanisms in the area. Environmental impacts on bottom substrates and
the water column are minimised in areas with strong current flow. However, the degree of
exposure must not exceed the physical tolerance of the production installations or the culture
organisms. It is therefore important to measure a range of hydrographic variables,
particularly during the planning or pre-licence phases. The most important information
required is as follows: current speed; current direction; neap and spring variations; current
residuals; bathymetry; winds and wave action; temperature; salinity; water stratification;
other regional factors (such as ice action and super-cooled water in cold-water areas).
Since hydrographic conditions are seasonally variable, measurements should be carried out at
certain time intervals, to take into account different sea temperatures and seasonal
stratification/upwelling of bottom water masses. In areas with significant tidal flows, current
measurements should be made over a full tidal cycle, preferably at both spring and neap
tides. Peaks in production activities should also be taken into consideration.
Further, where possible, hydrographic measurements should be carried out at several sites
within a given area to assess local variations in hydrography that could affect the aquaculture
activities. For example, small variations in topographical features could cause local
anomalies in current flow. Particular attention should be paid to such variability in sill-fjord,
sill-loch areas, or where there are small coves within a bay or gulf. In addition, it is essential
that accurate position fixing is used and that relocation of stations for time series analysis or
for specific spatial monitoring, is considered.
17
Sensory measurements (e.g. presence of gas bubbles, sediment colour, smell, consistence and
softness) are also important in providing a quick assessment of local environmental
conditions. In Norway, these are employed to assess environmental status in the local impact
zone, as part of the MOM system (modelling - ongrowing fish farms – monitoring), and a
score system is used to quantify the impact (Maroni 2000). In addition, redox measurements,
as mentioned below, provide a semi-quantitative measure to assist with the sensory
descriptors.
Chemical analyses
Chemical analyses of bottom sediments around aquaculture sites quantify the levels of
contaminants or the chemical properties. These can be compared with natural conditions in
the area as well as pre-defined levels of acceptability or consent.
Some measurements can be carried out in situ using probes for which the results are
immediately available. These include the following variables, all of which give information
on the sediment loading: pH, redox (Eh), oxygen. Laboratory analyses most often focus on
the following: organic content, hydrogen sulphide, sediment granulometry (indicative of
organic deposition, bottom current speeds and also used for normalisation of levels of
contaminants) and heavy metals. In addition, specific pesticides, medicinal agents and
antifoulants may be analysed according to individual requirements.
Benthic faunal analyses

Changes in the organic loading of an area result in marked changes in the fauna present on
the sea floor. Extensive work has been carried out in sedimentary areas, for which a model
framework has been developed in relation to an organic enrichment gradient (Pearson and
Rosenberg 1978). The normal situation in undisturbed areas is a high species diversity with
few dominant species and relatively few individuals representing each species. In general,
organic loading of the sediment leads to a reduction in species diversity and an increase in
abundance of opportunistic species. However, if the level of pollution becomes very severe,
even opportunistic species will disappear, such that there are no macro-organisms present in
extreme conditions. In such cases, if sedimentation is not very heavy, a white bacterial layer
may form on the sediment surface. This principle of macrofaunal responses to pollution
gradients in marine communities is explained in detail in Pearson and Rosenberg (1978). In
this way, the changing status of macrofaunal communities is a very sensitive indicator of
sedimentary conditions, allowing the detection of environmental impacts, where other
methods might not record them.
Specific methodology concerning benthic faunal analysis (Holme and McIntyre 1984) would
include, for example, specification of sieve mesh size (e.g. in Northern latitude coastal areas,
1mm should be used, whereas in similar situations in the Mediterranean, 0.5mm should be
used), sample preservation and level of taxonomic identification (for standard monitoring
practices in low sensitivity situations, a specific taxonomic resolution could be agreed, e.g.
Family level; (Kingston and Riddle 1989; Karakassis and Hatziyanni 2000)). Rigorous
analytical quality control procedures must be developed for all areas of practical work and
implemented.
18
5 Aquaculture Regulation
Marine fin-fish aquaculture continues to expand, although expansion has to some extent
plateaued in several of the developed countries where modern intensive aquaculture was
pioneered. For example, in Scotland production increased steadily reaching a peak in 2003
but has since been variable (figure 1). There are several reasons for this including disease
and market conditions, but one reason has been constraints placed on farmers by planners and
regulators.
180,000
160,000
140,000
120,000
100,000
80,000
60,000
40,000
20,000
0
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
Figure 1. Scottish annual salmon production, tonnes. (Frs, 2006)
Planners must ensure that aquaculture developments meet aesthetic, social and economic
criteria, and that there is harmonisation between new developments and local infrastructure
capacity or other resource use e.g. tourism. Planners and regulators have duties to ensure that
developments do not adversely affect the environment. The objectives of regulation can be
separated into three areas:
1. protection of legitimate users of the environment, such as tourists or fishermen, such that
resources are fairly distributed.
2. protection of the environment for its biological structure including protection of
important/rare habitats and species
3. protection of ecosystem functions such as the recycling of nutrients and the maintenance
of oxygen levels
The first of these is the subject of the evolving “discipline” of Integrated Coastal Zone
Management (ICZM) which has 8 broad principles (Defra, 2006). It is worth presenting these
here in full:
a. A broad holistic approach

