DOI: 10.18130/v3/rj4ewf
title: Freshwater Mussel Diet

description: Freshwater Mussel Diet

Freshwater Mussel Diet Repository for files used in Isabella J. Maggard; Kayla B. Deel; Tina W. Etoll; Rachel C. Sproles; Timothy W. Lane; A. Bruce Cahoon, (2024) Freshwater mussels prefer a diet of stramenopiles and fungi over bacteria, Scientific Reports 14, 11958, https://doi.org/10.1038/s41598-024-62245-2 . 

Freshwater mussels (Mollusca: Unionidae) play a crucial role in freshwater river environments where they live in multi-species aggregations and often serve as long-lived benthic ecosystem engineers. Many of these species are imperiled and it is imperative that we understand their basic needs to aid in the reestablishment and maintenance of mussel beds in rivers. In an effort to expand our knowledge of the diet of these organisms, five species of mussel were introduced into enclosed systems in two experiments. In the first, mussels were incubated in water from the Clinch River (Virginia, USA) and in the second, water from a manmade pond at the Commonwealth of Virginia’s Aquatic Wildlife Conservation Center (AWCC) in Marion, VA. Quantitative PCR and eDNA metabarcoding were used to determine which planktonic microbes were present before and after the introduction of mussels into each experimental system. It was found that all five species preferentially consumed microeukaryotes over bacteria. Most microeukaryotic taxa, including Stramenopiles and Chlorophytes were quickly consumed by all five mussel species. We also found that they consumed fungi but not as quickly as the microalgae, and that one species of mussel, Ortmanniana pectorosa, consumed bacteria but only after preferred food sources were depleted. Our results provide evidence that siphon feeding Unionid mussels can select preferred microbes from mixed plankton, and mussel species exhibit dietary niche differentiation. (2024-05-29)
description: Experimental Design: Mussels were placed into tanks with water collected from either the Clinch River (experiment 1) or a pond at the AWCC (experiment 2). Liters of water were filtered and DNA extracted from the microbes adhering to the filter. 16S (bacteria), 18S (microeukaryotes) and ITS (fungi) DNA barcode sequences were PCR amplified and sequenced by the commercial sequencing company, Genewiz, using paired-end Illumina next generation sequencing. 

Each sample is listed in the Freshwater_Mussel_Diet_Dataset_metadata spreadsheet. Each sample has two accompanying sequence data files representing the forward and reverse sequences generated from the environmental DNA barcodes for either bacteria, microeukaryotes or fungi collected from a water sample. This is an example file name, Exp1_16S_River_Water_01. The naming convention is as follows: Exp1 denotes the data was collected from the first experiment with water from the Clinch River, 16S is the barcode sequence in this data set, River_Water denotes that there were no mussels introduced into the tanks with this water (i.e. it was a negative control), and _01 represents the replicate. If the sample name contains two letters such as the “Op” in this file name, Exp1_16S_Op1_01, it represents the species of mussel that was introduced into the tank and allowed to feed on the microbes present. The full name of each species can be found in the metadata spreadsheet. 

Each data file is in FASTQ format, which is a common format for the sequence output of next-generation sequencing. These files can be opened and viewed by commercially available DNA reading software such as Geneious or CLC Genomics Workbench, to name only two. There are open-source DNA sequence readers that will allow users to visualize the contents of each file. Some text readers, such as BBEdit, will also open fastq files.

The abundance of each DNA marker (16S, 18S, and ITS) was measured using quantitative PCR (qPCR). These data are included in two files named, “Quantitative PCR readings – Figure 2” and “Quantitative PCR readings – Figure 6”. The figures refer to the published study cited at the top of this file.