Lotus-fish co-culture reshapes pond microbiota and improves ecological stability relative to fish monoculture

The lotus-fish co-culture ponds (LP) is a widely applied integrated aquaculture system in China. However, research on the micro-ecology of aquaculture in lotus ponds is still insufficient. This study explored the dynamic patterns of organic matter composition, as well as algal and bacterial community structures in LP and MP.

A total of six independent ponds were used in this study: three lotus ponds designated as the lotus-fish co-culture ponds group (A1, A2, A3), and the other three conventional earthen ponds serving as the fish monoculture ponds group (B1, B2, B3). Bacterial and algae community survey, environment factor survey, bacterial Biomarker selection, function prediction, and association analysis were used to analyze the effects of lotus-fish co-culture on algae, bacteria and sediment organic matter components of pond.

The sediments of LP had lower concentrations of total nitrogen (TN), total phosphorus (TP), total carbon (TC) and organic matter (OM), and the chlorophyll-a (chla) content in the water was also relatively low. The algal community in LP exhibited seasonal variations, while MP was predominated by Chlorophyta and Cyanobacteriophyta. The dominant bacterial phyla were the same in both pond groups, yet their abundances varied across months. Bacterial biomarkers in LP was c_Alphaproteobacteria, c_Vicinamibacteria, etc. (sediments) and c_Gammaproteobacteria (water), whereas MP was c_Desulfobacteria, c_Dehalococcoidia, etc. (sediments), and c_Verrucomicrobiia, c_Mycobacteriales, etc. (water). Functional analysis suggested that bacterial communities in LP were enriched in methanotrophy, nitrogen fixation, whereas MP communities were more closely associated with anaerobic respiration and phototrophic processes. The bacterial network in LP exhibited a modular structure reliant on keystone taxa, whereas MP harbored highly interconnected and cooperative bacterial communities. In the LP sediments, TC, TN, and TP collectively drive the broad differentiation of bacterial modules. Total nitrogen (TN) played a vital role in bacterial assembly in MP sediments, while total phosphorus (TP) acted as the primary negative driving factor in MP sediments. FBL and FBW were significantly greater in LP than MP, while CF was lower.

These findings indicate that microbial communities in LP and MP follow distinct assembly patterns, and they differ in core ecological functions and environmental preferences within their respective ecosystems.