KINGSTON, R.I. —July 23, 2025 — A study led by Associate Professor Kelton McMahon at University of Rhode Island’s Graduate School of Oceanography has found that food webs on tropical reefs are more fragile than we once thought. Instead of being part of a highly connected system where species can easily switch food sources, many reef creatures in these incredibly biodiverse ecosystems rely on surprisingly narrow, specialized energy pathways that link specific species to distinct sources of primary production.

Using compound-specific stable isotope analysis of amino acids (CSIA-AA), a cutting-edge technique McMahon helped pioneer that allows scientists to follow the path of nutrients as they flow through ecosystems over time, the team investigated three common reef-dwelling snapper species (Lutjanus kasmira, L. ehrenbergii, and L. fulviflamma). Though previously considered opportunistic predators, these fishes, and the food webs supporting them, turned out to be remarkably specialized:

• Lutjanus kasmira fed almost exclusively within a food web based on water column phytoplankton.
• L. ehrenbergii was tied to a macroalgae-based food web on the seafloor.
• L. fulviflamma primarily fed within a coral-based food web.

“When you dive on these beautiful Red Sea reefs, one of the first things that you’ll notice is these snapper species schooling together in perfect synchrony. We would never have guessed that each had carved out its own unique niche within these complex, biodiverse reef food webs.” said McMahon as he reflected on his first time diving on the study reefs. As abundant predators high in the food chain, they were long assumed to be generalists, roaming the reef together and feeding broadly on whatever prey was available.

But the study findings reveal a shockingly different story: the flow of energy from primary producers low on the food chain (like coral, macroalgae, and phytoplankton) to predators is highly compartmentalized. In other words, each species relies on a distinct “silo” of production, forming self-contained food chains within specific microhabitats on the reef, despite the ability and opportunity to feed on a much broader array of potential prey. “It’s one thing to see a species or two specializing on a specific food item, but to see entire food chains of potentially dozens or even hundreds of species form tight relationships connected to a single primary producer (e.g., macroalgae) when equally tasty coral is just inches away fundamentally reshapes how we think about biodiversity of coral reefs.” says McMahon

Implications for reef resilience and biodiversity

The study also sheds light on a classic ecological puzzle: how high species diversity persists in reef environments historically characterized as low in nutrients, particularly in warm, shallow tropical waters. Normally, we’d expect stable ecosystems to have a lot of overlap in where energy comes from, helping them bounce back from disruptions. But instead, this study shows that reef species often stick to their own isolated energy sources, what the researchers call “vertical silos.”

This kind of separation within reef ecosystems challenges long-held assumptions that coral reefs are naturally resilient because they have so many species serving similar, interconnected roles. In systems where multiple species can perform the same role, the loss of one part doesn’t necessarily collapse the whole. But in these vertically siloed reef food webs, if a single primary producer is disturbed by climate change, overfishing, or bleaching, it can fracture an entire food chain.

That makes coral reef food webs more structured and more fragile than we thought, offering new insight into how these ecosystems work, and how vulnerable they may be to rapid environmental change.

Novel methods: CSIA-AA

McMahon’s Ocean Ecogeochemistry Lab on the URI Narragansett Bay Campus uses stable isotopes to understand the life history of animals based on what they’ve eaten. The lab’s research dives into big questions about food security, coastal health and resilience, and how warming waters are redistributing ocean life. In this study, the team used CSIA-AA to trace how carbon and nitrogen move through the coral reef food web. Unlike traditional methods like stomach content analysis, which only offer a short-term snapshot of what an animal has eaten, CSIA-AA provides a longer-term, more precise view of how energy actually flows through an ecosystem.

“People have used isotopes to understand food webs for nearly a century, where they turn an organism into a single isotope value. I’ve spent my career developing knowledge and tools to isolate and analyze all individual compounds within complex organisms, unlocking a metabolic history of organisms in a way we have never done before. That gives us the power to track where different sources of energy come from, and, in doing so, reveal patterns in the food web we couldn’t see before,” says McMahon about the novel CSIA-AA methodology.

Patience is key

The samples used in this study were collected during fieldwork in the Red Sea, with fish tissue analyzed at GSO and partner labs including the Woods Hole Oceanographic Institution. McMahon noted that samples were archived for over a decade before advances in analytical tools made this analysis possible:

“I collected these samples 15 years ago as a postdoc at King Abdullah University of Science and Technology,” shared McMahon. “The data were there, but I didn’t yet have the tools or perspective to make sense of it in a meaningful way. Sometimes, you have to let an idea sit until the knowledge and methods mature enough to be impactful. Finally, I feel prepared to handle this work in the way it deserves, and the outcome definitely rewarded that patience.”

The team plans to expand this work to other reef systems, explore similar questions in kelp forests and deep-sea ecosystems, and integrate DNA metabarcoding to more precisely identify the prey species that connect these highly siloed energy channels.

“I get excited about opening up access to knowledge that people have been seeking for a long time,” McMahon added. “In my lab, we don’t specialize on a system or species; we’ve worked in Antarctica with penguins, on ancient human diet in MesoAmerica, and locally with the burgeoning jonah crab fishery. Our goal is to develop tools that solve vexing ecological problems, and make sure diverse people and approaches are effectively brought together.”

Citation: McMahon KW, Thorrold SR, Langan JA, Pi J, Berumen ML, 2025. Highly siloed nutrient pathways fuel meso-predator fishes on coral reefs, Current Biology (2025)

This story was written by Mackensie duPont Crowley, a digital communications coordinator in URI’s Graduate School of Oceanography.