Evaluation of Rice Yield Attributes, Loach Muscle Quality, and Soil Biochemical Composition Under Rice–Loach Coculture System

This study aimed to evaluate rice yield attributes, loach Paramisgurnus dabryanus muscle quality, and soil biochemical composition under rice monoculture (RM), rice–loach coculture (RLC), and loach monoculture (LM). This trial was conducted for 90 days, and then rice, fish muscle and soil were obtained for analyses. The results showed that there were no significant differences in rice yield attributes between the rice–loach coculture (RLC) and rice monoculture (RM) groups. However, rice–loach coculture (RLC) improved muscle quality-related parameters, including increased hardness and springiness of loach muscle. Meanwhile, muscle metabolomic analysis showed that all the differentially expressed metabolites (DEMs) in the significantly enriched pathways of lysine degradation and lysine biosynthesis were up-regulated in the rice–loach coculture (RLC) group compared with the loach monoculture (LM) group. Furthermore, the rice–loach coculture (RLC) improved soil physicochemical properties, including an increase in microbial biomass nitrogen (MBN) content and activities of soil N-acquiring enzymes (NAG and LAP). Moreover, soil microbiome analysis showed that the abundance of Candidatus Koribacter versatilis, Acidobacteria bacterium WX27 and Pseudolabrys taiwanensis was significantly increased in the rice monoculture (RM) and rice–loach coculture (RLC) groups compared with the loach monoculture (LM) group. Pairwise Spearman’s correlation analysis of the top 30 soil microbial species and soil physicochemical properties indicated that Terrimonas sp. H1YJ31 showed a highly significant positive correlation with the soil N-acquiring enzymes (N-acetylglucosaminidase, NAG; leucine aminopeptidase, LAP) and a soil C-acquiring enzyme (exo-β-1,4-glucanase C1), whereas Gaiella occulta, Methyloceanibacter marginalis and Anaerohalosphaera lusitana had a highly significant negative correlation with S-NAG, S-LAP and S-C1. In short, the improved fish muscle quality and soil biochemical composition were ascribed to the increased hardness and springiness of loach muscle and the abundance of soil Terrimonas sp. H1YJ31.