Plant Microbiomes

A bog in Northern Minnesota carpeted by Spagnum moss.

Plant microbiome research is in its infancy, at least a decade behind research into the human microbiome. Microbes (bacteria, archaea, and fungi) interact with live plants to complement their functional traits and primary productivity. Tens of thousands of microbial species associate with plants, and plant-microbe interactions are crucial to plant health. Broadly defined, plant-microbe associations include the microbes that live inside plant tissues (endophytes) as well as those that grow on the plant surface. Microbes demonstrate the potential to benefit plants in nutrient acquisition, disease suppression, and in the modulation of host immunity. Next generation sequencing technologies and omics-based approaches have recently enabled some of the first detailed studies of plant microbiomes. However, these studies have been hampered by methodological limitations and applied to relatively few model plant species. Thus, in order to achieve a predictive, systems-level understanding of the role of plant function in managed or natural ecosystems, an improved mechanistic understanding of plant-microbe associations is required.

In contrast to planktonic environments where the predominant microbial groups have been identified, the ecology of plant-associated microorganisms (including their abundance, distribution, diversity, and functioning) remains little studied. To achieve a mechanistic understanding of plant-microbe interactions, the Kostka Lab is investigating the following questions:

  1. What microbial groups are associated with the tissues of plants and where in the plant do these microbial groups reside?
  2. How do plants benefit from their microbiome?
  3. How do plant genotype, microbiome, and environment (i.e., climate and soil type) interact to regulate plant growth promotion?
  4. What are the signaling or communication pathways between microbiome and plant?
  5. Are these dependent on plant genotype, developmental stage, soil conditions or attack by insects or microbial pathogens?
  6. How do various soil types affect the populations and community structures of microbes residing therein?

Active projects are focused on the microbiomes of sugar cane (Saccharum) and peat moss (Sphagnum). Sugar cane is among the most important agricultural plants on Earth. Sugar cane is not only key for food production but is also used as a biomass feedstock for biofuel (ethanol added to gasoline). In the Kostka Lab, we are investigating nitrogen fixing bacteria as an environmentally friendly alternative to fertilizer use. In other words, we are developing biofertilizer inocula to reduce the economic and environmental costs of sugar cane production.

Peat mosses play an important role in the global carbon cycle. Sphagnum dominates the photosynthetic production in many peatlands, where much of the world's soil carbon is stored. Peat mosses are known to contain methanotrophic and nitrogen fixing bacteria that aid the plant in nutrient acquisition. We are studying the role of Sphagnum microbiome as a source of carbon and nitrogen to peatland ecosystems.