The objective of a holistic approach is to forego piecemeal management and decision
making in favour of a more strategic approach which looks at the ‘bigger picture’,
19
including cumulative causes and effects. This means considering the conservation value
of natural systems alongside the human activities which take place on land and coastal
waters.
Taking a holistic approach will also involve looking at the problems and issues on the
coast in the widest possible context, including looking at the marine and terrestrial
components of the coastal zone and considering how different issues conflict or interact
together.
b. Taking a long term perspective

Successful coastal management must consider the needs of present and future
generations. Therefore, administrative structures and policies required to manage the
environmental, social and economic impacts now, must also be adaptable to take account
of, and acknowledge, uncertainties in the future.
c. Adaptive management
The … coastline has been subject to constant physical and economic changes over the
years, and management of such a dynamic environment requires measures which are able
to adapt and evolve accordingly. Successful management should reflect this principle by
working towards solutions which can be monitored effectively.
d. Specific solutions and flexible measures

Coastal management measures for each stretch of coast must reflect and accommodate
the many variations in the topography, biodiversity and local decision-making structures.
Integrated management should therefore be rooted in a thorough understanding of the
specific characteristics of an area i.e. its local specificity.
e. Working with natural processes

The natural processes of coastal systems are continual, so it becomes necessary in some
instances to adopt a different approach which works with natural processes rather than
against them. By recognising the physical impacts and the limits imposed by natural
processes, decisions regarding the human impact on the coastal zone are made in a more
responsible manner and are more likely to respond to environmental change.
f. Participatory planning
In the past stakeholders may not have had sufficient opportunity to contribute towards the
development and implementation of coastal management measures or programmes.
Participatory planning incorporates the views of all of the relevant stakeholders
(including maritime interests, recreational users, and fishing communities) into the
planning process. It can also help to promote a real sense of shared responsibility and
coastal stewardship by reducing conflict as real issues, information and activities which
affect the coast can be aired more openly.
g. Support and involvement of all relevant administrative bodies

Administrative policies, programmes and plans (land use, spatial, energy, tourism and
regional development for example) set the context for the management of coastal areas
and their natural and historical resources. Addressing the problems faced by … coastal
zones will therefore require the support and involvement of all relevant administrative
bodies at all levels of government to ensure cooperation, coordination and that commons
20
goals are achieved. It is therefore essential to engage key bodies from the start so that
decisions are consistent and firmly based on local circumstances.
h. Use of a combination of instruments

