UNIVERSITY PARK, Pa. — Corals and the microorganisms they host have evolved together for hundreds of millions of years. Understanding this long-term relationship could add fresh insight to the fight to save the Earth’s embattled coral reefs, the planet’s largest and most significant structures of biological origin.

A paper describing these findings by an international team of researchers appears in the Nov. 22 edition of the journal Nature Communications.

“There has been a lot of recent focus on understanding microbiomes — the community of microorganisms that live on or in all other organisms — because of their importance for the health of their host organism,” said Mónica Medina, professor of biology at Penn State and an author of the paper. “Corals are critical to marine ecosystems, so we set out to survey the microbiomes of a large number of coral species. Our study was guided by the evolutionary relationships among the corals, so we could test whether corals and their microbiomes have evolved together.”

The study involved hundreds of samples of scleractinian corals — also known as stony corals — which since their first appearance approximately 400 million years ago have branched into more than 1,500 species. Many of those species are major builders of coral reefs, which are found in less than one percent of the ocean but are home to nearly one-quarter of all known marine species. Reefs also help regulate the sea’s carbon dioxide levels and are a crucial hunting ground that scientists use in the search for new medicines.

A modern coral colony is home to a complex composition of dinoflagellates, fungi, bacteria and archaea that together make up the coral microbiome. Shifts in microbiome composition are connected to changes in coral health. The study looked separately at the microbiomes from three different components of a coral — the animal’s soft tissue, its skeleton, and the mucus it secretes to form a protective layer around itself.

“This is one of the most extensive studies of coral microbiomes that’s ever been conducted,” said Joseph Pollock, co-first author of the paper and former postdoctoral researcher at Penn State, now Caribbean Coral Strategy Director at The Nature Conservancy. “We sampled from hundreds of corals across a very large geographical region and across a broad range of coral diversity. We identified the microorganisms present in the three coral components using DNA sequencing and then looked for patterns of coevolution of the microbiomes with their coral hosts using the known evolutionary relationships among the corals.”

The researchers sequenced the 16S rRNA gene, which is present in every living organism, but is slightly different across species and thus can act as a “molecular bar code” for each organism. From there, the scientists could look for patterns between different corals’ microbial communities and determine whether coevolution of the corals and their microbiomes had taken place.

“We found strong support for coral-microbe ‘phylosymbiosis,’ in which coral microbiome composition and richness is reflected in the coral host’s evolutionary history,” said Rebecca Vega Thurber, associate professor of microbiology at Oregon State University and an author of the paper. “Now we have a framework for analyzing scleractinian coral microbes that can reveal how the corals’ evolutionary history, host traits and local environment interact to shape microbiomes. In the coral world, there’s been a longstanding hypothesis that microbes and coral coevolved, but there hadn’t been a sufficient data set to test that before now.”

It was something of a surprise to researchers to find that the microbial communities of the corals’ calcium carbonate skeletons showed greater microbiome richness compared to the tissue and mucus microbiomes. Also, the skeletal microbiomes displayed the strongest signal of long-term phylosymbiosis — the pattern of coevolution between the microbiomes and their hosts.

“We originally thought corals would show signs of phylosymbiosis throughout their entire phylogenetic history, and the results support that for the skeleton and tissue but not the mucus,” said Ryan McMinds, a graduate student at Oregon State and the other co-first author. “Despite variability in the chemical composition of mucus between species and significant host-specificity in the mucus microbiome, host specificity was limited to relatively recent divergences.”

The study found a strong relationship between the microbiomes of the coral’s tissue and its skeleton with the evolutionary relationship among coral species. It also found similar microbiomes even when corals within the same species were far apart geographically and in very different environments. This coevolution over such a long period of evolutionary time suggests that disruptions to the relationship between corals and their microbiomes could have negative consequences for coral health and may provide new avenues to help threatened corals species.

“We now have the data to evaluate the symbiotic relationships between corals and their microbiomes across the diverse and ancient coral evolutionary tree,” said Pollock. “Understanding which microbial partners have been selected over hundreds of millions of years of evolution helps us target those with the greatest potential to bolster coral health — those most likely to promote coral resilience in the face of increasing environmental stress.”

In addition to Medina, Pollock, Vega Thurber, and McMinds, the research team included Styles Smith at Penn State; David G. Bourne and Bette L. Willis at James Cook University in Queensland, Australia; and Jesse R. Zaneveld at the University of Washington. The research was funded by the U.S. National Science Foundation.