Aquaculture

by Claude E Boyd and Julio F Queiroz

The role and management

of bottom soils in
aquaculture ponds
Soil and water management are the two basic tenants for successful land based
aquaculture. Many of the negative impacts of inherent soil characteristics and changes
in bottom soils resulting from aquaculture operations can be counteracted by
application of management practices. These practices are outlined in Tabular form for
easy reference.

T
he
importance
of soils in
pond aquaculture
begins with site
selection and
construction.
Because of
their ecological
significance,
wetland sites Claude E Boyd
usually should not
be converted to
other land uses
and particularly
to land intensive
endeavours such
as agriculture
and aquaculture.
Where soils are
acceptable, their
properties are Julio F Queiroz
important for
determining permissible side-slopes of Dried bottom of a shrimp pond.
pond earthwork, degree of compaction
and need for clay liners in bottoms etc embankments. In the case of excavated O horizon is the A horizon that typically
to discuss the role and management of ponds, an even greater depth of earth is the most fertile horizon. These two
bottom soils in existing ponds. may be removed from the bottom area. horizons usually are removed and the
The area to become the pond bottom In terrestrial soils, the O horizon is the pond bottom typically lies in the B
typically is cleared of vegetation and top-most layer that contains recent horizon or possibly in the C horizon.
the upper 25 to 75 cm layer of soil is organic matter additions such as leaves The B horizon is usually of relatively
removed to use as earth fill for dams or and leaf fragments. The layer below the high clay content and both the B and C

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 Aquaculture
horizons are of lower fertility than the O depth – typical rates of sedimentation in the S horizon. Beneath the aerobic
and A horizons that were removed. The older ponds are 1 to 2 cm/yr. In heavily- layer, fermentation by anaerobic
new pond bottom often is compacted aerated ponds, aerator-generated water microorganisms oxidises a portion of the
to reduce the tendency for seepage. currents may greatly accelerate erosion organic matter to carbon dioxide, but
Although the original, terrestrial soil and sediment accumulation. much of the organic matter is converted
profile is greatly altered during pond The typical soil profile in pond to soluble organic compounds such
construction, once the pond is filled bottoms is detectable in sediment cores as alcohols, aldehydes, ketones, and
with water and aquaculture operations of new ponds within 2 or 3 years and short-chain fatty acids. In absence of
initiated, formation of sediment or it is well developed within 5 to 10 year molecular oxygen, bacteria capable of
pond bottom soil profile begins. Dead where sediment is not removed regularly. using combined oxygen from inorganic
plankton, feces of culture species, Notice that the pond soil horizons are compounds such as nitrate, iron and
organic fertilisers and uneaten feed will identified by different letters than used manganese oxides and hydroxides,
settle to the pond bottom. Wave action, for describing terrestrial soil horizons. sulfate and even carbon dioxide in
disturbance of the bottom by aquatic The most active zone of organic matter respiration oxidise organic metabolites
organisms, aerator-generated water decomposition (and oxygen demand) from fermentation. Anaerobic microbial
currents and seine hauls to sample or occurs in the F and So horizons. In activity produces metabolites such as
harvest aquatic animals erode pond this aerobic zone, microorganisms use gaseous nitrogen (N2 and N2O), ferrous
bottoms and side slopes of dams and molecular oxygen to oxidise organic iron (Fe2+), manganous manganese
embankments. Soil particles suspended matter to carbon dioxide. However, (Mn2+), hydrogen sulfide, and methane.
by erosion and organic matter produced dissolved oxygen movement into the Hydrogen sulfide in particular can be
in or introduced into the pond settle to sediment by diffusion and via infiltrating troublesome in aquaculture because it is
the bottom, become mixed and form water is slow compared to the rate highly toxic to shrimp and fish.
a sediment layer. This sediment layer that microorganisms use oxygen in Microbial action oxidises much of
usually increases in depth most rapidly respiration and dissolved oxygen in the fresh organic matter that settles to
during the first 2 or 3 years in a new sediment pore water usually is depleted the pond bottom during a production
pond but it continues to increase in within the upper few millimeters of cycle and converts the remainder to

