The many challenges of disease management in aquaculture
Regardless of the aquatic species an aquaculture venture produces, there are significant risks to su...
Aquaculture has immense potential to support future food security and sustainability. The increase in aquaculture production has been significant but, at the current rate, will not be enough to cover the expected protein demand. Over the past decade, production increased by around 50%, but growth was only 2.7% in 2020. Most of the production occurs in developing countries, with major output from extensive and semi-intensive systems. Countries in Asia (83.4% of production) and Latin America (16.3%) account for the major share of shrimp production, based on two species: the Pacific white shrimp (Litopenaeus vannamei) with 83% of the production, and the tiger prawn (Penaeus monodon) with 12%. India and Ecuador have augmented their shrimp yields significantly, with the latter increasing production roughly by 100% in a decade, reaching over 1 million tons in 2021, valued by Ecuador's Central Bank at USD 5.3 billion (Ekos, 2022), without a significant increase in rearing area. Semi-intensive production in Ecuador still yields an average of around 1250 kg/ha/cycle (Marcillo, 2017), but farmers can now consistently operate 3 cycles/year and are working on implementing best-aquaculture practices in the industry. In spite of that, further increases in production will be difficult to achieve with the current system, as space is limited and higher impacts on the environment by semi-intensive systems are undesirable (Boyd et al., 2022). The challenge to increase production, improve nutrition, and food security while reducing space requirements and the impact on the environment requires improved, controlled, more resilient, and intensive production systems.
As aquaculture production increases, more species will enter commodity status and price of these products will decrease, requiring increased cost efficiencies for such businesses to survive economically, including efficient supply and processing chains. In the case of shrimp, in 1987, production was 250,000 thousand tons per year, mostly coming from extensive and semi-intensive farms. As we approach the 7 million ton mark, production comes mainly from more intensive systems. Yields of over 40 tons/ha/cycle can be consistently produced in RAS systems (Krummenauer et al., 2011), with published experimental production results of over 100 tons/ha/cycle showing the possibilities of super-intensification. Nevertheless, significant challenges remain. Over the last twenty years, the shrimp industry has advanced and overcome various problems. Results of polls of industry stakeholders of the Global Seafood Alliance show that diseases, production costs, access to disease-free broodstock, seed stock quality, trade barriers, and market prices are the leading reasons for the move towards intensification as a way to assert control over the value chain (Anderson et al., 2019).
We define the super-intensive system for white shrimp, L. vannamei, as one that uses lined ponds, raceways, or tanks for stocking densities of over 150 shrimp per m2 during growth and applies a significant level of technology. We further define an effective system as one that maximizes productivity for the energy expended without harming the environment and minimizes water utilization, typically less than 250 L/kg of production, which is only possible with zero water exchange and should yield over 1200 kilos of shrimp/kW of energy. To achieve that, most super-intensive systems use nurseries. Open ponds should produce 2–3 crops a year of >30 tons/ha (1.2 kg/m3), while raceways should produce at least 3 crops a year with densities of over 2.5 kg/m3, and greenhouses should generate 3+ crops a year with a density of around 4.5 kg/m3. To consistently achieve this, understanding the interactions between the production system design, biosecurity strategies, nutrition, and seed quality as well as the impact of technology development, climate change, and social compliance on shrimp culture intensification is essential, as capital investment is 5–10 times that of the typical semi-intensive system.
Biofloc is now the most commonly used technology for intensive shrimp culture. It relies on effective beneficial microbe manipulation to minimize the need for water exchange and propitiate in-pond nutrient reuse that contributes to reduce wastes and the need for supplemental protein requirements. Proficient microbial manipulation is needed to form aggregates that are key to successful system operation, which requires appropriate engineering, supplies, and management. The biofloc occupies significant space in the water column and colonizes the shrimp gut, thus limiting potential vacant niches for pathogen development and providing a more varied nutrient base, improving digestibility, nutrient availability, and intake. A recent review by Emerenciano et al. (2022) describes different biofloc systems depending on whether they are heterotrophic, chemoautotrophic, photoautotrophic, or mixotrophic. Scientific information available for these systems is limited, particularly in relation to the understanding of their dynamics and the interactions between the ecosystem and the cultured organism. While commercial intensive shrimp systems in Asia have shown good results (Taw, 2017), the commercial economic viability of super-intensive systems has not yet been proven. The challenges are both technological and in the value chain. We are still evaluating too many different technologies, which dilutes effort and also puts pressure on traditional suppliers to the industry who will need to meet the new demands from these systems. Recognized challenges in intensive shrimp systems include diseases, feeds, energy use, and genetic selection in terms of the organism and environmental, social, and welfare issues for the farmers.
