ABOVE: Global warming could be indirectly harming kelp forests in Australia’s Great Southern Reef by altering the composition of the kelp microbiome, a study finds.

Stretching 8,000 kilometers along the southern coast of Australia, the Great Southern Reef is an underappreciated biodiversity hotspot home to hundreds of endemic species. Here, a vast kelp forest clad in the browns, golds, and greens of its seaweed denizens dominates the rocky reef, forming a habitat for myriad fish, crustaceans, and mollusks. But one species reigns over the forest: the yellowish-brown kelp Ecklonia radiata.

“It’s massive, the spread of this single species,” says Ziggy Marzinelli, an ecologist at the University of Sydney who has been studying the kelp for more than a decade. “[E. radiata] underpins a lot of the biological diversity and ecological function in this part of Australia.”

The Great Southern Reef...

Surveying the damage out in the ocean, Marzinelli had noticed that the same groups of bacteria tended to hang around on kelp showing signs of disease such as blistering, bleaching, and tissue degradation. This got him thinking about whether the kelp microbiome might mediate disease and how microbiome-kelp interactions may play out as the seas warm in the years to come.

A few years ago, Marzinelli and colleagues decided to test the ideas. They secured the use of 12 experimental mesocosms—fiberglass tanks with water continuously pumped in from the ocean—on the coast north of Sydney. The scientists then went scuba diving in the ocean and brought roughly 70 kelp plants back to their new homes. Using ocean temperature and acidification predictions for the years 2081–2100 from a report by the Intergovernmental Panel on Climate Change, the team simulated futuristic environments by heating or bubbling carbon dioxide into the water upstream of the kelp.

Dividing their setup into four sets of three tanks, the researchers recorded how the kelp fared over the course of two weeks in warm (23.5 °C), acidified (pH a little below 8), or both warm and acidified seawater, as compared with ambient conditions (21 °C and a pH of around 8.2).

In the experiment, warming alone didn’t seem to make much of a difference to algae health, which the team monitored by counting blisters on the kelp’s fronds and by measuring how efficiently the kelp carried out photosynthesis. But under acidified conditions, regardless of the water’s temperature, the kelp’s health took a turn for the worse. “It’s kind of a bit nasty when they develop those blisters,” says study coauthor Zhiguang “Galaxy” Qiu, a postdoc at Western Sydney University who worked on this project during his PhD at the University of New South Wales. The blisters start as tiny bubbles that grow and develop all over a kelp’s surface, he says. “Then, in the final stage of the blistering, they disintegrate so the whole kelp is full of holes.” The progression of the blisters destroys the kelp’s cell structure and cuts into its ability to carry out photosynthesis, he adds.

E. radiata underpins a lot of the biological diversity and ecological function in this part of Australia.

—Ziggy Marzinelli, University of Sydney

The researchers also periodically swabbed the surface of the kelp to grab DNA to identify which microbes were consorting with the kelp and how the composition of that community changed over time. The DNA sequences revealed that changes in the kelp microbiome preceded the downturn in the kelp’s health, suggesting that some of the microbes may be culprits rather than bystanders (Proc R Soc B, 286:20181887, 2019).

The findings imply that climate change could be indirectly affecting kelp via alterations to the kelp microbiome, says Marzinelli. Environmental conditions can change the microbial community composition “and result in massive effects on the host by causing bleaching, tissue decay, and affecting photosynthesis. . . . If they cannot do [photosynthesis], then they’re in a very bad shape.”

About the possibility that microbes drive the disease, “the results are suggestive, but by no means conclusive,” says Laura Parfrey, a microbial ecologist and evolutionary biologist at the University of British Columbia who was not part of the work. Parfrey says that the changes in the microbial communities are quite small, but do suggest scientists should think about interactions with the microbiome when considering climate change’s effect on a species.

A role for the microbiome in kelp health ties to what scientists have learned studying other species, says Cathy Pfister, a marine ecologist at the University of Chicago who was not involved in the study. For example, “I think that [this] result is very possible, and echoes to some extent what we know about corals and their symbionts.” Corals host photosynthesizing algae, alongside an array of bacteria and other microbes, which recent studies suggest could play a role in resilience to bleaching.

The new study adds weight to the idea that this kelp system that researchers think of as single species may really be a holobiont—a sort of superorganism formed from the host and its plethora of microbes, Pfister adds. “We’re really only on the cusp of understanding that.” 

See “Opinion: Individuals Are Greater Than the Sum of Their Parts

Regarding the current study, “there is a rich microbial community associated with Ecklonia,” says Pfister. “I would like to know: How is this microbial consortium helping or hurting the kelp? And does the nature of that interaction change with changing environment?”

One surprise in the study’s results was that in the most drastic conditions—seawater that was both warm and relatively acidic—the microbiome of diseased kelp eventually resembled that of healthy kelp under ambient conditions. One possible explanation is that “the extreme environmental scenario kills the pathogens, then the original microbial communities bounce back,” Qiu posits. At that point, it was probably too late for the ravaged kelp to also make a comeback, but the finding underlines the complexity of interactions between a host, its microbiome, and environmental factors, Marzinelli explains.

Following this study, the scientists cultured some of the microbial species that their experiment identified as possible harbingers of disease, and then inoculated the kelp with them to see whether disease manifested. The unpublished results suggest that some microbial taxa “clearly do cause bleaching and tissue degradation,” Marzinelli says. “But some others don’t do anything.” While their abundances happen to be correlated with kelp disease, they don’t seem to play a direct causal role.

Teasing out which microbes do what, and how they contribute to a host’s health, will be quite a task. “It’s really complex because the diversity of microbes is stunning,” says Marzinelli, adding that the number of microbial cells in the ocean dwarfs the quantity of stars in the known universe. “Those numbers are mind-blowing.”

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