Table S1.xlsx

In this study, we comparatively investigated the micro-ecological environment characteristics in the rice root substrate, rearing water, and shrimp intestine of <em>Litopenaeus vannamei</em> in two different stock density ponds (75,000 ha⁻¹ and 150,000 ha⁻¹) under rice-shrimp saline culture conditions. We found that a 150,000 ha⁻¹ pond has a higher water purification treatment capacity and a better micro-ecological environment than a 75,000 ha⁻¹ pond. 16S rRNA high-throughput sequencing analysis revealed that the richness and diversities of bacterial species in all samples were ordered as follows: rearing water &gt; shrimp intestine &gt; rice root substrate. The composition of the dominant bacterial taxa was more complex in the rearing water and shrimp intestine than in the rice root substrate. Alternatively, Proteobacteria, Firmicutes, and Bacteroides (relative abundance &gt; 2% at least in one sample) were the dominant bacteria in the integrated rice-shrimp saline culture environments, while Bacteroidetes and Firmicutes tended to colonize the rice root substrate. Proteobacteria and Cyanobacteria were dominant phyla in the rearing water and Proteobacteria and Firmicutes were enriched in the shrimp intestine.