Researchers collected over 3,000 samples of microbes and microbiomes from the entire watershed of Waimea Valley on O’ahu, Hawai’i. Their research revealed three key findings: microbes follow the food web, the majority of microbial diversity in a watershed is maintained in the soil and stream water, and a microbe’s local distribution predicts its global distribution.
A team of researchers from the University of Hawai’i (UH) at Mnoa School of Ocean and Earth Science and Technology (SOEST) collected over 3,000 samples of microbes and microbiomes from the entire watershed of Waimea Valley on O’ahu, Hawai’i, in a massive field expedition. Their research revealed three key findings: microbes follow the food web, the majority of microbial diversity in a watershed is preserved in soil and stream water, and a microbe’s local distribution predicts its global distribution. The researchers’ findings were recently published in the Proceedings of the National Academy of Sciences.
Plants and animals are home to dozens to thousands of different microbes, which are referred to as microbiomes. They help to digest our food, detoxify contaminants, and fight disease. Microbes also inhabit every habitat around us and power the machinery that keeps the air we breathe, the water we drink, and the soil beneath our feet alive. Despite their importance, most plant and animal microbiomes are not present at birth and must be acquired. But where? And where do microbes go when they are not in their hosts?
Microbes that occur in only one or two organisms or environments in Waimea Valley are unlikely to be widespread globally. Some microbes were widespread in Waimea and are presumably adaptable to all sorts of hosts and habitats. Our analyses demonstrated that those generalist microbes were also most widely recovered from diverse habitats across the globe.
Craig Nelson
The research team conducted a microbiome “bioblitz” – a near-complete census of all environmental substrates and possible hosts to microbes within the watershed. They took samples from the wet summit of Puʻu Kainapuaʻa, the low floodplain of Waimea Valley, and even the clear waters of Waimea Bay. Researchers gathered samples from soil; stream and sea water; animals, including rats, crayfish, mosquitoes, and sea urchins; plants, including trees, ferns, and algae; and much more. They extracted and sequenced more than 800 million microbial DNA “barcodes,” to determine which microbes were present where.
The structure followed the food web when the team assessed where the most diversity of microbes was found and where there were fewer species — many types in soil and water, fewer in plants, and even fewer in animals.
“Furthermore, microbes found in animals tended to be a subset of microbes associated with plants, and microbes on plants tended to be a subset of microbes in soil, water, and sediment,” said Sean Swift, co-author of the study and doctoral student in the UH Mnoa Marine Biology Graduate Program. “It’s as if plants build their microbiome from the environment, and animals then choose their microbiome from the plants’. Organism microbiomes are typically subsets of organisms lower on the food chain.”
One obvious way to build a microbiome is to acquire microbes from a related host, such as when a human mother shares her microbiome with an infant.
“However, this model is insufficient to sustain microbiomes across a dynamic landscape,” said Nicole Hynson, associate professor at SOEST and director of the Pacific Biosciences Research Center (PBRC). “Many plants and animals are sparse, seasonal, or ephemeral, necessitating that their symbiotic microbes be able to live in alternate nearby hosts or environments at times. We discovered that soil, sediment, and water serve as microbial diversity reservoirs, acting as environmental waiting rooms for microbes to colonize hosts when they become available.”
Another key finding is that the local distribution of a microbial species predicts its global distribution.
“Microbes that occur in only one or two organisms or environments in Waimea Valley are unlikely to be widespread globally,” said Craig Nelson, co-author and associate research professor in the Daniel K. Inouye Center for Microbial Oceanography: Research and Education and Hawai’i Sea Grant. “Some microbes were widespread in Waimea and are presumably adaptable to all sorts of hosts and habitats. Our analyses demonstrated that those generalist microbes were also most widely recovered from diverse habitats across the globe.”
Both plants and animals need microbes to stay healthy. The recent work shines light on the diversity and distribution of microbiomes at a landscape scale, an approach made possible by the unique structure and habitat diversity of Hawaiian watersheds.
“Understanding the origins and assembly processes of symbiotic microbes and their role in preserving biodiversity and ecosystem services allows us to better understand the origins and assembly processes of symbiotic microbes and their role in preserving biodiversity and ecosystem services,” said Anthony Amend, lead author of the study and associate professor at PBRC. “If we want to restore native plants and animals to an area, we may also need to consider restoring the microbiome source environments. Microbes are yet another way that organisms are linked to their surroundings.”
