Microbiome in shrimp Litopenaeus vannamei aquaculture : dynamic changes and bacterial lifestyles

Abstract

The Pacific white leg shrimp Litopenaeus vannamei is the most frequently cultured shrimp species, comprising more than 70% of the world shrimp commodities since 2010. Shrimp indoor and outdoor aquacultures are affected by water quality deteriorations and bacterial diseases. These cultivation problems lead to a substantial annual loss of shrimp harvest. Traditionally, water quality is quantified by plankton density, total suspended solids/particulate matter, pH, salinity and inorganic nutrients, particularly ammonium, nitrite and phosphate. Especially, the quantitative assessment of the carbon cycle in shrimp aquaculture is required to determine oxygen demand and depletion. However, optimal and acceptable but potentially stressful conditions have not systematically been determined in pond aquaculture. Excess biomass formed by photosynthesis of phytoplankton and by heterotrophic bacteria in the microbial loop poses a particular problem in shrimp aquaculture. While particulate matter in pond water may serve as additional feed source for shrimps, it also provides niches for particle-associated bacteria, such as pathogenic Vibrio species. In this study, water quality parameters as well as bacterial community compositions were observed in Indonesian shrimp aquacultures over the complete rearing process. Semi-intensive and intensive aquacultures differed in suspended particulate matter content, chlorophyll a, pH, and dissolved oxygen, while inorganic nutrient concentrations and the population size of cultivable heterotrophic bacteria were comparable. Halomonas, Salegentibacter, and Sulfitobacter were the most abundant free-living bacteria, whereas particle-associated bacteria were dominated by Halomonas and Psychrobacter. Vibrio were more frequently found in the intensive aquaculture system, particularly in the particle-associated fraction and at low pH conditions. White feces disease (WFD) event, which is a disease repeatedly occurring in shrimp aquaculture, was further documented in this thesis. To better understand pond water conditions as well as bacterial community dynamics during the disease event, the quantification of physico-chemical water parameters was combined with molecular analyses of the microbiome of shrimps, feces, and aquaculture water including the particles. The WFD event coincided with a low water pH and a high proportion of Alteromonas in the feces. Virulence genes of Vibrio, i.e toxin regulator (toxR) and termolabile hemolysin (tlh) were detected in the particle fraction ( 3 AAmicrometre), in the intestine of healthy shrimps and feces of WFD-infected shrimps. An increase of pH above 8 via limestone addition enabled a recovery from WFD. In addition, the bacterial community composition also changed with the rise in pH. This observation led to a recommendation, that aquacultures of L. vannamei should maintain a pH above 8. Lastly, bacterial dynamic on aggregates, which form in large numbers in shrimp aquaculture, was investigated to monitor the growth of potential pathogenic Vibrio species. In the rolling tank experiments, the addition of carbon-rich molasses was shown to rapidly reduce toxic ammonium and nitrite pools. Furthermore, it enabled the fast growth of halophilic heterotrophic bacteria, such as Halomonas, Psychrobacter, and Salegentibacter. Conversely, in the presence of Chlorella vulgaris aggregates V. parahaemolyticus population remained constant without decay. The algal biomass seemed to maintain the Vibrio population and density. I conclude that water parameters such as salinity and pH shape bacterial communities in shrimp pond aquaculture, and that a deterioration of water quality may cause detrimental shifts in bacterial community composition. However, bacterial communities will recover to the initial composition if water parameters are adjusted to former condition. To improve shrimp farming practices, I propose to perform regular pond water assessment, not only for the physicochemical parameters, but also for bacterial community composition. For this purpose, I recommend to analyze the bacterial communities in the particle fraction, including virulence genes of pathogenic bacteria. In addition, sludge discharge and regular addition of lime stones are necessary to improve and maintain shrimp production. As consequence, sustainable shrimp pond farming systems should include sludge as well as clean water reservoirs.