“Who did you eat before I ate you?”: a metagenomic analysis of gut contents of the Arctic lamprey (Lethenteron camtschaticum) during its feeding phase (Gulf of Ob, Kara Sea)

In the cold, dark waters of the Arctic, a jawless fish known as the lamprey has lived for hundreds of millions of years, surviving by attaching itself to other fish and feeding on their blood and flesh. While these creatures are ancient and well-known, scientists have long struggled to understand exactly what they eat in specific regions. Traditional methods of looking inside a lamprey's stomach often fail because the soft tissues of their prey are digested so quickly that no bones or scales remain to identify the meal. To solve this, researchers have turned to a modern technique called shotgun metagenomics. Instead of looking for physical remains, this method reads the genetic code, or DNA, found within the gut contents. By sequencing every fragment of genetic material present, scientists can identify the species of the fish that was eaten, even if the meal has been reduced to a liquid paste. Understanding these diets is crucial for managing fish populations and maintaining the balance of marine food webs, especially in the rapidly changing Arctic environment.

In August 2018, researchers collected two Arctic lampreys from the Gulf of Ob, a massive estuary in the Kara Sea of Russia. These fish were caught as part of a standard research survey, and their intestinal contents were carefully preserved for analysis. The material inside was not a collection of recognizable parts but a semi-digested, reddish-brown paste, consistent with blood and crushed muscle tissue. To uncover the identity of the lampreys' last meals, the team extracted all the DNA from this paste and sequenced it using a powerful method that reads millions of genetic fragments at once. The challenge was that the gut contained a mix of DNA from the lamprey itself, bacteria, and the researchers who handled the samples, all of which had to be filtered out to reveal the true dietary signal.

After removing the genetic noise from humans, bacteria, and the lamprey host, the remaining data revealed a clear picture of what these predators had consumed. The analysis showed that the primary food source for the Arctic lamprey in this region is the whitefish, a large group of fish belonging to the genus Coregonus. In one of the lampreys, whitefish DNA made up nearly two-thirds of the identifiable fish genetic material, while in the other, it accounted for more than four-fifths. This finding confirms that in the Gulf of Ob, these lampreys act as predators of large, abundant fish rather than just parasites of smaller species. The study also detected traces of other fish, including the nine-spined stickleback, the Arctic char, and members of the cod family, though these appeared in much smaller amounts.

The researchers had to be careful in interpreting these results because the genetic databases they used to identify the fish were not perfect. The initial data contained genetic matches to fish species that do not live in the Arctic, such as tropical species found in the Americas or Africa. These were identified as errors caused by gaps in the scientific reference libraries, which are heavily biased toward well-studied, economically important fish and lack sufficient data on Arctic species. To correct for this, the team developed a system that weighed the genetic findings against what is known about the fish that actually live in the Gulf of Ob. This approach allowed them to confidently dismiss the exotic, impossible matches and focus on the local species that were genuinely present in the lampreys' guts.

The diet found in the Gulf of Ob stands in sharp contrast to what has been observed in other parts of the world. In the Bering Sea, for example, Arctic lampreys have been found to feed mostly on small, schooling fish like capelin and herring. The lampreys in the Russian Arctic, however, are clearly targeting the large whitefish that dominate their local waters. This difference highlights the flexibility of the lamprey's feeding habits; they do not stick to a single type of prey but instead adapt to whatever large, nutritious fish are most available in their specific environment. The study also noted that the two individual lampreys examined had slightly different diets, with one having eaten a more varied mix of fish while the other had fed almost exclusively on whitefish. This suggests that individual feeding history and local availability play a significant role in what each lamprey eats.

While the study provides the first molecular glimpse into the diet of Arctic lampreys in the European Arctic, the authors acknowledge that their sample size was very small, consisting of only two fish from a single location and time. They caution that this is an exploratory look at the species' feeding ecology rather than a complete census of their diet. The presence of some fish DNA, such as that from the stickleback, might also be the result of secondary consumption, meaning the lamprey may have eaten a fish that had recently eaten a stickleback, rather than eating the stickleback directly. Despite these limitations, the research successfully demonstrates that shotgun metagenomics is a powerful tool for studying the diets of animals where traditional methods fail. It also underscores the urgent need for scientists to build better, more complete genetic libraries for Arctic species to ensure future studies can identify prey with even greater accuracy.