Genomic time machine: From sponge microbiome, insights into evolutionary past

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The red barrel sponge, Xestospongia muta — pictured here during collection trip in belize — harbor a dense and diverse microbial community that evolved repeatedly during sponge evolution and is linked to increased predation defense. Credit: Sabrina Pankey.

Sponges in coral reefs, less flashy than their coral neighbors but important to the overall health of reefs, are among the earliest animals on the planet. New research from UNH peers into coral reef ecosystems with a novel approach to understanding the complex evolution of sponges and the microbes that live in symbiosis with them. With this “genomic time machine,” researchers can predict aspects of reef and ocean ecosystems through hundreds of millions of years of dramatic evolutionary change.

“This study shows how microbiomes have evolved in a group of organisms over 700 million years old,” says Sabrina Pankey, a postdoctoral researcher at UNH and lead author of the study, published recently in the journal Nature Ecology & Evolution. “Sponges are increasing in abundance on reefs in response to and they play an enormous role in and nutrient fixation.”

The significance of the work transcends , though, providing a new approach to understanding the past based on genomics. “If we can reconstruct the evolutionary history of complex microbial communities like this we can say a lot about the Earth’s past,” says study co-author David Plachetzki, associate professor of molecular, cellular and biomedical sciences at UNH. “Research like this could reveal aspects of the chemical composition of the Earth’s oceans going back to before modern even existed, or it could provide insights on the tumult that experienced in the aftermath of the greatest extinction in history that took place about 252 million years ago.”

The researchers characterized almost 100 sponge species from across the Caribbean using a machine-learning method to model the identity and abundance of every member of the sponges’ unique microbiomes, the community of microbes and bacteria that live within them in symbiosis. They found two distinct microbiome compositions that led to different strategies sponges used for feeding (sponges capture nutrients by pumping water through their bodies) and protecting themselves against predators—even among species that grew side by side on a .

“The types of symbiotic communities we describe in this paper are very complex, yet we can show they evolved independently multiple times,” says Plachetzki.

And, adds Pankey, “there’s something very specific about what these microbial communities are doing … sponges dozens of times have decided that this diverse arrangement of microbes works for them.”

Leveraging this new genomic approach, the researchers found that the origin of one of these distinct microbiomes, which had a high microbial abundance (HMA) of more than a billion microbes per gram of tissue, occurred at a time when the Earth’s oceans underwent a significant change in biogeochemistry coincident with the origins of modern coral reefs.

While machine learning and genomic sequencing generated the findings Plachetzki calls “a tour de force of microbial barcode sequencing,” this research began far from the lab, in the warm waters of the Caribbean.

“We dove for all 1,400 of these samples,” says Pankey, who went on five expeditions in 2017 and 2018 to collect sponges. “It was a monstrous collection,” she adds, acknowledging that SCUBA diving in the Caribbean has its rewards. The duo credits co-author Michael Lesser, UNH research professor emeritus, for establishing field work techniques, and their co-authors from the University of Mississippi and the Universidad Nacional del Comahue in Argentina for assisting with sponge collection and molecular identification. Former graduate student Keir Macartney also contributed to the study.

More information:
M. Sabrina Pankey et al, Cophylogeny and convergence shape holobiont evolution in sponge–microbe symbioses, Nature Ecology & Evolution (2022). DOI: 10.1038/s41559-022-01712-3

Genomic time machine: From sponge microbiome, insights into evolutionary past (2022, April 14)
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Hexbyte Glen Cove Genomic data 'catches corals in the act' of speciation and adaptation thumbnail

Hexbyte Glen Cove Genomic data ‘catches corals in the act’ of speciation and adaptation

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A) Porites lobata (yellow massive morphology) shown next to Porites compressa (blue-grey branching morphology) side by sidein the same habitat; (B) example of variation in bleaching susceptibility of P. compressa in Kāne’ohe Bay. Credit: Forsman, et al. (2020)

A new study led by the University of Hawai’i at Mānoa’s Hawai’i Institute of Marine Biology (HIMB) revealed that diversity in Hawaiian corals is likely driven by co-evolution between the coral host, the algal symbiont, and the microbial community.

As have rapidly collapsed around the globe over the past few decades, there is widespread concern that corals might not be able to adapt to changing , and much of the biodiversity in these ecosystems could be lost before it is studied and understood. Coral reefs are among the most highly biodiverse ecosystems on earth, yet it is not clear what drives speciation and diversification in the ocean, where there are few physical barriers that could separate populations.

The team of researchers used massive amounts of metagenomic sequencing data to try to understand what may be some of the major drivers of adaptation and variation in corals.

“Corals have incredible variation with such a wide range of shapes, sizes, and colors that it’s really hard for even the best trained experts to be able to sort out different species,” said Zac Forsman, lead author of the study and HIMB assistant researcher. “On top of that, some corals lose their algal symbionts, turning stark white or ‘bleached’ and die during marine heatwaves, while a similar looking right next to it seems fine. We wanted to try to better understand what might be driving some of this incredible variation that you see on a typical coral reef.”

Forsman and colleagues examined genetic relationships within the coral genus Porites, which forms the foundation and builds many around the world. They were able to identify genes from the coral, algal symbionts, and bacteria that were most strongly associated with coral bleaching and other factors such as the shape (morphology) of the coral colony. They found relatively few genes associated with bleaching, but many associated with distance from shore, and colony morphologies that dominate different habitats.

“We sought out to better understand and place it in the context of other sources of variation in a coral species complex. Unexpectedly, we found evidence that these corals have adapted and diverged very recently over depth and distance from shore. The algal symbionts and microbes were also in the process of diverging, implying that co-evolution is involved. It’s like we caught them in the act of adaptation and speciation.”

“These corals have more complex patterns of variation related to habitat than we could have imagined and learning about how corals have diversified over various habitats can teach us about how they might adapt in the future,” he explained. “Since is the raw material for adaptation, there is hope for the capacity of these corals to adapt to future conditions, but only if we can slow down the pace of loss.”

More information:
Z. H. Forsman et al, Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae), Scientific Reports (2020). DOI: 10.1038/s41598-020-73501-6

Genomic data ‘catches corals in the act’ of speciation and adaptation (2020, November 2)
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