Diseases were responsible for a significant shrimp production decline from 2009 to 2014, when around 1 million tons were lost, mainly in Asia and Latin America. White spot syndrome virus, acute hepatopancreatic necrosis disease, enterocytozoon hepatopenaei, and white feces syndrome, have impacted the industry with substantial economic losses (Shinn et al., 2018), so that producers look for more controlled intensive systems with higher biosecurity in an effort to mitigate this risk. Nevertheless, some large producer countries rely on semi-intensive or intensive systems where farms lack biosecurity. Indiscriminate use of antibiotics has been a significant problem, and diseases have become established so that original strategies, like the use of specific pathogen free (SPF) broodstock used to contain and mitigate diseases, have become less effective. Disease pressure causes these farmers to increasingly favor survival over growth. Several large broodstock producers market specific lines as being tolerant to disease. Over time, differences in survival will become more evident, separating programs based on solid genetic selection from those relying on the multiplication of surviving individuals. The challenge will be to prove higher survival rates while maintaining acceptable levels of growth, feed conversion, physiological resilience, and fecundity.
Recently, D'Abramo (2021) summarized nutritional advances in aquaculture. In super-intensive systems, information for new SPF lines, genetically selected to thrive in these systems, is still needed. Particularly in relation to nutrient requirements, a better understanding of protein and amino acid use, the impact of alternate protein and lipid sources, and the interaction with microbes and microalgae in biofloc-based systems. While the feed industry has made remarkable advances to deliver a high-quality product to the farm, these diets are still based on available macro ingredients such as fish, soybean, and wheat meals, fish and vegetable oils, complemented by a mix of vitamins and minerals. One challenge is to develop alternate protein sources at volumes and production costs that represent a feasible alternative. Current substitutes still represent a limited, high-carbon footprint source, while new alternatives (e.g., insect meal) are costly and lack sufficient volumes. Vegetable-based proteins also hold significant promise but require specific genetic selection of lines where enzyme activity is redirected towards this and better use of compound carbohydrates. The need for vitamins and minerals in the diet has to be established for flow-through clear-water systems and its relevance is defined for efficient biofloc-based systems. Significant reductions in protein, amino acid, and the vitamin-mineral mix will reduce costs significantly. Similarly, the goal to control C:N ratios (15:1 for photoautotrophic or chemotrophic systems; 20:1 for heterotrophic systems) in intensive systems frequently leads to over-use of carbon sources that results in an excess of organic matter in the ponds that needs to be eliminated. More in-depth analysis of the microbe-based systems is needed to reduce these wastes in systems that were, ironically, originally developed to use and eliminate wastes. From an environmental and social license perspective, there is a need to convert this high nutrient load, which includes uneaten feed, feces, and other organic matter, into microbial biomass, proteins, and nutrients that can be used effectively in the system, or in secondary production systems (such as mollusk, fish, or vegetable cultivars). Another challenge is to balance the requirement to deliver high-quality water-stable pelletized or extruded feeds to the farm with the production dynamics, where the feeding behavior of the shrimp (i.e., manipulating the feed to select specific particles) and the required organic matter load needed by the biofloc system must be met, as natural feeds still represent a significant contribution to actual feed consumption.
