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Background  Fish culture in rice paddies can contribute to increasing yields of rice and surplus fish products. Environmental impacts and food-safety issues have become important topics in aquaculture, and organic foods currently were paid attention by researchers and industry practitioners. But the mechanism of differences in quality of Loach ( Paramisgurnus dabryanus ) reared in rice fields and ponds remains largely uncharacterized. In this study,digestive enzyme activity, intestinal mucosa cells and the gut microbial community of loach were determined under the two separate cultivation modes.    Results  The levels of intestinal digestive enzyme activity of fish reared in the paddy-cultivated mode (PACM) were higher ( P  < 0.05) than those in the pond-cultivated mode (POCM). It was extremely significant ( P  < 0.01) for the activity of lipase in the liver, foregut and midgut, and for the activities of amylase and trypsin in the hindgut. Acid mucous cells in the loach foregut in PACM were fewer than in POCM ( P  < 0.01). In summer, the abundance of the Firmicutes,  Lactobacillus  spp.,  Aeromonas hydrophila , Enterobacteriaceae and  Streptococcus  spp. in loach intestinal mucosa in PACM was higher than in POCM. In fall, the abundance of total bacteria, the Bacteroidetes,  Bifidobacterium  and Enterobacteriaceae in the intestinal mucosa in PACM was likewise higher than in POCM. These differences were significant ( P  < 0.05 or  P  < 0.01) between loach in the two separate culture modes for all microorganisms except for  A. hydrophila  and  Streptococcus  spp. In addition, quantitative PCR assays showed that some microorganisms presented consistently similar abundances in the gut as in the culture water.    Conclusions  These results showed some enzymatic activities involved in digestion in liver and intestine of loach in PACM were higher than those in POCM, as using digestive enzyme analysis and histological observation of intestinal sections. These findings suggest most of the microorganisms examined in the gut mucosa of loach in the two culture modes significantly differed in abundance between summer and fall. However, some pathogenic bacteria in the gut, particularly  A. hydrophila , presented lower abundance in PACM in fall, yet did not differ in abundance between loach in the two cultivation modes .

Differences in the digestive enzyme activity, intestinal mucosa and microbial community in loach cultivated in two separate environments