Introduction

Beneficial microbes in agriculture

The long-term application of fertilizers and pesticides can damage soils and pollute water, and further can cause health problems to farmers. Beneficial microbes are less toxic and typically less regulated than many of these chemicals, and therefore can be a nice substitute for chemicals in some cases. As climate change and human population growth threaten agriculture, sustainably improving agriculture is essential. Major companies such as Novozymes, Monsanto, AgBiome, etc. actively look for beneficial microbes and have found some useful ones to sell in their products, but the search process is inefficient because we still have a poor understanding of how and under what conditions beneficial microbes will work. 

Sphingomonas as a potential bacterial inoculant

Named after membrane sphingolipids (which are somewhat rare in bacteria) the bacterial genus Sphingomonas is widely-distributed in the environment, on plant surfaces, and inside the leaves, roots, and seeds of many major crops. Plants tolerate Sphingomonas well, and it does not cause any important plant diseases. In fact, many Sphingomonas have been recently recognized for plant-beneficial features. Unfortunately, we know very little about how they actually interact with plants and other microbes. Learning the secrets to their success will help to identify beneficial microbes more efficiently. 

Specific Research Directions

1) Sphingomonas genetics 

• Bacterial mutant screens and tests of mutants on plants (Arabidopsis thaliana, barley, and poplar)

• Transciptomes of bacteria and plants living together.

The goal is to prioritize a set of strains for other work and find the genes defining Sphingomonas’ colonization and microbial interaction potential. These genes will be relevant for understanding why Sphingomonas does not overgrow its niche and harm plants — see below. They also could be used to bioengineer mutualists in future studies. 

2) Sphingomonas pathogenic potential 

• Bacterial growth in immune-compromised and injured plants

To reveal the extent to which Sphingomonas strains may become opportunistic plant pathogens in permissive conditions, to what extent the survival interests of the genus are aligned with those of the plant, and to identify genes affecting growth in such conditions.

3) Sphingomonas host preference 

• Assembly of wild bacterial populations on plants of different genetic background

• Sphingolipid interaction with plants

To inform inoculation strategies and help identify plant loci that can potentially be bred to support beneficial strains. To uncover to what extent bacterial sphingolipids interact with these plants. 

4) Changing field conditions

• Performance of strains and plants outdoors, and in conditions simulating future climate change

To reveal the biotic and abiotic factors that affect the ability of each strain to survive and persist on the plant, and the effect of these factors on the health of the plant. To portfolio of candidate robust beneficial strains, along with profiles of their limitations across environments.

Overview of work plans in currently-running grants