Research Accomplishment Reports 2011

Functional Metagenomic Analysis of Soil-dwelling and Plant-associated Microbial Communities

L.A. Moe
Department of Plant and Soil Sciences

 

Non-Technical Summary

This work will use cutting-edge, high-throughput technologies to further understanding of two essential areas of research in agriculture:

• the biochemical communication mechanisms between plants and bacteria, and
• the biotransformation of nitrogen fertilizers in agricultural settings.

Soil-dwelling and plant-associated bacteria have a profound impact on the health and agricultural yield of plants. These bacteria can promote mutualistic interactions that benefit both the bacteria and plant host. Benefits provided to the plant include an increased capacity for nutrient uptake and the ability to fend off pathogens, among others. Conversely, bacteria can colonize and kill plants through pathogenic interactions. A poorly understood language of small molecules links plants and bacteria, and it is this language that is understood by pathogens and mutualists alike. While the plant may be exuding small molecule signals with the intention of recruiting beneficial bacteria, these signals can be recognized by other members of the plant-associated microbial community.

Our work aims to further understanding of the small molecule signaling language by looking at the response of an entire microbial community to the presence of compounds produced by the plant for signaling purposes. We aim to identify the bacterial response to these compounds by the overall microbial community to determine what the net effect of the signaling event is, and understand how microbial communities can potentially be manipulated to enhance plant health and agricultural yield.

Synthetic nitrogen fertilizers have a profound effect on agricultural yields, yet the majority of nitrogen applied in these fields is not taken up by the plants. The fate of the excess nitrogen is of significant interest owing to the impacts that this can have on downstream ecosystems. This includes eutrophication of bodies of water, which is a major problem in the Mississippi river basin. Microbial biotransformation of nitrogenous fertilizers plays a major role in the speciation and mobility of the nitrogen, yet little is known about the microbes and microbial communities that effect this biotransformation in agricultural soils.

The proposed work aims to further understanding of microbial communities in agricultural soils and to identify and characterize the genes that are essential in this biotransformation process. A greater understanding of this process can lead to more effective methods for plant fertilization that minimize excessive nitrogen application, benefiting both the farmer and the ecosystem. The work proposed here aims to create knowledge that will impact agriculture in the US by advancing understanding of agriculturally relevant microbes and the roles they play in plant health as well as agroecosystem health.

2011 Project Description

This is the first 6-month period of the project. The data generated to this point is preliminary in nature, and does not warrant dissemination to a larger audience. Activities during this reporting period include recruitment of graduate and undergraduate students to work on the project during the school year, research on the project, and mentoring students on the project.

Preliminary research outputs include a collection of genes from the rhizosphere metagenome that are upregulated in the presence of plant hormone compounds found in the rhizosphere, we are currently looking over the genetic data to interpret the potential impact of the data. This work has also provided a collection of bacterial genes responsive to plant hormones.

Work during this period has resulted in a number of collaborations with experts in the relevant fields including the following faculty at the University of Kentucky: Mark Coyne (Plant and Soil Sciences), Seth DeBolt (Horticulture), and David McNear (Plant and Soil Sciences).

We have constructed and validated a plasmid vector that we have found to be effective in operon-trap functional metagenomic screens.

2011 Impact

Research activities have been focused on developing techniques for studying the impact of soil-dwelling microbial communities on plant health and on biotransformation of nitrogenous fertilizer. Because the research is basic in nature and because the project is in its infancy, the impacts are limited at this point.

The primary impact at this point is the development of metagenomic methodologies for studying agriculturally-relevant soil-dwelling microbial communities. We aim to use this our metagenomic methodology in conjunction with basic genetic and biochemical studies of culturable microbes to further advance knowledge on the importance of microbial communities to plant health and agricultural yield.