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

Abstract

1. Freshwater mussels are important for nutrient cycling and ecosystem health as they filter feed on their surrounding water. This filter feeding makes these bivalves especially sensitive to conditions in their environment. Gut microbial communities (microbiomes) have been recognised as important to both host organism and ecosystem health; however, how freshwater mussel microbiomes are organised and influenced is unclear.2. In this study, the gut bacterial microbiome of Threeridge mussel, Amblema plicata, was compared across two river basins, five rivers, and nine local sites in the south-eastern U.S.A. Mussel gut tissue was dissected, DNA extracted, and the microbiome characterised by high throughput sequencing of the V4 region of the 16S ribosomal RNA gene.3. Planctomycetes, Firmicutes, and Cyanobacteria were the most common bacterial phyla within the guts of all sampled A. plicata. However, the relative abundances of these major bacterial phyla differed between mussels sampled from different rivers and river basins, as did the relative abundance of specific bacterial operational taxonomic units (OTUs). Despite these differences, a core microbiome was identified across all mussels, with eight OTUs being consistent members of the A. plicata microbiome at all sites, the most abundant OTU identifying as a member of the family Planctomycetaceae. Geographic distance between sites was not correlated with similarity in the structure of the gut microbiome, which was more related to site physicochemistry. 4. Overall, these results suggest that while physicochemical conditions affect the composition of transient bacteria in the Threeridge mussel gut microbiome, the core microbiome is largely unaffected, and a portion of the A. plicata microbiome is retained regardless of the river system. 5. How long transient bacteria remain in the gut, and to what extent these transient microbes aid in host function is still unknown. Core microbiota have been foundto aid in multiple functions within animal hosts, and within freshwater mussels this core microbiome may aid in nutrient processing and cycling. Therefore, it is important to look at both transient and core microbes when studying the structure of freshwater invertebrate microbiomes.

Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation

“…An increasing number of studies have characterized the gut microbiome of freshwater mussels [3,[42][43][44][45][46][47][48][49]. Many of these studies report similar findings to the current study in that the most abundant bacterial phyla in the guts of freshwater mussels are Firmicutes, Proteobacteria, and Planctomycetes [3,45,47].…”

A multi‐study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation

“…Stevick et al (2021) observed that the gut microbiomes of non‐depurated C. virginica vary spatially over their range in Narragansett Bay with important covarying environmental factors such as temperature, salinity, dissolved oxygen and nutrients. Similar effects of the site have been observed in the gut microbiomes of non‐depurated freshwater bivalves (Chiarello et al, 2022; Lawson et al, 2022). The gut microbiomes of non‐depurated bivalves have also been demonstrated to vary temporally over both years (McCauley et al, 2021) and seasons (Akter et al, 2023; Conceição et al, 2021).…”

“…A ‘core’ microbiome, as it is most commonly defined (i.e., taxa present in most or all samples), is not synonymous with a resident microbiome. In the bivalve‐associated microbiome literature, researchers have identified ‘core’ microbial communities and either directly implied that the ‘core’ taxa were residents or indirectly implied it by using ‘core’ as the opposite of transient (King et al, 2012; Lawson et al, 2022; Zheng et al, 2021). Even if a taxon is recovered in all samples across spatial or temporal spectra, if the host had not voided transient material at the time of sampling, then the ‘core’ taxa could be transient.…”

Freshwater mussels prefer a diet of stramenopiles and fungi over bacteria

“…Other studies have relied upon the presence of bacterial fatty acids such as C18:1 to assess the consumption of bacteria but these fatty acids are also abundant in algal chloroplasts 58 raising the possibility that algal fatty acids could have been mistaken as bacterial. Freshwater mussels also sustain an endosymbiotic gut microbiome 59 which is established from bacteria filtered from the environment that are not digested 60 , 61 . Therefore it is possible that some earlier studies mistook the microbiome for consumed bacteria 23 .…”