Reader enquiry number 7

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 Aquaculture
pond bottoms or in moist soil. Therefore, Such soils neutralise alkalinity and lessen
pond bottom dry-out between crops also pH in pond water. A soil with iron pyrite
is an excellent disinfection practice but will be particularly acidic because of
it requires that soils be dried thoroughly oxidation of the pyrite and overlaying
enough to kill the majority of organisms pond water may become too acidic for
through desiccation. Desiccation survival of fish and shrimp. On the other
affects both desirable and undesirable hand, a soil that contains limestone will
organisms and when a pond is refilled have base saturated clay minerals and
following thorough dry-out, there will water of moderate to high alkalinity.
be a paucity of benthic organisms, some It is very important to maintain
of which serve as food for post larvae or aerobic conditions at the soil-water
fingerlings. Moreover, water to fill ponds interface. This thin zone acts as a barrier
often has relatively low abundances of to the diffusion of hydrogen sulfide,
nutrients and plankton. nitrite and other potentially toxic
Once a pond is refilled, sediment metabolites of anaerobic, microbial
exchanges substances with water respiration into the water column. In
through several processes to include shallow areas of ponds benthic algal may
dissolution of minerals, adsorption- grow on the sediment and underneath
desorption of substances by clay these mats of algae, microbial
minerals and ion-exchange. In many decomposition of dead algal cells may
cases, the equilibrium concentration cause anaerobic zones. Benthic animals
of a substance in water is quite low in grow in the sediment utilising organic
comparison to the concentration of matter from dead algal and other pond
a form that decomposes slowly (the the substance in the solid phase (soil waste as food. Benthic organisms serve
refractory fraction) and has less effect on minerals). For example, the concentration as natural food for many species and
pond oxygen dynamics. Nevertheless, of soluble reactive phosphorus in the especially for shrimp.
there is an accumulation in organic water may be only 5 to 10 µg/L, while the
soil may contain 1 000 mg/kg or more
matter in sediment overtime and the
phosphorus bound in insoluble forms.
Bottom soil management
concentration of labile organic matter
is greatest in the F and S horizons and Certain clay minerals in soil also may between crops
especially at the end of a production fix cations, especially potassium, within
cycle. When ponds are drained for their structure. Thus, depending upon Pond bottom soil management often
harvest, labile organic matter in the F the characteristics of the bottom soil, is quite intensive in marine shrimp
horizon is removed in outflowing water, the concentrations of ions in the water culture but less management is applied
but a considerable amount remains in added to ponds may increase, decrease in most types of fish culture. The best
the S horizon. Drying of bottoms allows or remain the same depending upon the opportunity for applying bottom soil
air to replace water in pore space in the characteristics of the bottom soil. management is during the period
sediment. At 20oC, 1 litre air contains 252 The soil has a pronounced influence between crops while ponds are empty
mg O2 as compared to 9.07 mg in 1 litre on acid-base relationships in water. and bottoms are accessible. The length
of freshwater. More oxygen within the An acidic soil has low base saturation of time required to thoroughly dry-out
soil mass enhances oxidation of organic – a large percentage of acidic, the bottom of a pond varies with several
matter by bacteria as well as accelerating exchangeable aluminum ion compared factors and especially weather conditions
the chemical oxidation of ferrous iron to to basic, exchangeable cations (calcium (warm, dry, windy conditions favor rapid
ferric iron (Fe3+), manganous manganese magnesium, potassium, and sodium). drying), soil texture (coarse texture soils
to manganic form (Mn4+), nitrite to
nitrate, and sulfide to sulfate. Dry-out
is beneficial because it allows most
of the labile organic matter from the
previous crop to be oxidised lessening
the sediment oxygen demand at the
beginning of the new crop. The oxidised
inorganic compounds also can be used
again in anaerobic respiration during
the next crop. One should realise that
after about 2 or 3 weeks of drying most
of the labile organic fraction will have
decomposed and the soil will be too dry
for further microbial activity.
Pathogens, their vectors and other
unwanted organisms can survive
between crops in puddles of water in Coarsely ground agriculture limestone. Finely ground agriculture lime stone.

