Mussel Mass Mortality and the Microbiome: Evidence for Shifts in the Bacterial Microbiome of a Declining Freshwater Bivalve

Abstract

Freshwater mussels (Unionida) are suffering mass mortality events worldwide, but the causes remain enigmatic. Here, we describe an analysis of bacterial loads, community structure, and inferred metabolic pathways in the hemolymph of pheasantshells (Actinonaias pectorosa) from the Clinch River, USA, during a multi-year mass mortality event. Bacterial loads were approximately 2 logs higher in moribund mussels (cases) than in apparently healthy mussels (controls). Bacterial communities also differed between cases and controls, with fewer sequence variants (SVs) and higher relative abundances of the proteobacteria Yokenella regensburgei and Aeromonas salmonicida in cases than in controls. Inferred bacterial metabolic pathways demonstrated a predominance of degradation, utilization, and assimilation pathways in cases and a predominance of biosynthesis pathways in controls. Only two SVs correlated with Clinch densovirus 1, a virus previously shown to be strongly associated with morality in this system: Deinococcota and Actinobacteriota, which were associated with densovirus-positive and densovirus-negative mussels, respectively. Overall, our results suggest that bacterial invasion and shifts in the bacterial microbiome during unionid mass mortality events may result from primary insults such as viral infection or environmental stressors. If so, bacterial communities in mussel hemolymph may be sensitive, if generalized, indicators of declining mussel health.

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure

“…These results also support the idea that agricultural CECs such as atrazine and metolachlor may alter the growth of bacterial species (Seghers et al, 2003), and encourage microbes that can harm unionids and decrease unionid (e.g. L. cardium) health over time including contributing to die off events (Richard et al, 2021). Currently, the function of many bacterial species for mussel health remains unknown, therefore we suggest the possibility that alterations from the original gut microbiota pre-exposure could be impactful to unionid health.…”

The gut bacterial microbiome of the Threeridge mussel, Amblema plicata, varies between rivers but shows a consistent core community

“…The 16S rRNA gene sequences identified as Methylocystis and Rhizobiales have been identified as being members of the core microbiome of other Unionid mussels (Obovaria unicolor and Cyclonaias asperata ; Weingarten et al., 2019). No members of the core microbiome were bacterial genera such as Aeromonas , Salmonella , or Yokenella that have been associated with stressed or diseased mussels (Aceves et al., 2020; Richard et al., 2021). This putative core microbiome of A .…”

“…with stressed or diseased mussels (Aceves et al, 2020;Richard et al, 2021). This putative core microbiome of A. plicata accounted for approximately 10% of the identified sequences.…”

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea)

“…Dual-indexed barcoded primers were used to amplify the V4 region of the 16S rRNA gene of the extracted DNA from each sample following established techniques ( Kozich et al, 2013 ; McCauley et al, 2021 ). This hypervariable region was chosen following previous work on unionid microbiome using Illumina MiSeq technology ( Weingarten et al, 2019 ; Aceves et al, 2020 ; Richard et al, 2021 ), and recommendations from the Earth Microbiome Project 2 (01/2022). The amplified 16S rRNA gene fragments were combined and spiked with 20% PhiX before being sequenced on an Illumina MiSeq at the University of Mississippi Medical Center Molecular and Genomics Core Facility.…”

“…The unionid microbiome has been increasingly studied over the past few years, suggesting some degree of species-specificity, where mussel species collected from the same environment have distinct microbiomes ( Weingarten et al, 2019 ; Liu et al, 2020 ; McCauley et al, 2021 ). However, while opportunistic bacteria are detected within moribund mussels or during mass mortality events, little is known about potential bacterial pathogens of mussel populations in the wild ( Grizzle and Brunner, 2009 ; Leis et al, 2019 ; McElwain, 2019 ; Richard et al, 2021 ), or the risk of a transmission of such pathogens from exotic species such as C. fluminea . Whether C. fluminea likewise harbors its own distinctive microbiome, influences the microbiome of native freshwater mussels, or has acquired a microbial community that reflects that of the local environment and/or one of the native mussels remains unknown.…”