For shrimp farmers, biosecurity efforts often focus on water quality management, stocking density, and feed protocols. However, an often-overlooked factor that could be compromising shrimp health lies below the surface, namely the pond sediment.
Acting as a biological reservoir, sediment houses everything from essential microbes to dangerous pathogens. When left unmanaged, it can quietly trigger recurring disease outbreaks, slow growth rates, and poor survival, often before visible symptoms appear.
So, what’s lurking in your pond sediment? More importantly, how can you turn this hidden risk into an opportunity for disease prevention?
The Role of Pond Sediment in Disease Outbreaks
Shrimp ponds naturally accumulate organic matter over time, for example uneaten feed, faeces, molted shells, and microbial biofilms. This material settles at the pond bottom, forming a complex ecosystem that supports both beneficial and harmful microorganisms.
When properly managed, pond sediment can help maintain a healthy microbial balance that benefits shrimp growth and immunity. However, when conditions deteriorate due to factors such as low oxygen levels, high ammonia concentrations, or stagnant water, the sediment transforms into a breeding ground for harmful pathogens.
Continue reading: Get to Know the Total Organic Matter (TOM) Parameter
Research has shown that pond sediment plays a major role in the persistence of serious shrimp diseases. White Spot Syndrome Virus (WSSV) can remain viable in sediment for months, only resurfacing when environmental stressors, such as sudden temperature drops, create the perfect conditions for an outbreak (Kumar et al., 2013). Similarly, Infectious Myonecrosis Virus (IMNV) has been detected in pond soil even after harvest, indicating a high risk of disease carryover from one production cycle to the next. Perhaps one thing that is most concerning is the ability of Vibrio species to thrive in nutrient-rich sediment, making them a leading cause of Early Mortality Syndrome (EMS/AHPND) (Tran et al., 2013).
Even with regular water exchange and pond flushing, disease-causing microorganisms can persist in sediment for extended periods, lying dormant until conditions become favourable for reinfection.
How Sediment Management Affects Shrimp Health
The impact of poor sediment management on shrimp health is often gradual but severe. As organic matter accumulates and decomposes, it releases ammonia, hydrogen sulphide, and methane, creating an environment where shrimp experience chronic stress. This stress weakens their immune system, making them more susceptible to opportunistic infections.
Another overlooked risk is pathogen resuspension. Activities such as aeration, pond draining, or bottom-feeding behaviours can stir up dormant pathogens, reintroducing high infectious loads into the water column. This is particularly concerning when stocking postlarvae, as young shrimp are highly vulnerable to disease outbreaks.
Beyond pathogens, a disrupted microbial balance within the sediment can interfere with shrimp digestion and gut health. Beneficial bacteria, which play a crucial role in breaking down organic matter and supporting shrimp immunity, may be outcompeted by harmful microbes. Without intervention, this microbial imbalance can lead to poor feed conversion rates and higher mortality risks.
Understanding Pond Bottom Quality
Monitoring pond bottom condition is just as important as checking your water quality, and it can make or break your next crop. A basic visual assessment, including looking for blackened sludge, strong hydrogen sulphide odours (rotten egg smell), or bubbling gases, is a good starting point and often signals anaerobic conditions and excess organic load. While these sensory indicators do provide helpful insights, it often means the problem has already developed.
Ideally, farmers should check the condition of the pond bottom at the end of each cycle. This can include simple tests like measuring pH and organic matter and microbial composition. The goal is to make sure you’re not unknowingly carrying over issues from one cycle to the next. With the right information, you can take action early and avoid carrying yesterday’s problems into tomorrow’s pond.
A Data-Driven Approach to Pond Sediment Biosecurity
Traditional sediment management practices, such as drying ponds, liming, and increasing aeration, are important but often rely on visual assessments rather than scientific data. While these methods help, they don’t always address specific pathogen risks lurking in the sediment.
With advancements in molecular diagnostics, shrimp farmers can now analyse the microbiome and pathogen profile of their pond sediment before stocking. Understanding the microbial composition at the sediment level allows for targeted interventions rather than general guesswork.
By using data-driven insights, farmers can determine whether their pond conditions favour beneficial bacteria or if harmful pathogens, such as Vibrio spp., are dominating. This information helps in adjusting probiotics, aeration strategies, and sanitation methods to create a healthier production environment.
Pond Preparation: Setting Up for a Disease-Free Season
A well-managed pond doesn’t just start with a clean slate. It starts with controlled conditions that minimise the risk of disease. The first step in effective pond preparation is to analyse sediment, water, and shrimp samples before harvesting the current crop. This pre-harvest pathogen assessment provides a clear understanding of what microbes and viruses have been present throughout the production cycle. If harmful pathogens are detected, farmers can take immediate action to neutralize them before the next stocking phase.
Continue reading: The Application of Biosecurity in Shrimp Farms: Cleaning and Sterilization
Another essential strategy is sediment microbiome profiling, which examines whether the pond’s microbial community is supporting shrimp health or creating conditions that favour disease outbreaks. By validating probiotic use and monitoring bacterial diversity, farmers can make informed adjustments to their water sanitation protocols and organic matter management.
Finally, targeted pond preparation based on scientific data ensures that corrective actions, such as adjusted pond drying cycles, specific probiotic applications, or enhanced aeration techniques, are truly effective. Rather than applying a one-size-fits-all approach, farmers can tailor their biosecurity measures to their specific pond conditions.
Look Beneath the Surface for Better Shrimp Health
Shrimp biosecurity doesn’t end with water quality management. It extends down to the pond floor. By analysing sediment composition, identifying persistent pathogens, and managing microbial balance, farmers can prevent outbreaks before they start.
A data-driven approach to pond sediment management isn’t just about avoiding losses. It’s about optimizing shrimp production for long-term sustainability. When it comes to disease control, the best defence is always early detection and proactive biosecurity.
References
Satheesh Kumar, S. et al. (2013) ‘Viability of white spot syndrome virus (WSSV) in sediment during sun-drying (drainable pond) and under non-drainable pond conditions indicated by infectivity to shrimp’, Aquaculture, 402–403, pp. 119–126. doi:10.1016/j.aquaculture.2013.04.001.
Tran L, Nunan L, Redman RM, Mohney LL, Pantoja CR, Fitzsimmons K, Lightner DV. Determination of the infectious nature of the agent of acute hepatopancreatic necrosis syndrome affecting penaeid shrimp. Dis Aquat Organ. 2013 Jul 9;105(1):45-55. doi: 10.3354/dao02621. PMID: 23836769.
