The Newest Dirt on Microbial Communities

Have you ever struggled to keep a house plant alive? Or are the flowers in your garden wilting? New research in microbial communities that live just below the surface of these plants may give us the answer to growing bigger and better plants. 

In October of 2017 the ISME journal for microbial ecology published an article from University of Wyoming graduate student Charley Hubbard. His research was focused on how a plants circadian clock influences microbial community structure and function. After joining Cynthia Weinig's lab at UW Hubbard was able to combine his experience with bacteria with his interest in plants. Studies across disciplines have shown that microbes are extremely beneficial for their hosts.

"In plants, microbes can affect plant nutrient access, response to stress, the timing of important life history events, gene expression, growth and so much more," Hubbard explains.

Figure 1: Changes within the human circadian rhythm

In addition to microbes, the circadian rhythm is another important component of Hubbard's research. Also known as the inner biological clock, the circadian rhythm is found in a variety of organisms, including humans. This rhythm operates within the 24 hour period, and helps to regulate our sleep patterns, feeding behavior, and other physiological changes.

Hubbard's findings suggested that there was a difference in microbial communities depending on the plants circadian clock. In turn, the different microbes living in the soil affected the growth of the plant.

Figure 2: The Rhizosphere is where microbial communities live

"I think it is a Goldilocks and the three bears kind of scenario, where the three bears (plants with a 20, 24, and 28 hour circadian period) have selected their beds (microbial communities) and Goldilocks (plant with a 24 hour circadian period) prefers (grows largest in) a certain bed," Hubbard explains.

Hubbard looked specifically at the rhizosphere, the area where the root meets the soil, and where many microorganisms live.

"Essentially, we pull plants out of their pots, shake the roots until only the soil closely adhering to the roots remains, use specialized kits to take the DNA for the closely adhering soil, and then send that DNA to a lab in Massachusetts," Hubbard explains.

When they receive results from the lab, they are given huge files of DNA sequencing. This sequencing information is run through a special software to determine what microbes are associated with the plant.

Hubbard's publication comes out at a time when many other researchers are exploring the circadian rhythm in organisms. The 2017 Nobel Prize in Physiology or Medicine was awarded to a group of scientists who studied the circadian rhythm in fruit flies. These findings, as well as other findings focused on plant's circadian clocks, helped to inform Hubbard's project.

Hubbard is running follow up projects on this paper's findings in the context of natural variation in the circadian clock. The circadian clock within a plant may change depending on it's elevation, which would also affect the microbial community it lives with.

"If differences in the circadian clock lead to differences in microbial communities, then it is possible that plants at differing elevations associate with different microbial communities," Hubbard adds.

Figures 1, 2