This is beta v.7 (Post-expert review), so the citations and tone are off, we're just getting info down.
Preface As human population grows, the demand and need for fish will grow alongside it. As such, despite developments in fishing technology, the demand and need for fish will almost certainly exceed sustainable levels. Aquaculture is poised to fill the gap between fish needs and sustainable fishing, and to be scalable to meet future demands.
Aquaculture is already economically viable, with 40% of all food fish and 22% of all trade in fish already raised in aquaculture facilities, mostly from developing countries(1). However, some forms of aquaculture are far from sustainable. Some of the most pressing environmental issues are antibiotics used on fish forming resistant strains of disease and the aquatic ecosystem around aquaculture facilities collapsing. Some other issues that must be resolved are genetically modified fish escaping into the wild, and the need to feed fish in aquaculture facilities(2). Our goal was to develop guidelines for an individual country to follow when creating an aquaculture industry, that would remove as many environmental dangers as possible, while remaining scalable to meet growing fish demand in the future in an economically viable way.
Since our goal for aquaculture was to replace wild fish as a food source with farmed fish, we focused primarily on fish farming, rather than all forms of aquatic organism farming. For the purposes of this plan, we looked at two general types of fish farming. The first type is cage farming, which uses cages in large bodies of water, relinquishing control over water quality for a cheaper, simpler system. The second type, intensive, used closed or nearly closed-loop water filtering systems, so that the fish do not interact with any natural environments. Extensive Aquaculture Cage farming has the virtue of being comparatively simple to set up and maintain, as there is no need for advanced water quality control systems. However, the reliance on nature for water management causes many greater environmental problems, notably the risk of algae blooms caused by the concentrated waste and nutrients and then remove nearly all nutrients from the ecosystem(2). The level of these risks are very dependent on site selection and the staying within the carrying capacity of the body of water and the levels of pollution from industrial and other sources. Near-shore waters with good tidal flushing can be suitable, however more exposed sites and attention to cage density can prevent risks to the environment. Other solutions we have found are either to use shellfish, sponges, or other filter feeders for local water quality management(3), or to make the cages mobile so waste does not concentrate in any one location(4). The first option would work well for countries where the right species are already native to the area, while the second option would allow landlocked nations or nations with little coastline a shot at aquaculture, as the mobile cages can be deployed in the open ocean in international water. There remains the question of the economic feasibility of the system described in (4), especially in regards to developing nations. While we are not currently able to provide an answer, we believe that should sufficient commercial and governmental pressure develop, means of reducing the cost of mobile-cage aquaculture would arise. These two options should provide most nations a means of performing extensive aquaculture while preserving the environment.
To attempt to reduce the risks from genetically modified fish, we recommend that genetically modified fish not be used in extensive systems, as the risk of escape is too great. Instead, we recommend that low-trophic level fish that also naturally school are farmed, especially herbivores and omnivores (such as tilapia). Many of these fish also tend to be more resistant to disease than other fish given similar disease prevention techniques(5), as they are used to living with poor water quality. When coupled with vaccines (already used in Norwegian salmon farms(1)), clever fish selection will reduce or eliminate the need for antibiotics and the corresponding risk of resistant strains. Since they are herbivores, they can also be fed plants from land or sea, meaning that fish would not have to be taken out of the ocean to support the farming. While these fish are not necessarily popular in the open market, they can certainly provide necessary protein for many people, and can be used as feed for higher trophic level farmed fish. Intensive Aquaculture The second form of aquaculture we want to integrate is intensive, closed-loop systems. In these systems, almost all the water is recycled, with at most 5-10% of water being replaced each day(1). This also means that escape of genetically modified stock is nigh impossible, and that, with careful monitoring, antibiotic-resistant diseases can be contained, and not spread into the wild. Furthermore, as the water is in a closed loop, the waste and nutrients from the fish do not impact the surrounding environments. The ability to stack shallow tanks makes intensive farming particularly well suited to flat fish such as flounder. The primary downside is the complexity of the recycling systems. However, intensive aquaculture provides an opportunity for landlocked nations to become involved, and stacking tanks allows for more fish in a given footprint. Genetics and Feeding There is a growing fear that genetically modified fish escaping from cage farms could seriously impact the surrounding environment. As fish from aquaculture come from broodstock, this broodstock is often selected to produce the best fish for aquaculture. Sadly, these traits are often less useful, if not harmful, in the natural environment. As such, there is a fear the escaped fish from farms may displace natural species, either through interbreeding or putting too much pressure on the local ecosystem (http://www.nature.com/embor/journal/v5/n7/full/7400197.html). 
