Microbiome analysis of rice-crayfish integrated system using 16S and 18S rRNA gene sequencing Targeted loci

This project employs a multi-kingdom amplicon sequencing approach to investigate the aquatic microbiome of the Rice-Crayfish Integrated (RCI) system, a widespread and sustainable agro-ecosystem. The study aims to mechanistically understand how microbial communities, particularly keystone taxa, maintain ecosystem stability and drive nutrient cycling under high-frequency agricultural disturbances.We characterized the prokaryotic (bacteria and archaea) and microbial eukaryotic (protists, fungi, and metazoans) communities using 16S (V3-V4 region) and 18S (V9 region) rRNA gene sequencing, respectively. A powerful contrasting ecosystem design was implemented, comparing the multitrophic RCI system against both crayfish monoculture (CM) and rice monoculture (RM) controls. This design allows for the identification of microbiome signatures specifically attributed to the integrated management practice.The central goal is to test the hypothesis that the RCI system enriches for a unique consortium of multitrophic keystone taxa which stabilize water nutrient cycling primarily through a top-down, diversity-mediated mechanism. Our analysis integrates co-occurrence network analysis to identify keystone taxa and partial least squares path modeling (PLS-PM) to quantitatively test the causal pathways linking keystone taxa, microbial diversity, and nutrient cycling efficiency.Sample Overview:All samples are composite water matrices collected from the paddy fields and perimeter ditches of the RCI, CM, and RM systems in Jianli County, Hubei Province, China. Sampling was conducted synchronously across key management stages throughout a full production year.