Another relevant topic that needs to be evaluated is the relationship between total energy available and physiological resilience of selected lines for super-intensive production systems. Several producers have stressed the need for high dissolved oxygen (DO) levels to maximize yields (>6 mg/L). Genetic selection of highly adapted lines to specific rearing conditions (salinity, temperature, pH, density, feed type, etc.) is essential. In terms of DO, the carrying capacity of the systems is affected by all these factors. Villarreal et al. (2022) presented data where a 12-h reduction in aeration results in a 42% reduction in final weight for a no-water exchange super-intensive photoheterotrophic system, even when DO levels were consistently over 3 mg/L. Villarreal-García (2022) indicated that this was because of a 48% increase in routine metabolic demand for shrimp in limited aeration ponds, which also resulted in a higher threshold for the shrimp to conform to critical oxygen saturation. Shrimp growth is discrete and depends on molting. This creates a significant challenge during very intensive culture, as the organism requires an extraordinary amount of energy to complete the molting process and leaves the animal exposed to cannibalism, diseases, and death through exhaustion, particularly in systems that are unable to maintain sufficient DO levels, or whose microbe system is unbalanced in terms of potentially harmful bacteria (or fungi and parasites). These chronic stresses have a significant impact on shrimp. Shelters and other hiding places developed for vulnerable animals (such as freshwater crayfish) allow aggressive interactions and cannibalism during culture to be controlled (Villarreal & Naranjo, 2006). These have led to consistently higher yields. Information on multilayer systems for super-intensive shrimp production is still limited.
High fecundity and genetic variability are important traits for selective breeding of aquatic species during the process of domestication. To ensure those post larvae are well suited to conditions in super-intensive systems, breeding has an important role that can be enhanced through genetic improvement. Gjedrem et al. (2012) mention that most commercial shrimp breeding programs are based on full- and half-sib family structures that focus on the improvement of growth traits and survival rate. Clean pathogen-free organisms are critical during the domestication process as they reduce the risk of disease development during farming. Shrimp lack adaptive immunity and rely on innate immune responses. This means that vaccination to manage the disease is not yet possible. On the other hand, heritability for specific pathogen tolerance traits in L. vannamei is low to moderate. However, Roy et al. (2020) have reviewed some of the advances in shrimp genomics that are contributing to improve breeding programs, including post-transcriptional gene silencing or RNA interference, which regulates the expression of specific protein-coding genes involved in resistance to pathogenic nucleic acids (Robalino et al., 2005). Castillo-Juárez et al. (2015) report that survival time to a disease challenge using these techniques was up to 2.6 times greater than that of phenotypic sib selection. Apart from disease, genetic selection programs often consider other traits, such as physiological tolerance, reduced routine metabolic demand, specific nutrient digestibility, and growth. The relative importance of each of these traits is based on economic benefit/cost analyses for the specific production system. To develop genetic lines that perform well for different traits (e.g., growth, reproduction, and pathogen tolerance) for different production systems and environmental conditions, knowledge of the correlation between them is needed. For super-intensive systems, the information is still limited.
According to Giri et al. (2022), semi-intensive aquaculture of exotic shrimp (L. vannamei) in India has much higher unit-area profitability than other types of agribusiness but involves greater financial risk. On the other hand, there is little incentive for current users of semi-intensive technologies for shrimp production (e.g., in Ecuador) to intensify production, as their business model is currently economically successful and most super-intensive technologies have not demonstrated economic viability. Of particular consideration is the high capital expenditure needed, the high production costs, and current commodity market prices for shrimp based on frozen value chains rather than on fresh, never-frozen, product demand. In addition, some question the ability to offer a shrimp product that complies with animal welfare guidelines. At issue are topics like broodstock ablation, animal management during super-intensive rearing, and humane sacrifice at harvest. The industry also questions the advantages of certifying operations if that does not result in higher sale prices for their product.
It is evident that replication of current models for semi-intensive shrimp production will be limited. Certainly, countries like Ecuador and China should not expect to be able to double production volume using the same cultural systems. Intensification of shrimp farming requires that the cultured animals have health, physiological, metabolic, and genetic status suited to thriving in these environments. Focused scientific knowledge development will be highly relevant to achieve this. From an environmental sustainability perspective, current super-intensive systems use less water per kilogram of shrimp produced, reuse water, have lower feed conversion ratio, and optimize farmland and water resources. They need to be socially responsible, engage in local communities effectively, and offer a traceable and certifiable product harvested from high-technology systems that mitigate carbon footprint and comply with welfare and humane practices.
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