Subcuticular and biofilm microbiomes in Holothuria tubulosa and their potential for denitrification

Abstract

Holothurians, as benthic invertebrates inhabiting marine ecosystems, have a crucial function in that they actively process organic detritus in the sediments. Previous works have provided evidence of the capability of holothurians to reduce nitrate and ammonium concentrations in aquaculture tanks. However, the mechanisms underlying this nitrogen decrease still need to be elucidated and might be related to bacterial symbionts in the holothurians. Here we characterize the community of bacterial symbionts in the biofilm and subcuticle of Holothuria tubulosa and explore the presence of nitrification and denitrification genes. To characterize these bacterial symbionts, we extracted DNA and amplified the V3-V4 hypervariable region of the 16S rRNA gene. We obtained a notable contribution of Bacteroidota, Alphaproteobacteria (mostly Rhodobacterales), and Gammaproteobacteria (mostly Pseudomonadales) both within the biofilm and subcuticle of H. tubulosa. Subsequently, we tested the presence of specific genes encoding enzymes involved in nitrification (i.e. archaeal amoA and bacterial amoA) and denitrification (i.e. nirS and nosZ). Our results confirm the presence of denitrification genes in the holothurian biofilms. These findings indicate that the holothurians house a diverse community of bacterial symbionts, which includes species with the potential for nitrogen removal. Therefore, holothurian holobionts may play a multifaceted ecological role, both processing organic detritus and reducing nitrogen levels in coastal areas. These roles could be extended to sustainable aquaculture, making them valuable ecosystem engineers with significant implications for ecosystem and aquaculture health.