Microbial ecology related to agriculture and biotechnology
We have an interest in understanding the ecology of microbes as this relates to plant health, agricultural productivity, and post-harvest crop quality. Projects have focused on the microbial inhabitants of the rhizosphere, phyllosphere, and endosphere, and include both model plants as well as major agricultural crops. We are fortunate to collaborate with agronomists, plant molecular biologists, soil and rhizosphere scientists, and phytochemists at UK and at the Kentucky Tobacco Research and Development Center.
The rhizosphere plays a key role in plant health and nutrient acquisition, but the process by which plants recruit and maintain microbes at the soil-root interface or as root endophytes is not well understood. We use both culture-dependent and culture-independent tools to explore the ecology of these microbes and the biochemical language shared between plant and microbe in this environment.
Representative publications:
Szoboszlay, M., White-Monsant, A., & Moe, L. A. (2016). The Effect of root exudate 7,4′-dihydroxyflavone and naringenin on soil bacterial community structure. PloS ONE, 11(1).
Saleem, M., Law, A. D., & Moe, L. A. (2015). Nicotiana roots recruit rare rhizosphere taxa as major root-inhabiting microbes. Microbial Ecology, 1-4.
Szoboszlay, M., Lambers, J., Chappell, J., Kupper, J. V., Moe, L. A., & McNear, D. H. (2015). Comparison of root system architecture and rhizosphere microbial communities of Balsas teosinte and domesticated corn cultivars. Soil Biology and Biochemistry, 80, 34-44.
We have a particular interest in the phyllosphere microbial communities of tobacco, owing to the fact that tobacco is one of the minority of major agricultural crops in which the leaf is the agronomic quantity. Following harvest, burley tobacco is air-cured in dedicated curing barns for several weeks. Carcinogenic tobacco-specific nitrosamines (TSNAs) are mostly absent from fresh leaves, but accumulate during the air-curing process. This is especially true under high heat, high humidity conditions – conditions that presumably select for optimal microbial activity. We have noted a shift in microbial communities that develop under high heat, high humidity conditions and that correlate with increases in TSNA content. We are currently exploring the ecology and biochemistry of tobacco phyllosphere microbes under fresh and curing conditions to identify the mechanism by which this occurs.
Representative publications:
Law, A. D., Fisher, C., Jack, A., & Moe, L. A. (2016). Tobacco, microbes, and carcinogens: correlation between tobacco cure conditions, tobacco-specific nitrosamine content, and cured leaf microbial community. Microbial Ecology, 72, 120-129.
In addition to agricultural microbial ecology, we explore how microbial ecology impacts major biotechnological processes such as bioethanol fermentation. In collaborative work with scientists at the Danville, KY-based company Ferm Solutions, Inc., we seek to understand how the bacterial communities in large scale yeast-based fermentations can impact the overall success of the process. Bioethanol fermentations, in contrast to most food and beverage fermentations, are optimal under conditions in which bacterial activity is kept to a minimum. However, these fermentations take place in massive fermentation vats (~500,000 gallons) that are not sterilized. Under certain conditions, bacteria can outcompete the fermentation yeasts and result in a “bacterial bloom” event that can have devastating effects on the production facility. We explore the ecology of these fermentations to gain an understanding of the native bacterial communities and to identify conditions under which an “optimal” bacterial community may prevent bloom events in the future.
Representative publications:
Li, Q., Heist, E. P., & Moe, L. A. (2015). Bacterial community structure and dynamics during corn-based bioethanol fermentation. Microbial Ecology, 1-13.
Murphree, C. A., Heist, E. P., & Moe, L. A. (2014). Antibiotic resistance among cultured bacterial isolates from bioethanol fermentation facilities across the United States. Current Microbiology, 69(3), 277-285.
Biology of D-amino acids in microbes
Of the 20 proteinogenic amino acids, 19 are chiral about their alpha carbon. Nature has selected for L-amino acids as the building blocks of ribosomally-produced proteins as as major metabolic intermediaries. In contrast, D-amino acids are less abundant, and their roles in biological systems are much less understood. We use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore the synthesis and catabolism of D-amino acids. Enzymatic racemization of L-amino acids is the primary mechanism for synthesis of D-amino acids, but the roles of the D-amino acids produced through this process are not always clear. We are currently exploring the genomics and biochemistry of amino acid racemization to understand which D-amino acids are synthesized and why they are synthesized. Regarding D-amino acid catabolism, we have recently shown that catabolism of a diverse collection of D-amino acids is a common trait shared by soil-dwelling bacteria, and we are following up on the mechanisms by which this occurs.
Representative publications:
Radkov, A. D., McNeil, K., Uda, K., & Moe, L. A. (2016). D-Amino acid catabolism is common among soil-dwelling bacteria. Microbes & Environments, 31, 165-168.
Radkov, A. D., & Moe, L. A. (2014). Bacterial synthesis of D-amino acids. Applied Microbiology and Biotechnology, 98(12), 5363-5374.
Radkov, A. D., & Moe, L. A. (2013). Amino acid racemization in Pseudomonas putida KT2440. Journal of Bacteriology, 195(22), 5016-5024.
Genetics and biochemistry of phosphate solubilization by soil-dwelling bacteria
Some soil-dwelling microbes exhibit a plant-beneficial trait whereby they make insoluble mineral phosphates available for plant uptake. This process (phosphate solubilization) occurs through secretion of organic acids into the soil matrix where they act to chelate cations, releasing inorganic phosphate. In the Pseudomonas putida KT2440, gluconic acid carries out this role. Gluconic acid is synthesized from glucose by a periplasmic glucose dehydrogenase (GDH) enzyme that requires pyrroloquinoline quinone (PQQ) as a cofactor. We are exploring the mechanisms by which GDH activity is regulated in P. putida KT2440. In particular, we have an interest in regulation of gene expression for glucose dehydrogenase and the pqq operon genes according to growth conditions and available phosphate levels. We are also extending this work to explore the genomics of PQQ biosynthesis and phosphate solubilization among a library of soil-dwelling bacteria.
Representative publications:
An, R., & Moe, L. A. (2016). Regulation of PQQ-dependent glucose dehydrogenase activity in the model rhizosphere dwelling bacterium Pseudomonas putida KT2440. Applied and Environmental Microbiology, 82, 4955-4964.