Discerning differences in diets of reef fishes with DNA

Written by Matt Tietbohl

If you wanted to know what I ate for breakfast, there are a few different ways you could do this. You could simply find me, then ask what I ate for breakfast or maybe ask my flat mate, who knows me well, what I ate that morning. Perhaps if you were adventurous, you might find a comfortable place to watch me eat. If you were very serious and unconcerned for human safety, you could hunt me down, cut me open, and look inside my stomach to know exactly what I ate. Though you have a range of options, you would most likely opt for the simplest and just ask me what I ate (I hope)!

While it is easy to talk to people to learn about what they eat, when it comes to animals, it can be much more difficult determining their preferred foods. This is especially true of marine animals, like fish, where observations of feeding events can be even more difficult. Because conversation with fishes is not an option, scientists typically use similar means mentioned above: they will follow fish and observe feeding events or catch fish and dissect them to see exactly what they have eaten. These different methods yield different information, with dissections and stomach content evaluation often giving the most detailed assessment. However, even this can be tricky because lots of times a fish’s food will be partially digested and broken up so that identifying the mushy, disarticulated remains is a serious challenge.

One way around this problem, is to look at the genetic material of food items instead of the food items themselves. Using DNA barcoding techniques for gut contents allows scientists to determine differences in diet between fishes, which can offer key insight into how they divide resources (Casey et al. 2019). This is especially true for species that ‘chew’ their food thoroughly or those that are very small. 

A great, recent example of this comes from Brandl et al. (2020), where gut content DNA metabarcoding was used to compare dietary niche overlap (amount of similarity in diet components) and species richness (number of different species consumed) between four species of cryptobenthic (small, living near the bottom) reef fishes (two tube-dwelling blennies and two triplefins). Cryptobenthic fishes include small species that are often well-camouflaged and hidden among the rocks and corals of reefs. This group of fishes may be small in appearance, but play a key role as food for other fishes on coral reefs (Brandl et al. 2019b). However, despite their importance, there is actually surprisingly little known about their own feeding ecology and how much they may partition food resources between themselves to limit competition. By analyzing the DNA of their stomach contents, Brandl et al. were able to show a high degree of partitioning between species (Figure 1). Though all species shared some overlap in diet, triplefins fed on more mollusks, worms, decapods and amphipods while tube-blennies consumed more copepods and flatworms. The use of DNA barcoding demonstrated finer-scale partitioning than other studies using broader taxonomic categories too.

The authors were also able to identify differences in prey richness between species, with Acanthemblemaria spinosa (the spinyhead blenny) and Enneanectes matador (the matador triplefin) consuming a higher richness of prey crustaceans. These species were only found on exposed reefs and also overlapped more than expected by chance. The authors hypothesized these fishes would be able to thrive in high energy reef environments requiring a higher metabolism by ingesting a greater diversity of food items, demonstrated by the higher richness of prey species in their diets. Here, the authors are able to use these subtle differences detected in diet from DNA barcodes to help inform actual ecological differences between these fishes we find in their habitat. This allows them to hypothesize that differences in diet of these cryptic fishes, combined with metabolic and energetic differences likely play a key role in allowing these, at a glance, similar species to coexist. 

The use of DNA metabarcoding on small, cryptic fish shows great potential for scientists in understanding fine-scale differences in diets that may allow these fish to thrive together. This technique gives us a clearer window into their ecology, and is more informative in many ways than attempting to identify tiny, chomped-up crustaceans under a microscope. Though this technique is still being refined as a tool for investigating the feeding ecology of fishes, it shows great promise and potential to be a key tool for ecologists in the future. 

Figure 1. Bipartite network tree of the linkages between the four fish species and their crustacean prey items based on presence/absence. Colors represent the four fish species and their various combinatory linkages, while symbol shapes correspond to crustacean taxa. Each species ingested a large portion of unique taxa (peripheral symbol clouds), while a smaller number of OTUs were shared among different combinations of the four fishes. Fish are pictured to the right (from top to bottom: Acanthemblemaria aspera, A. spinosa, Enneanectes altivelis, E. matador), and scale bars represent 10 mm. Figure modified from Brandl et al. (2020).


Brandl SJ, Casey JM, Meyer CP (2020) Dietary and habitat niche partitioning in congeneric cryptobenthic reef fish species. Coral Reefs https://doi.org/10.1007/s00338-020-01892-z

Brandl SJ, Tornabene L, Goatley CHR, Casey JM, Morais RA, Côté, IM, Baldwin CC, Parravicini V, Schiettekatte NMD, Bellwood, DR (2019b) Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning. Science, 364:1189–1192

Casey JM, Meyer CP, Morat F, Brandl SJ, Planes S, Parravicini V (2019) Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs. Methods in Ecology and Evolution 10: 1157-1170

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