Microbial community dynamics and nitrogen transformation associated with turbid-turned culture stage of Pacific white shrimp, Litopenaeus vannamei in small greenhouse farms

Abstract

Small greenhouse farms have experienced rapid expansion of Litopenaeus vannamei culture in China in recent years. To investigate microbial community dynamics and nitrogen transformation during the early critical stage, known as the turbid-turned stage in small greenhouse farms, microbial samples from the water column of small greenhouses were analyzed by 16S rRNA and 18S rRNA high-throughput sequencing, along with the detection of ammonia nitrogen in water. The results of water quality analysis revealed that accumulated ammonia nitrogen was converted to nitrite as the water color transitioned from clear green to turbid brown. High-throughput sequencing data demonstrated a shift in dominant microorganisms from zooplankton to algae and bacteria during the turbid-turned stage, and the main functional microbial taxa, such Marivita and Chlorella, were enriched. The results of Linear Discriminant Analysis Effect Size and canonical correlation analyses indicated that the compositions of key microbial communities were correlated with environmental factors. Furthermore, analysis of functional genes indicated that ammonia-oxidizing bacteria were present in the early growth stage, while the abundance of nitrite-oxidizing bacteria was low during the early culture stage. Overall, the findings suggest that microorganisms during the turbid-turned stage in small greenhouses may play a crucial role in regulating water quality and promoting shrimp health within a stable small greenhouse environment.