The dynamic features and microbial mechanism of nitrogen transformation in small greenhouse farming system of Pacific white shrimp, Litopenaeus vannamei

Abstract

The proliferation of small greenhouse farms for Litopenaeus vannamei cultivation in China represents an emerging dominant paradigm in shrimp aquaculture. However, inorganic nitrogen accumulation in water during cultivation significantly impacts yield and economic benefits. In this study, water quality analysis, particle size analysis, quantitative Real time-PCR and metagenomics were employed to investigate the main nitrogen transformations, the characteristics of surface sediment (SS) and suspended particulate matter (SP), the attached microbial communities, and the response characteristics of the main functional genes in the small greenhouse. The results indicated that the changes in inorganic nitrogen concentration in the small greenhouse exhibited phased characteristics. The increase in the abundance of ammonia-oxidizing and nitrite-oxidizing bacteria reduced the ammonia and nitrite concentrations in water to less than 1 mg/L during the turbid-turned stage. During the maturity stage, the abundance of key denitrification functional genes (nirS and nirK) both increased to more than 1 × 10⁸ copies/g, promoting the removal of nitrate from the water. SS and SP were mainly composed of silt and clay, providing abundant ecological niches for nitrifying and denitrifying bacteria. The metagenomic results indicated that Defluviimonas, Rhodohalobacter, Nitrosomonas and Nitrobacter were the main nitrifying and denitrifying functional microorganisms in SS and SP. These findings demonstrated that SS- and SP-mediated nitrification and denitrification processes served as primary mechanisms for inorganic nitrogen transformation and removal in small greenhouse farming systems. This study provided critical insights into microbial nitrogen transformation processes in small greenhouse shrimp aquaculture, establishing a theoretical framework for enhanced water quality management and aquaculture practices.