There are reasons for and against having aquatic plants in your aquaculture ponds but, overall, the reasons against them outweigh the reasons for having them. It does depend to some extent on the level of farming that you wish to operate, the fish species and the type of plant. Generally the farming level can be categorised into three levels, extensive or subsistance (farm dam/wild fishery level), semi-intensive (managed drainable ponds with high stock densities) or intensive (totally artificial environments with a high degree of control and very high stock densities). The fish species can essentially be broken up into two categories finfish and crustaceans. The plants can be broken up into three groups, submerged, emergent and floating. It is important to remember that while plants produce oxygen during the day they use it up at night.
In semi-intensive and intensive farming you do not want any aquatic plants as they can interfere with the management of the system and are an uncontrolable variable when analysing production. Submerged plants while creating habitat/shelter for juveniles also provide an ideal habitat for dragonfly larvae which are highly predatory on juvenile crustaceans.If shelter is required it is better to use an artificial weed bunch which is easily cleaned between stockings. The submerged plants are also said to supply a good food (as in the case of Vallisneria [ribbon weed] and marron) but there only is anecdotal evidence to support this idea and it is an inefficient, uncontrollable and unprofesional method of feeding stock at these higher production levels.
Obviously some fish species (possibly silver perch) may do well by having this feed supply but at commercial densities one would expect this to be rapidly consumed. Submerged aquatic plants also have the potential to greatly restrict water flow and therefore cause overnight oxygen depletion. At harvest time the draining of these ponds results in the collapse of the plant on top of the farmed species so the harvest is made extremely difficult by having to sift through this tangled mess searching for your valuable fish/crustacean stock. A mass of weed in the bottom of the pond also makes cleaning and rejuvenation of the pond extremely difficult if not impossible. Submerged plants are ideal in low yield extensive farming systems where these other issues are of no concern.
Emergent plants in semi-intensive farming and intensive farming are again undesireable for similar reasons to submerged plants. Because this type of plant can grow to a large size (up to 4 meters eg cumbungi and some reeds) they can create very effective wind breaks which can greatly reduce the amount of wind aeration. They also reduce water circulation, even with the use of paddlewheel aerators, causing pockets of low oxygen water which are then not utilised by the fish/crustacean species being cultured (in effect increasing the fish/crustacean density). Although most (due to their having to be able to grow above the surface) do not collapse the same as submerged plants (some such as water ribbons, caldesia and water poppies can collapse) when the pond is drained they can pose formidable problems in trying to harvest, clean and rejuvenate the pond. In the case of plants like cumbungi (Typhaceae) this work can be almost dangerous due to the sharp edges of the leaves. This group of plants also has a tendency to rapidly take over and choke the shallow pond systems (some can grow in up to 2 meters of water eg cumbungi and some reeds) resulting in costly, time consuming removal programs. It is wise to remove these types of plants as they appear and due to the nature of extensive ponds they will appear.
Floating plants are again undesirable in intensive and semi-intensive ponds for similar reasons to both of the above. When the pond is drained they again smother the important fish stock, they are of little value to bottom feeding fish or crustaceans except possibly at the shallow fringes of the pond.The worst affect is the smothering of the air water interface resulting in dramatically reduced oxygen/carbon dioxide exchange and greatly reduced wind aeration. Suprisingly a cover of floating plants does not reduce evaporation as people believe, it actually increases evaporation due to the transpiration/respiration cycle and is called evapotranspiration. They also reduce the amount of light penetration into the water column due to the effects of shading as well as competing for nutrients, resulting in lower phytoplankton productivity which leads to a lower production in the natural food chain (phytoplankton is the major base in pond food chains). It has been reported that up to 50% reductions in fish production have resulted due to waterhyacinth cover in tilapia ponds. For these reasons they are also undesirable even in extensive systems. These types of plants are often included in the lists (by waterway managers) of noxious weeds around the world due to the choking effect they often have on waterways (eg waterhyacinth and salvinia). On the positive side however these types of plants are very usefull in macrophyte ponds for treating eutrophic effluent water due to their ability to take up high quantities of nitrogen and phosphorous.
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