Census of ridge-to-reef ecosystem reveals hidden reservoir for microbiomes

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In a monumental field expedition, a team of researchers from the University of Hawai’i (UH) Mānoa School of Ocean and Earth Science and Technology (SOEST) collected more than 3,000 samples of microbes and of microbiomes present throughout the Waimea Valley watershed. on O’ahu, Hawaii. Their investigation revealed three key findings: microbes follow the food web, most of the microbial diversity in a watershed is maintained in soil and stream water, and a microbe’s local distribution predicts its worldwide distribution. Their findings were recently published in the Proceedings of the National Academy of Sciences.

Plants and animals are each host to tens to thousands of different microbes, collectively called microbiomes. They metabolize our food, detoxify contaminants and help fight disease. Microbes also inhabit all the habitats around us and operate the machinery that maintains the air we breathe, the water we drink, and builds the soil beneath our feet. Despite their importance, most plant and animal microbiomes are usually not present at birth and are instead acquired. But from where? And where do microbes live when they are not in their hosts?

The research team conducted a microbiome “bioblitz” – a nearly complete census of all environmental substrates and possible hosts of microbes in the watershed. They took samples from the wet summit of Puʻu Kainapuʻa, the lower floodplain of the Waimea Valley, and even the clear waters of Waimea Bay. Researchers collected soil samples; stream and sea water; animals, including rats, crayfish, mosquitoes and sea urchins; and plants, including trees, ferns and algae; and much more. They extracted and sequenced more than 800 million “barcodes” of microbial DNA to determine which microbes were present and where.

When the team assessed where the greatest diversity of microbes was and where there were fewer species, the structure followed the food web – many types in soil and water, fewer in plants and still less in animals.

“Additionally, the microbes found in animals tended to be a subset of the microbes associated with plants and the microbes on plants tended to be a subset of the microbes in soil, water, and sediment” , said Sean Swift, co-author of the study. and PhD candidate in the Marine Biology Graduate Program at UH Mānoa. “It’s like plants assembling their microbiome from the environment, and then animals selecting their microbiome from that of plants. The microbiomes of organisms are usually subsets of those found lower in the environment. the food chain.”

An obvious way to assemble a microbiome is to acquire microbes from a related host – like a human mother shares her microbiome with an infant, for example.

“However, this model is insufficient to maintain microbiomes in a dynamic landscape,” said Nicole Hynson, associate professor at the Pacific Biosciences Research Center (PBRC) at SOEST. “Many plants and animals are rare, seasonal, or ephemeral, requiring their symbiotic microbes to be able to occasionally reside in nearby alternate hosts or environments. We have found that soil, sediment, and water serve as reservoirs for microbial diversity – providing environmental waiting rooms for microbes to colonize hosts when available.”

Another key finding is that the local distribution of a microbial species predicts its global distribution.

“The microbes found in one or two organisms or environments in the Waimea Valley are unlikely to be widespread globally,” said Craig Nelson, co-author and associate research professor at the Daniel K. Inouye Center for Microbial Oceanography. : Research and Education and Hawaii. ‘I Sea Grant. “Certain microbes were widespread in Waimea and are likely adaptable to all kinds of hosts and habitats. Our analyzes demonstrated that these generalist microbes were also the most widely recovered in various habitats around the world.”

Plants and animals need microbes to stay healthy. Recent work sheds light on the diversity and distribution of microbiomes at the landscape scale, an approach made possible by the unique structure and diversity of Hawaiian watershed habitats.

“Understanding the sources of shared microbial diversity in ecosystems allows us to better understand the origins and assembly processes of symbiotic microbes and their role in maintaining biodiversity and ecosystem services,” said Anthony Amend, lead author of study and associate professor at PBRC. “If we want to restore native plants and animals to an area, we may also need to think about restoring the source environments of their microbiomes. Microbes are another way in which organisms are connected to the environment.”

Source of the story:

Material provided by University of Hawaii at Manoa. Original written by Marcie Grabowski. Note: Content may be edited for style and length.

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