Abstract: Microorganisms play an important role in the shrimp aquaculture ecosystem and are closely related to the health and quality of shrimp. Little is known about the dynamics of bacterial and archaeal community in the pond water associated with different growth phases of Penaeus vannamei. In this study, we examined the abundance, diversity and community structure of bacteria and archaea in the initial （May）, middle  （June-July）, and late phase （August） using realtime fluorescence quantitative PCR (qPCR) and Illumina Miseq highthroughput sequencing. The responses of bacterial and archaeal community to environmental factors were analyzed. Carbon and nutrients (N, P, Si) concentrations in the water increased with increasing food consumption. NH₄⁺ concentration rose up to 8.17 mg·L^-1 in the midlate phase, while the dissolved oxygen (DO), pH and the redox potential (ORP) decreased to 2.92 mg·L^-1, 6.66 and 29.10 mV, respectively. The abundance of bacteria (1.67×10⁸-3.91×10⁹ copies·mL^-1) was two orders of magnitude higher than that of archaea (3.08×10⁵-2.77×10⁷ copies·mL^-1), and both of them were stable from May to July, but significantly higher in August (ANOVA test,P<0.05). The abundance of both bacteria and archaea positively correlated with nutrient levels (P<0.05). Bacterial and archaeal community compositions shift obviously during the growth cycle. Rhodobacteraceae always dominated in bacteria (on average 27.93%). Flavobacteriaceae, Microbacteriaceae, and Actinomycetales had higher relative abundances in the middle phase. The proportion of Saprospiraceae descended first and then increased during the whole cycle, while that of Enterococcaceae decreased from 5.61% in the initial phase to about 1% in the late phase. DHVEG6 was the most dominant group of archaea (on average 67.17%), the relative abundance of which rose up to 90% in August. The proportion of ammoniaoxidizing archaea Candidatus Nitrosopumilus dropped rapidly in the late phase from 29% in May to 4.5% in August. In short, water bacteria and archaea cooperate to maintain the ecological balance of shrimp ponds. Our results can provide a theoretical basis for technology optimization, disease prevention, and yield guarantee of intensive shrimp aquaculture.

Key words: shrimp pond, aquaculture water, bacteria, archaea, dynamic succession.