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 Aquaculture
Summary of pond bottom soil management practices

Action Practice
Empty ponds between production cycles
Effect dry-out • Drain ponds and let them dry for 2 to 3 weeks.

Sediment removal • Remove sediment from areas where it is too deep to dry completely.

• Measure pH of soil.
Correcting soil pH
• Apply agriculture limestone if pH < 7.5 – unless the purpose is to disinfect the soil.

Improve drying and aeration of soil • Use a disk harrow or other tillage implements to fragment the surface soil and break up clods.

• Use lime to disinfect entire pond bottom, or apply it only at wet areas that will not dry completely.
Soil disinfection • If lime is used over entire pond for disinfection, agriculture limestone treatment usually is not
needed for correcting low soil pH.

• Use fertilisers containing N and P to stimulate phytoplankton.

Improving natural productivity in
• Apply plant meal or fish meal to improve zooplankton growth.
recently-filled ponds
• Use organic matter to encourage benthic growth.

Grow-out period

• Lime ponds with agriculture limestone if total alkalinity falls below 50 to 60 mg/L in fish ponds or
Maintaining total alkalinity below 80 to 90 mg/L in shrimp ponds.
• Use sodium bicarbonate in lined ponds.

Control decline in potassium

• Apply muriate of potash fertiliser.
concentration

Minimising embankment • Install aerators in a way to avoid erosion of embankments.

erosion while effecting adequate • Reinforce easily erodible areas of embankments with grass cover, stone, or geotextile.
oxygenation and circulation • Use enough aeration to provide good circulation of water over pond bottoms.

Raising redox potential of soil in un-

• Apply sodium nitrate or other nitrate compound.
aerated ponds

dry faster than fine textured soils), and the weight of the tiller. Thus, sediment slows, phosphorus applied in fertilizers
sediment depth (a deeper sediment removal from ponds may be necessary, is less available, benthic productivity
layer inhibits drying). In addition, ponds there is however, no research finding to may decline and bottom soil acidity
may have depressions from which water support the removal of sediment from may cause a drop in total alkalinity.
does not drain sufficiently to allow the ponds after each crop as often done in The best liming material for general
area to dry, water can seep into empty Asian shrimp farming. purposes is agricultural limestone
ponds from adjacent full ponds or water The pH of pond soils should be made by pulverising limestone to a fine
supply and groundwater may infiltrate measured on a sample of surface soil particle size. There are two basic forms
into ponds constructed in low-lying (0-5 cm layer) prepared by mixing 10 or of agricultural limestone. One is made
areas. As a general rule, in tropical and more subsamples of soil taken randomly from calcitic or ordinary limestone that
subtropical zones, most ponds can be over the pond bottom. This sample contains mostly calcium carbonate
dried out in 2 to 3 weeks during the should be thoroughly air-dried (or at and usually a smaller proportion of
dry season. Tilling with a disk harrow or 60oC in an oven) and pulverised to pass a magnesium carbonate; the other is made
similar tillage implements can break up 60 mesh sieve (0.85 mm openings). The of dolomitic limestone that is essentially
the soil mass to allow greater contact pH should be measured in a 1:1 mixture a 1:1 mixture of calcium carbonate and
with the air and encourage evaporation, of distilled water and pulverised soil magnesium carbonate. Agricultural
tilling is especially beneficial in drying using an electronic pH meter and glass limestone also can be produced from
heavy clay soils. Where sediment is over electrode following intermittent stirring marl, chalk, and seashells. There is
10 to 15 cm deep, it may be impossible for 20 minutes. Hand-held, battery- no advantage of one of these liming
to dry-out ponds thoroughly. The operated soil pH testers are not accurate, materials over the others providing they
sediment dries on the surface creating especially in soils of shrimp ponds. have similar neutralising values; pure
a barrier to evaporation and tilling may Ponds with a pH below 7.5 should be calcium carbonate has a neutralising
not be possible because the wet soil limed; because, as pH declines below value of 100 percent.
beneath the dry surface will not support this level, organic matter decomposition Soil testing laboratories have

