Co-culture of red swamp crayfish Procambarus clarkia influenced glycoside hydrolase families and fungal communities in the rice-paddy soils

Integrated rice-crayfish farming has expanded rapidly, and an in-depth understanding of this model is urgently required. In the present study, metagenomics and real-time polymerase chain reaction were carried out to determine whether and how the introduction of the red swamp crayfish Procambarus clarkia affected glycoside hydrolase (GH) families and the abundance and community composition of fungi in soils. Investigations comprised the ecosystems of rice-crayfish co-culture fields, crayfish culture ponds, and rice paddy fields. Further, we sought to investigate the influence of the fungal community on bacterial chitinase gene abundance. The results showed that although rice cultivation induced variations in GH families and fungal communities in rice paddy soils, the introduction of crayfish was the main factor responsible for these variations. Additionally, the proliferation of bacteria with chitinase genes was not induced by the crayfish exoskeleton (in the form of living animals) but by the abundance of fungi in the soils. Therefore, bacterial chitinase in soils may not affect the exoskeleton of living crayfish but is likely the main regulator of the abundance of soil fungi. The impact of crayfish on fungal diversity was likely due to direct biological effects, while its inhibitory effect on fungal abundance was mainly attributed to the low nitrogen content in soils.