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In Corvallis, Oregon, Posy Busby works in a garden planted with 3,000 black cottonwood trees that represent 1,000 unique genetic specimens, each originally found somewhere on the West Coast of North America, from California to Canada. Cottonwoods are some of the fastest-growing trees in the world, and the garden looks a lot like a timber company plantation. But Busby, an ecologist at Oregon State University, studies something on a much smaller scale than trees\u2014the microbes that live inside their leaves.<\/p>\n\n\n\n
Busby started paying attention to microbes because she wanted to understand why wild plants plagued by a disease, such as leaf rust, fall ill in one place and not another. Genetics and environment could explain only part of this puzzle. But inside a plant is a whole world of microorganisms, and some of the cottonwoods\u2019 resident microbes seemed to have an impact on the severity of the leaf rust.<\/p>\n\n\n\n
At first Busby thought of these bacteria and fungi as individuals that could be either troublesome or beneficial to the plants, like the fungus that causes leaf rust. But as she read up on the human microbiome, she realized that the microbial communities within plants were as complex as those within us. \u201cWe\u2019re really dealing with the same thing,\u201d she says.<\/p>\n\n\n\n
Scientists have known for centuries that soil is packed with microscopic organisms and, since the late 1800s, that some plants form symbiotic relationships with fungi. But now they are finding that microorganisms live not just around but inside plants\u2014in their roots, stems, and leaves\u2014in greater numbers and with more diversity than anyone realized.<\/p>\n\n\n\n
Busby\u2019s cottonwood trees, for instance, were known to have a handful of microbial pathogens. \u201cBut when we looked at the overall diversity of the fungi in the leaves, it was more like a thousand or 1,500 different fungi living in and on these leaves,\u201d across the tree\u2019s range, she says. \u201cSo that was an astounding number.\u201d<\/p>\n\n\n\n
Just as we have learned that the human microbiome has a greater influence on human health than anyone imagined, there\u2019s an emerging understanding that the plant microbiome could be the key to floral health. One initial goal of exploring the plant microbiome has been to determine who\u2019s part of this community and what they\u2019re doing for the plant. The answer, it turns out, depends on location. If you\u2019re a plant, the place you live changes the ecosystem inside you, and that can affect your whole life.<\/p>\n\n\n\n
\u201cThe plant\u2019s microbiome is strongly determined by where that plant is growing. It matters whether you\u2019re on one side of the mountains or the other. It even matters if you\u2019re 30 miles a way.\u201d<\/p>\n\n\n\n
As an example, about an hour north of Corvallis, there\u2019s another scientific garden of cottonwood trees, and, Busby says, \u201cwe see very different communities form in those two different places.\u201d<\/p>\n\n\n\n
No one knew much about the microorganisms that colonize plants\u2019 external surfaces\u2014and internal tissues\u2014until the arrival of relatively cheap DNA sequencing. A single cottonwood leaf, for instance, might have 50 species of fungi and bacteria living inside. Roots and leaves in the same plant can have notably different microbial communities, but for any particular plant species, there are certain types of microorganisms that make up the community\u2019s core. But across a plant\u2019s range, this can vary greatly.<\/p>\n\n\n\n
Some of the best-known mushrooms in the world are the fruits of mycorrhizal fungi, which grow in association with plant roots. When people raised in Europe or in the eastern half of America traveled west, they thought the mushrooms they found were the same as the ones they already knew. But now we understand that they\u2019re different species. \u201cYou find very regionally distinct communities of mycorrhizal fungi depending on where you are,\u201d says Kabir Peay, an assistant professor of biology at Stanford. These fungi, by the way, live both inside and outside a plant. They have filaments that reach out into the soil to fetch nutrients, but they also form what Peay calls \u201cthese really intimate structures, where they come in close proximity with plant cells,\u201d inside the plant.<\/p>\n\n\n\n
Those regional variations in microbial or fungal communities, in turn, affect the structure of plant communities. Disease-causing microbes, for example, can keep one tree species from becoming dominant, but their impact depends on the mix of other microbes they live among. \u201cWhat does it mean on a large scale when you change the composition of these communities and decrease their diversity?\u201d says Peay. \u201cI don\u2019t think we have the answer quite yet.\u201d But there are indications that it will matter\u2014in a big way\u2014as environments begin to shift. It seems like different microbes are \u201cdoing wildly different things\u201d to forests, says Colin Averill, a postdoctoral researcher at Boston University, in Jennifer Bhatnagar\u2019s lab. \u201cIf you know which types of fungi are on the roots of trees, you can better predict the ability of the forest to sequester carbon and forecast [the effects of] climate change.\u201d<\/p>\n\n\n\n
How exactly a plant\u2019s microbiome makes changes like this is still a mystery, but last year a group of scientists, Busby included, proposed an agenda \u201canalogous to the Human Microbiome Project,\u201d to promote research that could start answering these questions. Scientists are beginning to discover how incredibly diverse the metabolism of plant-associated microorganisms is, says Bhatnagar, an assistant professor at Boston University, with a potential impact on a variety of fields, such as drug discovery and environmental management. \u201cThat\u2019s one of the treasures of the plant microbiome that\u2019s still untapped\u2014all the molecules these guys can make and how we can help make them,\u201d she says.<\/p>\n\n\n\n
And keeping plants healthy is, in the end, a matter of human health, too. Understanding how to promote or manipulate a plant\u2019s microbiome so that it\u2019s healthier and more productive could lead to breakthroughs in agriculture and give farmers powerful tools other than fertilizers to boost production. If we can understand plant microbiomes, it might help us manage the rocky environmental future. \u201cThese cryptic organisms that live in plants contribute in meaningful ways to plant growth, plant development, and plant immunity,\u201d says Busby. \u201cThey could be the key to growing enough food for our human populations in the future.\u201d<\/p>\n\n\n\n