Within this research theme, we seek a fuller understanding of the mixed and complex microbial communities (‘microbiota’) that naturally associate with plant surfaces, both above- and below-ground. These communities, also known as the ‘phytobiome’, are important to the sustainability of US agriculture, not only as a source of many current and future economically important plant pathogens, but also as a natural supply of bacteria, fungi and other microorganisms with the individual or collective capacity to promote plant health (Kim2011).
Research in Lab Leveau seeks to quantify the spatial and temporal variation in the types, abundances, and functions of microorganisms that colonize plant leaves and roots, and identify the factors that drive such variation. We have several completed and ongoing projects that aim to profile microbial communities that associate with the leaves and/or roots of plants such as grape (Leveau2011), lettuce (Rastogi2012), spinach, tomato, strawberry and citrus. We use culture-independent (Rastogi2010) as well as culture-dependent (Scheublin2013) approaches to describe and compare the size and diversity of plant microbial populations in the phyllosphere (Rastogi2013) and rhizosphere (Leveau2007). We are also interested in the gene functions and adaptations that allow bacteria to survive and compete with each other on plant surfaces, especially leaves, and that may have practical applications. By a combined approach of genome mining (RemusEmsermann2013), transcriptional profiling (Scheublin2014), and mutant screening of phyllosphere-competent bacterial species, we are revealing novel genes and gene clusters with a possible function in leaf surface survival and future use in the (bio)control of plant and human pathogens on plant foliage. One of our projects builds on the lab’s discovery of a so-called iac gene cluster (Leveau2008) that allows bacteria to destroy and grow at expense of the plant hormone indole 3-acetic acid or IAA (Leveau2005). We recently proposed the pathway by which this gene cluster codes for the conversion of IAA to catechol (Scott2013). We are interested to discover the selective advantage of this gene cluster, which can be found not only in plant-associated bacteria, but also in bacteria from other environments, such as the human body, hospitals, and soils.