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 Aquaculture
procedures for determining the lime
requirement of soil samples (the same
sample taken for soil pH can be used).
In the likely event that such a service
is unavailable; the liming rate can
be ascertained from soil pH and soil
texture. The liming material should be
spread uniformly over the bottom of
the empty pond while the soil is still
moist. In cases where the pond bottom
is to be tilled, the liming material
should be applied before tilling so
that it will be mixed into the soil mass.
However, it is not necessary to till the
soil for liming to be beneficial.
In shrimp farming and some types
of fish culture, producers commonly
apply burnt lime or hydrated lime
to pond bottoms to increase the pH
above 10 or 11 to kill pathogenic
bacteria, vectors of viral diseases and
other unwanted organisms that may
survive dry-out. When this practice
is employed, it is not necessary to
apply agricultural limestone to ponds microbial respiration can be accelerated may be applied to pond bottoms at
with pH < 7.5. Burnt lime is made by application of nitrogen fertiliser. rates of 250 to 500 kg/ha to encourage
by incinerating limestone in a kiln at Urea or other nitrogen fertiliser can be benthic organisms. Chemical fertiliser
high temperature to drive off carbon applied at 200 to 400 kg/ha (20 to 40 g/ may be applied to the water to promote
dioxide; the remaining material consists m2) to provide supplemental nitrogen phytoplankton blooms. An N: P2O5 ratio
of oxides of calcium and magnesium. for microbial activity. Urea and ammonia of 1:2 or 1:3 in fertilisers is acceptable,
Burnt lime can be treated with water fertilisers should not be applied when but the nitrogen input should not
to produce hydrated lime. When soil pH is above 8, because much of exceed 8 kg/ha. There are, however,
applied to ponds, either type of lime the nitrogen will be lost to the air by many opinions about the optimum
will cause a rapid increase in pH, but ammonia volatilisation. fertilisation rate. Zooplankton growth
the pH will decline within a few days Some farms, particularly intensive typically lags phytoplankton growth and
as the lime reacts with carbon dioxide. shrimp farms, have reservoirs in which plant meal or fish meal can be applied
This reaction converts lime to calcium water can be held and disinfected. At over the water surface at 10 to 20 kg/
and magnesium carbonates, the same small farms without reservoirs, water ha to encourage rapid development of
compounds in agricultural limestone. may be disinfected directly in ponds zooplankton communities.
Recent studies have shown that at before stocking. The most effective Once an adequate plankton bloom
least 3 000 kg/ha and up to 5 000 kg/ disinfecting agent likely is calcium has been established, post larvae or
ha of lime are needed to increase the hypochlorite, often known as high fingerlings may be stocked. It is not a
pH of pond soils to 11 and maintain it test hypochlorite (HTH) but there are good practice to stock small animals
at this level for a few hours so that most several other products in common in clear water ponds even where feed
soil organisms are killed. Because of the use as disinfectants. A frequently is offered. Natural food organisms are
large amount of lime needed to treat recommended treatment is 10 mg/L an important supplement to the diet of
pond bottoms, the most practical way of available chlorine [15 mg/L of calcium post larvae and fingerlings that cannot
using lime in disinfection is to treat only hypochlorite (65 percent chlorine)], use manufactured feed as efficiently as
those areas that will not dry adequately. but a concentration of 15 to 20 mg/L can older and larger animals. Of course,
Of course, in the rainy season, ponds available chlorine might be more care must be taken to avoid excessive
cannot be dried completely and farmers generally reliable for disinfection. phytoplankton growth in ponds that
may desire to treat the entire bottom Many other disinfectants are used but could lead to stressfully low dissolved
area. Lime will not be effective as a only chlorine has been subjected to oxygen concentrations at night.
disinfectant if not applied at high rates, investigation and shown to be effective.
most farmers only use a fraction of the Pond bottoms and waters often
rate recommended above. Moreover, are essentially sterile following dry-
Bottom soil management
lime will not increase pH in dry soil, out and other disinfecting efforts, during grow-out
lime should be applied while the soil is and fertilisation to promote benthic
still moist. organisms and plankton for natural During the grow-out period, there
Ponds sometimes are built in organic food organisms before stocking culture are fewer opportunities to manage
soils that have a wide C:N ratio and animals is advisable. Organic matter pond soils. In areas with highly acidic

