Microbiome Analysis Reveals Microecological Balance in the Emerging Rice–Crayfish Integrated Breeding Mode

Abstract

The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.

Metagenomics Analysis Reveals Compositional and Functional Differences in the Gut Microbiota of Red Swamp Crayfish, Procambarus clarkii, Grown on Two Different Culture Environments

“…Among the factors, the planting of rice may be especially important, as different crayfish-plant co-culture ecosystems have been shown to result in distinct bacterial communities in the intestines of crayfish ( Wei et al, 2021 ). The ecological interactions between the microbial communities in the intestines of crayfish and the environments cause variations in the gut microbiota composition between these two culture environments ( Wang et al, 2021 ). Nevertheless, bacterial communities that perform major functions in the guts of red swamp crayfish can change significantly, even at the phylum level.…”

Healthier Communities of Phytoplankton and Bacteria Achieved via the Application of Modified Clay in Shrimp Aquaculture Ponds

“…Bacteria play an important role in nutrient circulation, water quality maintenance, and the health of cultured animals [ 52 ]. In contrast to terrestrial animals, aquatic animals and microorganisms share the same water environment in the aquaculture ecosystem [ 53 ]. Therefore, aquatic animals are highly vulnerable to the changes in the surrounding bacterial community [ 54 ].…”

“…Among the pathogens, Vibrio and Pseudoalteromonas accounted for a relatively high proportion, and their proportion in the control pond was large and fluctuated significantly over time, while the proportion in the MC-treated pond was small. Vibrio and Pseudoalteromonas are considered opportunistic pathogenic bacteria [ 53 , 55 ], and opportunistic pathogenic bacteria are pervasive in seawater and become dominant when the aquaculture water quality deteriorates [ 7 , 56 ]. In fact, the high mortality of shrimp is attributed to the proliferation of opportunistic pathogenic bacteria [ 57 , 58 , 59 ].…”

The Microbiome Structure of a Rice-Crayfish Integrated Breeding Model and Its Association with Crayfish Growth and Water Quality

“…The 16S rRNA high-throughput sequencing approach has been used to assess the composition and diversity of bacterial communities in crayfish gut, water, or sediment in the RC model ( 16 – 20 ). Two previous studies have suggested that there was no significant difference in gut, water, and sediment microbiomes between the RC and crayfish monoculture (CM) models ( 18 , 19 ). Zhang et al suggested that overutilizing the RC model can lead to the destruction of soil microbial ecology ( 20 ).…”