When a Maine reef loses its kelp forest to turf algae, the change is obvious to anyone who dives it: a canopy of towering kelp blades gives way to a low, carpet-like mat. What’s much harder to see is that the reef’s entire microbial community changes with it. A new study in the Proceedings of the National Academy of Sciences, led by Shane Farrell, a former University of Maine PhD student, with senior author Doug Rasher and co-author Tim D’Angelo of Bigelow Laboratory for Ocean Sciences, is among the first to actually measure that invisible shift, and it found the microbial world of a turf-dominated reef looks fundamentally different from a kelp-dominated one.
The team compared six sites along the Maine coast, three still dominated by kelp and three that had already flipped to turf algae, surveying each during spring and summer. Rather than just counting species, they used metagenomics to identify which microbes were present and what biochemical processes they were capable of, paired with metabolomics to measure the actual chemical compounds present on the reef. One finding stood out: Synechococcus, a type of photosynthetic cyanobacteria, was rare on kelp-dominated reefs but abundant on turf-dominated ones, a shift the authors interpret as a sign that turf reefs may be leaning on a different primary source of energy than kelp reefs do.
That matters because Maine’s coast has been quietly living through this exact transition for years, as warming water and other stressors push kelp forests toward turf-dominated states across large stretches of the Gulf of Maine. If the microbial community underpinning a reef changes as fundamentally as this study suggests, it could alter how efficiently that reef cycles nutrients and stores carbon, effects that would be easy to miss if researchers only tracked which seaweed was on top. As D’Angelo put it, “Every habitat is an integrated system of all the organisms it contains, even those that cannot be seen.”
The authors are careful about what their data can and can’t say: the study captured a snapshot of each reef’s microbial and chemical makeup rather than measuring metabolic rates directly, so it shows that kelp and turf reefs run on different microbial systems without yet pinning down exactly how much that difference affects carbon storage or nutrient cycling in practice. Untangling that is the logical next step, and it carries some urgency, since it would mean the consequences of losing a kelp forest extend well past the visible loss of the kelp itself.
Further reading: Farrell, S.P., D’Angelo, T., Yiu, D.S. et al., “Kelp forest collapse alters the reef microbiome and associated metabolome,” PNAS (2026).