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 Aquaculture
soils, especially acid-sulfate soils, total pond bottoms with impermeable plastic
alkalinity may decline gradually and liners. In ponds that are completely lined,
it should be measured occasionally. If phosphorus is not removed from water
the concentration is below 50 to 60 by bottom soils, and the potential for
mg/L in fish ponds or 80 to 90 mg/L in dense phytoplankton blooms increases.
crustacean ponds, agricultural limestone Large amounts of dead plankton and
should be applied. other wastes accumulate in the bottoms
Aerators should be positioned in of such ponds, and some producers
ponds so that they do not damage use suction devices to remove this
earthwork by erosion and suspend material and discharge it outside
large amounts of soil particles. However, ponds. This practice lessens the oxygen
aerator-generated water currents should demand of organic matter in ponds and
be adequate to thoroughly circulate allows more of the dissolved oxygen
pond water and provide a continuous supplied by aeration to be used by the
movement of oxygenated water across aquaculture crop. Of course, the oxygen
the sediment-water interface to maintain demand is exported to the surrounding
a So horizon that serves as a barrier to environment.
the diffusion of reduced substances from Lined ponds often are operated
the Sr horizon into the water column. without water exchange and there is no
Some shrimp producers apply contact of water with bottom soil. Thus,
sodium nitrate to ponds for the purpose when ammoniacal nitrogen from the
of poising the redox potential at the cultured species is oxidised by nitrifying
soil-water interface to lessen the bacteria creating acidity, alkalinity
possibility of hydrogen sulfide and other declines because there is no input of
metabolites of anaerobic, microbial replacement alkalinity in incoming
respiration entering the water column. water or from dissolution of carbonate
Nitrate is used by denitrifying bacteria minerals in pond bottoms. Alkalinity
in the sediment and as long as nitrate should be checked regularly in lined
is present, the redox potential will not ponds and liming materials applied to
fall low enough for the existence of maintain the desired concentration.
anaerobic microbial metabolites and Because of the limited solubility of
especially hydrogen sulfide at the traditional liming materials, sodium
sediment-water interface. This practice bicarbonate that dissolves quickly and
probably is beneficial in some un-aerated completely is an excellent alternative. The
ponds. amount of sodium bicarbonate needed
During inland culture of shrimp or to neutralise acidity is around 45 g/kg
other marine organisms in low-salinity of feed. However, the application rate
water, potassium in water of some ponds usually is made at frequent intervals to
may decline to an unacceptably low maintain a relatively stable alkalinity.
concentration, because it is removed Each milligram per liter of sodium
from water by cation exchange with bicarbonate is equivalent to 0.60 mg/L
bottom soil and by fixation within certain of total alkalinity (expressed in terms of
clay minerals. Muriate of potash fertiliser calcium carbonate).
(potassium chloride) must be applied
periodically to such ponds to maintain
adequate potassium for good survival Dr Claude Boyd is Professor
and growth of the cultured species. in the School of Fisheries,
The treatment rate usually is calculated Aquaculture and Aquatic Sciences
to raise potassium concentration to at Auburn University, Alabama,
the level that would occur in normal USA. He is the author of several
seawater diluted to the salinity of the books on water and soil quality
culture system. The target potassium management in aquaculture. Dr
concentration in milligrams per liter can Julio Queiroz is Researcher for
be estimated by multiplying the salinity Brazilian Agriculture Research
in the culture system (in ppt) by 10.7, Corporation. He works on
the ratio of potassium concentration to environmental management of
salinity in seawater. Each unit of muriate aquaculture and development of
of potash is equal to about 0.5 units of BMPs.
potassium.
In intensive aquaculture, it is
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