Nitrogen Fixing Bacteria in Sugar Cane Fields

The field of canes that the researchers are researching.
Collecting and analyzing samples in the sugarcane fields.
Dr. Joel Kostka with other researchers.

Soil, ocean water, and even the human gut are teeming with bacteria. These environments can harbor thousands of species of bacteria, each one performing a unique set of key functions. One function of interest in agriculture is the transformation of nitrogen gas from air into ammonia, a chemical form that plants and bacteria can absorb. Nitrogen is essential for life because it is part of the structure of cellular macromolecules like proteins and DNA. Nitrogen is usually the nutrient which first limits growth of crops because it is required more than any other soil nutrient. Nitrogen fertilizers can alleviate this limitation, but they are expensive to produce because the industrial process for nitrogen fixation requires high temperatures and the addition of hydrogen obtained from natural gas. Furthermore, the addition of nitrogen fertilizer to crops results in runoff which contaminates water supplies, and soil denitrification (the transformation of nitrate back to nitrogen gas through a series of biologically mediated enzymatic steps) can generate intermediate forms of nitrogen which are potent greenhouse gases. However, some bacteria have an enzyme capable of transforming nitrogen into ammonia. These bacteria are known as nitrogen fixers, of which there are thousands of species, and only a fraction of known to exist have been successfully isolated and studied in culture. Nitrogen fixers can be found free-living in the environment, symbiotically associated with plants as in the case of the rhizobia that live inside legume root nodules, and associated with the root surface or within plant tissues. Sugarcane, while not exhibiting a direct symbiosis with nitrogen fixers as for legumes, does harbor abundant and diverse nitrogen fixers that have been shown to contribute significant amounts of fixed nitrogen to the plant.

Using state-of-the art molecular techniques combined with enrichment and cultivation-based approaches, we are working to:

  1. Characterize the nitrogen-fixing bacteria that live in association with sugarcane
  2. Determine the environmental variables that shape communities of nitrogen-fixing bacteria, and
  3. Obtain cultures of representative nitrogen-fixing bacteria that grow in association with sugarcane.

We have implemented an enrichment approach which allows simultaneous screening of multiple inoculum sources with various growth substrates. Using this approach, we have succeeded in isolating numerous unique strains of Proteobacteria known to associate with plants and that have the molecular marker for nitrogen fixation (the nifH gene). We have also developed a bioinformatics pipeline for analysis of nifH gene sequences obtained from rhizosphere soils, roots, and stems of sugarcane. We can thereby identify the many species of nitrogen-fixers found in association with sugarcane and begin to determine which factors in the environment (e.g. pH, soil texture, sugarcane variety, etc.) favor the proliferation of particular species of nitrogen fixers. Through a deeper understanding of the ecology of nitrogen fixers associated with a model crop like sugarcane, we can begin to formulate ways to stimulate the abundance and activity of this beneficial group of microbes in order to increase crop yields and to ultimately reduce the need for economically and environmentally costly fertilizers.

From the Kostka Lab:

From the Jordan Lab:

Participants from Colombia: