Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem.

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Effects of Stocking Density on the Growth Performance, Physiological Parameters, Antioxidant Status and Lipid Metabolism of Pelteobagrus fulvidraco in the Integrated Rice-Fish Farming System.

Pelteobagrus fulvidraco is a freshwater fish commonly raised in rice fields, yet the optimal stocking density for this species remains unknown. Therefore, this study aimed to investigate the appropriate stocking density of P. fulvidraco in integrated rice-fish farming systems. Three different stocking densities--low density (LD, 125 g/m2), middle density (MD, 187.5 g/m2), and high density (HD, 250 g/m2)--were set up to evaluate P. fulvidraco's growth performance, stress indices, immune function, antioxidant status, and lipid metabolism after 90 days of farming. The results indicated that HD treatment had a detrimental effect on P. fulvidraco's growth parameters. HD treatment led to an increase in cortisol (Cor) and lactate (La) levels, but a decrease in glucose (Glu) content in serum. After 90 days of farming, an immune response accompanied by the increase of complement 3 (C3), C4, and immunoglobulin M (IgM) was observed in the HD group. Meanwhile, HD treatment induced oxidative stress and altered antioxidative status evidenced by the levels of catalase (CAT), glutathione peroxidase (Gpx), glutathione (GSH), malondialdehyde (MDA), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) in serum or liver. Additionally, the lipid metabolism-related genes including lipoprotein lipase (lpl), peroxisome proliferators-activated receptor (pparα), carnitine palmitoyltransferase-1 (cpt-1), and sterol regulatory element binding protein-1 (srebp-1) were markedly downregulated in the HD and/or MD group after 90 days of farming. In conclusion, this study contributes to a better understanding of P. fulvidraco's response to different stocking densities in integrated rice-fish farming systems. We suggest that the appropriate stocking density for P. fulvidraco in these farming systems should be below 250 g/m2, considering both fish growth and physiological responses.

Effects of stocking density on the growth performance, mitophagy, endocytosis and metabolism of Cherax quadricarinatus in integrated rice-crayfish farming systems.

Red claw crayfish (Cherax quadricarinatus) is an economic freshwater shrimp with great commercial potential. However, the suitable stocking density of C. quadricarinatus is still unclear in integrated rice-crayfish farming system. Thus, this study aimed to investigate the effects of stocking density on growth performance, mitophagy, endocytosis and metabolism of C. quadricarinatus. The C. quadricarinatus was reared at low density (LD, 35.73 g/m2), middle density (MD, 71.46 g/m2) and high density (HD, 107.19 g/m2) in an integrated rice-crayfish farming system. After 90 days of farming, the growth performance of C. quadricarinatus significantly decreased in the MD and HD groups relative to that in the LD group. The HD treatment caused oxidative stress and lipid peroxidation at the end of the experiment in hepatopancreas. Transcriptome analysis showed that there were 1,531 DEGs (differently expressed genes) between the LD group and HD group, including 1,028 upregulated genes and 503 downregulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis indicated that the DEGs were significantly enriched in endocytosis and mitophagy pathways. Meanwhile, four lipid metabolism pathways, including biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, glycerolipid metabolism and glycerophospholipid metabolism, exhibited an upregulated tendency in the HD group. In conclusion, our data showed that when the stocking density reached up to 207.15 g/m2 in HD group, the growth performance of C. quadricarinatus was significantly inhibited in this system. Meanwhile, the data indicated that C. quadricarinatus may respond to the stressful condition via activating antioxidant defense system, endocytosis, mitophagy and metabolism-related pathways in hepatopancreas.