Examining invasive lionfish diet and trophic position in the Northern Gulf of Mexico via DNA barcoding of unidentifiable prey items

End Date: 03/31/15

Professors William Patterson, Alison Robertson and Alice Ortmann, all of University of South Alabama, are looking to determine what lionfish in the Gulf of Mexico are eating. They will examine unidentified stomach contents of lionfish samples using DNA barcoding analysis to determine what it is the invasive species is eating. The study will include lionfish collected on artificial reefs and natural reefs.


The objectives of this study are to 1) examine lionfish diet at natural versus artificial reefs in the northern Gulf of Mexico (nGOM); 2) apply DNA barcoding to characterize unidentifiable prey in lionfish stomach samples; and, 3) test for differences in lionfish diet and trophic position at natural versus artificial reef sites.


During spring, summer, and fall 2013, 702 lionfish were sampled by divers with spears at natural and artificial reef sites in the nGOM, and additional samples will be collected in winter 2014 for a total sample size of approximately 1,000 fish. Greater than 50% by mass of prey items present in stomach samples analyzed to date were too digested to be identified. These unidentified prey items were placed in vials and fixed in 100% ethanol for DNA barcoding analysis. Standard protocols will be employed for cytochrome c oxidase subunit I (COI) DNA barcoding of muscle samples from unidentifiable prey items. COI barcode sequences generated for unidentifiable samples and searched against a regional database, GenBank, and other available repositories to positively identify lionfish prey items. Differences in fish diet between habitat types and size classes will be tested with permutational MANOVA. Results of diet analysis including DNA barcode-identified prey items will be compared to results obtained without those data to examine the increase resolution DNA barcoding of unidentified prey items provides for diet analysis.


Lionfish in the western Atlantic constitute the most successful marine fish invasion to date, and dramatic shifts in reef fish community structure have occurred among US South Atlantic Bight and Caribbean reefs where lionfish populations have become established. While the lionfish invasion in the nGOM is still in its early stages, we have already observed significant shifts in reef fish community, size, and trophic structure where lionfish have become established. Furthermore, lionfish densities on nGOM artificial reefs already are among the highest reported throughout the western Atlantic; their densities at natural reefs have been an order of magnitude lower. Substantial shifts reef fish community structure have been detected following the first occurrence lionfish in the nGOM, with small (<100 mm) demersal planktivores that are likely prey for piscivorous lionfish showing the most dramatic declines (e.g., >95%). It is possible, if not likely, that predation by invasive lionfish is having a substantial impact on these ecologically important fishes and will continue do so in the years to come.

The goal of this study will be to determine exactly what lionfish are eating on nGOM reefs, thus what their potential trophic and community-scale impacts are likely to be. Stomach content analysis of animals collected to date (n = 702) has revealed a significant difference in lionfish diet between natural and artificial reefs (PERMANOVA, p < 0.001). However, greater than 50% by mass of prey items present in stomach samples were too digested to be identified. Therefore, diet analysis may be biased if more labile prey items are more rapidly digested thus unidentifiable in stomach samples. DNA barcoding of these unidentifiable prey items will enable an unbiased assessment of lionfish diet and trophic position, and comparisons of those parameters between natural and artificial reefs.

The ultimate end-users of the proposed research will be everyone who derives their recreation, livelihood, or nutrition from nGOM reef fish resources. Intermediate to that are ecosystem modelers who are currently developing Ecopath with Ecosim and Atlantis models of the nGOM food web, and resource managers who are mandated to transition toward multispecies assessment and management of marine resources. Study participants include charterboat fishermen, technical divers, and recreational divers who will facilitate sample collection. Project co-sponsors and supporters include the Alabama Department of Conservation Marine Resources Division, the University of South Alabama’s Foundation, the Gulf of Mexico Fishery Management Council, and nGOM charterboat owner/operators.