Managing the different activities which take place on the coast requires the use of a
number of different policies, laws and voluntary agreements. While each of these
approaches is important, achieving the right combination is key to resolving conflicts, as
these instruments should work together to achieve coherent objectives for the planning
and sustainable management of coastal areas.”
The second objective, the protection of ecosystem structure, may be intimately linked to the
third, protecting ecosystem function, especially where the structure of habitats have dominant
functional roles. For example, mangroves have been shown to have key functional roles in
flood protection, nutrient recycling and as nursery areas (Holmer, 2003; Primavera, 1998;
Primavera, 2005). However, habitats may be deemed worthy of protection when their
precise contribution to ecosystem function is unknown but they are considered to be rare or
have rare species assemblages e.g. cold water corals and moves to protect them from trawling
damage (Roberts et al., 2006).
Interactions between aquaculture and sensitive habitats or species can be minimised by
establishing aquaculture zones in areas with less sensitive/important/rare habitats, or by
designations that more closely regulate developments with respect to their interactions with
particular features of concern. In Europe, Special Areas of Conservation (SACs) have been
established under the Habitats Directive (92/43/EEC) for the protection of specific habitats.
As this is an important piece of legislation, with wide ranging impact, it is worth exploring
this further. The UK Joint Nature Conservation Council gives the following background on
its website (www.jncc.gov.uk).
“In 1992 the European Community adopted Council Directive 92/43/EEC on the
Conservation of natural habitats and of wild fauna and flora (EC Habitats Directive).
This is the means by which the Community meets its obligations as a signatory of the
Convention on the Conservation of European Wildlife and Natural Habitats (Bern
Convention). …The provisions of the Directive require Member States to introduce a
range of measures including the protection of species listed in the Annexes; to
undertake surveillance of habitats and species and produce a report every six years on
the implementation of the Directive. The 189 habitats listed in Annex I of the
Directive and the 788 species listed in Annex II, are to be protected by means of a
network of sites. Each Member State is required to prepare and propose a national list
of sites for evaluation in order to form a European network of Sites of Community
Importance (SCIs). Once adopted, these are designated by Member States as Special
Areas of Conservation (SACs), and along with Special Protection Areas (SPAs)
classified under the EC Birds Directive, form a network of protected areas known as
Natura 2000. The Directive was amended in 1997 by a technical adaptation Directive.
The annexes were further amended by the Environment Chapter of the Treaty of
Accession 2003.
The Habitats Directive introduces for the first time for protected areas, the
precautionary principle; that is that projects can only be permitted having ascertained
no adverse effect on the integrity of the site. Projects may still be permitted if there
are no alternatives, and there are imperative reasons of overriding public interest. In
21
such cases compensation measures will be necessary to ensure the overall integrity of
network of sites.”
In Loch Creran on the west of Scotland, for example, an SAC has been implemented to
protect the unique reefs of the tube building polychaete Serpula vermicularis and reef
forming horse mussels Modiolus modiolus. Several management principles are invoked in
marine SACs (www.argyllmarinesac.org):
• Management should enable the natural habitat types and the species habitats
concerned to be maintained or, where appropriate, restored at a favourable
conservation status.
• Steps must be taken to avoid deterioration or disturbance of the habitats and species
for which the site has been designated.
• Activities, plans or projects likely to have a significant effect upon the features of the
site must be subject to an appropriate assessment. A development that would have an
adverse effect on the conservation interests of the site should only be permitted if
there is no alternative solution and there are imperative reasons of over-riding public
interest, including those of a social or economic nature.
• Monitoring must be undertaken at each site to monitor the condition of the
conservation features and to assess the effectiveness of management measures.
• Management of the site must take into account the economic, social, cultural and
recreational needs of the local people.
Loch Creran was one of the original sites in Scotland developed for fish farming with
continuing major aquaculture activity both from shellfish and salmon faming. However, any
proposed change to the aquaculture activity must be assessed against these principles. In
practice, the operator has found it possible to continue to farm in Loch Creran, despite the
SAC, by being able to show that any proposed changes will have little impact on the
conservation feature.
In general, the science of interactions between sensitive habitats and aquaculture is not well
developed, and it is only where catastrophic impacts occur on relatively visible habitats, such
as mangroves or sea grasses (Holmer et al., 2003; Orth et al., 2006), that research effort is
focussed. Thus for many habitats, neither the precise functional significance nor the
sensitivity to aquaculture is known with any certainty and regulation is more problematic.
In addition to loss of habitats, reduction in genetic diversity can also be regarded as having a
structural component that may or may not also have a functional aspect. For example, the
release of genes, disease organisms and parasites for salmon culture and their effects on wild
populations has received considerable attention. Wild Atlantic salmon maintain their high
degree of population structure by homing to natal rivers for breeding. The resulting genetic
diversity has been shown to be important in terms of fitness and can be severely eroded by
interbreeding with escaped cultured salmon or from intentional translocations of fish with
maladapted genes (Mcginnity et al., 2003). Modelling work has shown that under high rates
of intrusion of cultured fish significant changes to populations will occur that may not
recover even if the intrusion rate is reduced (Hindar et al., 2006). For marine species, such as
Atlantic cod and European sea bass, the consequences of genetic interactions on populations
are not well established.
22
The potential interactions between parasitic sea lice on wild and cultured populations have
also received considerable attention and publicity. Salmon host ectoparasitic parasitic sea
lice Lepeophtheirus salmonis and Caligis elongatus which feed on the skin and underlying
tissue. In salmon culture these can increase rapidly to high abundance if left untreated and
infestations can result in severe legions and mortality. Sea lice larvae are adept at find hosts
and increasing infestations on juvenile Atlantic salmon and sea trout Salmo trutta were
blamed on infection pressure from salmon farms. This in turn was linked to reduced survival
and population declines of these salmonids. While causal links are extremely difficult to
prove (Mcvicar, 1997), there seems little doubt that sea lice from farmed salmon can (Murray
and Gillibrand, 2006) and do (Bjorn et al., 2001) infect wild salmonids and cause mortality,
particularly to sea trout.
Different approaches have been taken to regulating escapes and parasites in different
countries. In Scotland, the government now require statutory declaration of escapes
including the approximate number and size of fish, the location and date of escape (Scottish
Statutory Instrument 2002 No. 193, The Registration of Fish Farming and Shellfish Farming
Businesses Amendment (Scotland) Order 2002). In the planning process, developments of
farms near important salmon rivers is discouraged, and farmers are obliged to show how they
have taken steps to minimise escapes and improve containment. In Scotland, there is no
statutory limit at present for the average lice infestation of salmon that is permitted before
treatment with anti-parasitic medicines, although there are several voluntary agreements in
place between the fishfarming sector and the fisheries sector (Area Management
Agreements). This is in contrast to Norway where when statutory lice limits are exceeded,
treatment is compulsory (Heuch and Mo, 2001). The situation is likely to change in Scotland
as new legislation, aimed at ensuring farmers keep lice levels low is enacted (Aquaculture
and Freshwater Fisheries Bill). This will require fish farmers to record levels of parasites and
to ensure that burdens are kept low, but the precise mechanism for achieving this has yet to
be announced.
The state of knowledge of the structural effects of fish farming and their sound regulation is
rather weak. In contrast, the third objective of regulation, to protect ecosystem function from
the consequences of aquaculture, is often better understood and quantified. We now briefly
review the current state of knowledge for the main environmental outputs from aquaculture,
focussing on marine fish farming, and for each of these we comment on issues related to
regulation.
In general, the environmental interactions posed by intensive marine shellfish culture are
fewer than for fin fish culture owing to the fact that shellfish are net extractive of nutrients.
However, they do concentrate organic material and deposit wastes as faeces and
pseudofaeces causing enrichment of the local benthos (Chamberlain et al., 2001) and, if
cultured in sufficiently high density, in some areas can clear the water to such an extent that
they reduce productivity (Smaal et al., 2001). Regulation on shellfish farming is, however,
less well developed than for marine finfish farming owing to its lower perceived
environmental risk.
6 Conclusions
The regulation of aquaculture in developed countries has developed considerably over the
past decade. This has been driven by the need to improve the scientific basis for
23
management of this very high economic value sector. Regulators must base their decisions of
good science in order to protect the environment and but at the same time allowing
development with its economic benefits. This has particularly been the case for the major
salmon growing countries, although Chile perhaps has still to catch up in a regulatory sense
with its rapidly expanding industry. In the developing world, where aquaculture products are
primarily for export, market pressures are increasingly brought to bear to ensure food safety,
for example concerning residues, and there is also a growing awareness of environmental
issues, particularly relating to habitat destruction related to shrimp farming. In the
Philippines, regulation of the very large number of small scale fish farms where the market is
local represents a significant regulatory challenge, but the potential environmental costs
make rational regulation essential for the future of this industry. In this paper we have
outlined some of the approaches being taken by aquaculture regulators in other countries. It
is highly likely that some of these approaches will be relevant and adaptable to the Philippine
industry.
Acknowledgements
This review is primarily based on papers by Kenny Black of the Scottish Association of
marine Science, Yannis Karakassis et al of Biology Department of the University of Crete,
and Sabina Cochrane of Akvaplan-niva.
24
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A Review of