; However, there is little evidence to support these claims. Though some farmed fish may interbreed with wild fish, there is little evidence that these news genes are harmful. However, the risk still exists, so we recommend mixing randomly selected wild fish with the broodstock, to minimize the divergence between the two groups.
On the issue of feed, there is great work being done on the subject of replacements for wild caught fish in farm feed. According to ( http://soyaqua.org/quickfacts.html ) "Soybean meal can replace all or most animal meals in the feeds for the majority of cultured omnivorous freshwater fish." We encourage such efforts, as they may prove key to separating aquaculture from wild fisheries and allowing near indefinite scalability. Solving the Problem on a Global Scale To solve these problems, we propose that developing countries use cage farming to raise a large number of low trophic fish, using plants as feed and our previous suggestions to prevent negatively impacting the environment. These fish would be used both as a source of protein for locals, as well as food for higher trophic level fish farmed in more wealthy nations. The purchase of fish from developing nations would allow those nations to keep the fish farms operating, thus (hopefully) providing food, for free, to their citizens. Corporations in developed nations, then, would use the fish from developing nations to raise higher tropic-level fish, selling them for a profit to consumers in wealthier nations. In this manner, developing nations would have food for their citizens as well as a new revenue stream, while developed nations could continue to consume higher trophic level, with very little negative environmental impact. Enforcing this plan would hinge on encouraging companies in developed countries to move to intensive high trophic level farming, thus producing a marked for extensive farming in developing nations and encouraging them to participate. In the United States, NOAA, due to the Merchant Marine Act, is already authorized to provide loans to help build aquaculture facilities(6), if nessecary to get the market started. By controlling the types of facilities they grant loans to, they could encourage the creation of intensive, high trophic level farms. However, this suggestion is tentative, as the manner of best enforcement is highly dependent on other aspects of the solution, particularly in regard to international treaties and bodies. On the issue of international bodies, we propose an international team of aquaculture experts to assist nations in farm design and placement, ensuring the most environmentally friendly farm possible.
There still remains the question of scale. Farms have produced anywhere from 63,000 to over two million pounds of tilapia per year(http://www.ag.ndsu.edu/pubs/alt-ag/tilapia.htm). At an average per capita consumption of about 35 pounds, a single farm could feed as many as 50,000 people. (http://www.who.int/nutrition/topics/3_foodconsumption/en/index5.html). Using the Maldives as an example, assuming an average per capita fish consumption, their population of 369,031 (http://www.aneki.com/Maldives.html) could be fed with as few as eight large fish farms. Addendums In some cases, it may be possible to produce a better system for a given nation. In the case of India, some cities have integrated their waste water treatment and aquaculture systems, so that human waste is used as feed for the fish, thus solving two problems simultaneously(1). However, such specialized multi-trophic solutions are dependent on many factors including local climate, species involved and , and are thus hard to create general guidelines for. We encourage any nations setting up aquaculture facilities to consider the possibility of multi trophic systems, which must be handled on a case-by-case basis.
As a final note, NOAA recently released a 10-year plan for aquaculture in the United States(6). We agree with their goal of increased usage of farming, particularly in terms of educating the public and in using aquaculture to rebuild stocks of wild fish. As their plan seemed to be focused more on production and research goals, we feel it can still work under our plan, and as such encourage its adoption.
1-World Bank report
2- http://www.britannica.com/eb/article-92632/Aquaculture-Fulfilling-Its-Promise
3-http://www.ugc.edu.hk/rgc/rgcnews10/Pages/2b%20Biofilter-E.html
4-http://seagrant.mit.edu/cfer/oceandrifter/Israel_paper.pdf
5-http://www.americulture.com/Disease.htm
6-http://aquaculture.noaa.gov/pdf/finalnoaa10yrrweb.pdf
Low trophic fish:
catfish
tilapia
grey mullets
carp
trout
anchoveta
herring
mackerel
sardinella
anchovy
http://www.esa.org/science_resources/issues/FileEnglish/issue8.pdf