Metagenomic-based observations regarding the inhibition effect of viruses on resistance genes in aquaculture system

Abstract

Viruses widely existing in the nature play important role in the various ecosystem. However, rare information is available regarding the quantitative effect of viruses on resistance genes in recirculating aquaculture system (RAS) which is an artificially-regulated advanced aquaculture mode. This study investigated the potential effect of viral community on both antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in a typical RAS based on metagenomic analysis. The results showed that viruses averagely accounted for 24.6%/0.1% of microbial community in water/residues of RAS operational units. Caudovirales were the predominant annotated order covering 32.5% of viral orders while Ligamenvirales and Picornavirales were not detected in residue samples. The total relative abundances of ARGs in the water/residue samples of RAS were in the range of (0.044–0.144)/(0.029–0.162) copies/16S rRNA copy while those of MRGs in the water/residue samples of RAS were in the range of (1058.6–2020.0)/(2263.2–3744.7) copies/16S rRNA copy. Caudovirales and Herpesvirales were frequently negatively related with ARGs in residue samples while Herpesvirales were often negatively related with MRGs in water. Viruses showed inhibition effect on ARGs and MRGs in RAS according to both the network analysis and pathway analysis. This study provided new insight on the relationship between viruses and resistance genes, regarding inhibition effect of viruses on resistance genes.

Graphical abstract

Keywords

Virus / Resistance genes / Recirculating aquaculture system / Metagenetic analysis / Inhibition effect

Highlight

	● Viruses averagely covered 24.6%/0.1% of microbial community in water/residue of RAS.
	● Caudovirales were the predominant annotated virus order in RAS.
	● Caudovirales and Herpesvirales were often negatively related with ARGs in residues.
	● Herpesvirales were often negatively related with MRGs in water.
	● Viruses showed inhibition effect on ARGs and MRGs with negative pathway coefficients.

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