Abstract
Traditional approaches to dietary assessment in fish necessitate the collection of stomach contents through either gastric lavage or lethal sampling. The Atlantic bonefish (Albula vulpes) is an economically important sportfish in the western central Atlantic region for which a minimally invasive, non-lethal alternative to morphological dietary assessment would be extremely useful. Here, we compare dietary DNA metabarcoding from cloacal swabs of 16 A. vulpes to dietary composition data obtained using traditional morphological classification techniques and metabarcoding of homogenized stomach contents. Further, we compare the performance of two commonly used barcoding genes (18S rRNA and COI) at inferring A. vulpes diet composition. We found that detection of taxa and the resolution of taxonomic annotation varied between markers, suggesting a multi-marker approach is likely to provide the most complete results. Importantly however, the number of dietary OTUs identified and the taxonomic composition of the core diet were not significantly different between molecular markers. Dietary compositions identified using metabarcoding approaches differed in both diversity and composition from matched dietary data obtained from morphologically analyzed stomach contents; however, the same core prey classes were identified using both methods, suggesting that metabarcoding does indeed offer a viable alternative to morphological dietary assessment. Importantly, dietary compositions identified by metabarcoding of cloacal swabs did not differ significantly from those identified by metabarcoding of stomach contents. Metabarcoding of minimally invasive cloacal swabs should be considered for dietary studies of bonefish and other fish species for which invasive or lethal sampling is problematic.
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Data availability
Raw sequence data associated with this work are available from the sequencing read archive under BioProject PRJNA874874.
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All bonefish handling and processing techniques follow the approved Florida International University protocol IACUC-21-058 and permit numbers: SAL-22-2100-SRP, BISC-2021-SCI-0010, EVER-2021-SCI-0025.
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Figure S1
Stacked bar chart of the percent abundance of dietary prey classes per fish for each molecular marker. (PNG 185 kb)
Figure S2
Stacked bar chart of the percent abundance of dietary prey classes per fish for each sampling method. G = Homogenised gut contents, M = Morphological stomach contents analyses, S = Cloacal swabbing. (PNG 189 kb)
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Campbell, L.J., Castillo, N.A., Shenker, J. et al. Bone appétit: DNA metabarcoding as a non-lethal alternative to morphological dietary assessment in Atlantic bonefish (Albula vulpes). Environ Biol Fish 106, 337–348 (2023). https://doi.org/10.1007/s10641-022-01328-3
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DOI: https://doi.org/10.1007/s10641-022-01328-3