Characterizing the Microbiome of Scottish Freshwater Pearl Mussels (Margaritifera margaritifera)

: A Metabarcoding Analysis using Next-Generation Sequencing

Abstract

Bivalves, such as the freshwater pearl mussel (Margaritifera margaritifera), are keystone species in freshwater habitats, functioning as ecosystem engineers, biological indicators, and flagship species. Despite their ecological significance, M. margaritifera populations are undergoing rapid declines, resulting in low reproductive success and limited juvenile recruitment. Addressing research gaps, particularly the understudied microbiome, may be crucial for effective conservation. With their filter-feeding lifestyle exposing them to diverse microbial communities, these mussels serve as an excellent model for investigating host-microbiome interactions. This study provides the first taxonomic characterization of the microbiome in Scottish M. margaritifera populations. Microbial communities from three distinct mussel populations were compared to those in river water, with geographic and ecological factors evaluated as potential drivers of community composition. Samples were collected using non-invasive DNA swabbing of mussels and water eDNA sampling from reference habitats, with microbial profiling conducted via 16S rRNA gene metabarcoding. Two sequencing platforms were utilized: the MinION (Oxford Nanopore Technology) for full-length amplicons and MiSeq (Illumina) for short amplicons, enabling a comparative analysis of platform performance at the species level. Results revealed that the mussel microbiome was distinct from that of river water, with significant differences even at high taxonomic levels. Proteobacteria were the most prevalent group within the mussel microbiome, with unique genera such as Aeromonas and Pseudomonas identified. While bacterial diversity was consistent across individual mussels, community composition varied significantly between populations, likely influenced by site-specific factors. Nanopore sequencing provided greater species-level detection but faced challenges with lower accuracy and difficulty in processing both sample types compared to Illumina. These findings highlight the distinctiveness of the mussel microbiome, shaped by extrinsic factors, and emphasize the potential crucial role of associated microbes. By providing baseline data, this study lays the groundwork for a more holistic conservation strategy, underscoring the urgent need to protect this imperilled species whose extinction would have profound and lasting consequences for freshwater ecosystems.

Date of Award	11 Apr 2025
Original language	English
Awarding Institution	University of the Highlands and Islands