The scientific principles

2 Environmental impacts from Aquaculture

Environmental awareness and sustainability

Table 1. Current environmental concerns arising from marine aquaculture operations

Types of waste and effluent deposition

Wastes from fish farming are usually considered in 3 overlapping categories:

3.1 Soluble wastes

"the enrichment of water by nutrients especially compounds of nitrogen and phosphorus,

The undesirable consequences of eutrophication include(Black et al., 2002):

• increased abundance of micro-algae, perhaps sufficient to discolour the sea and be

A variety of terminal electron acceptors are used by different bacterial communities in

resuspension processes are accommodated in the model. The output is visualised as a

250 Group 3 2500

In Scotland, as in several other countries, the regulator (Scottish Environment Protection

Table 2 Sediment Quality Criteria (SEPA Fish Farm Manual, Annex A)

Determinand Action Level Within Action Level Outside

Copper* Probable Effects 270 mg/kg dry 34 mg/kg dry sediment

Loss on Ignition 27%

3.1.1 Organic matter

Chemicals and other additives

Effects on wild fish populations

3.1.3 Parasites and diseases

3.1.4 Escapees and genetic transfer

Direct impacts on wildlife

Implications for biodiversity

4 Scientific rationale behind monitoring methods

Benthic faunal analyses

a. A broad holistic approach

b. Taking a long term perspective

d. Specific solutions and flexible measures

e. Working with natural processes

g. Support and involvement of all relevant administrative bodies

h. Use of a combination of instruments

Cabello, F. C. (2006). Heavy use of prophylactic antibiotics in aquaculture: a growing

Pearson, T. H. and Stanley, S. O. (1979). Comparitive measurement of redox potential of

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