Microarray Analysis and functional assays to assess microbial ecology and disease suppression in soils under organic or sustainable management

Final Report for LS05-173

Project Type: Research and Education
Funds awarded in 2005: $250,000.00
Projected End Date: 12/31/2009
Grant Recipient: North Carolina State University
Region: Southern
State: North Carolina
Principal Investigator:
Dr. Frank Louws
NC State University
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Project Information


First, we are engaged in sustainable agriculture research, teaching and extension at multiple levels – from the field to national and international programming. We support Southern SARE’s desire to conduct component research, farming systems research and more recently research that involves sociological questions and advancing agriculture within a sustainable society. Advances need to occur at all levels. This project focused on component research and sought to advance the fundamental understanding of the impact of farming systems on microbial communities and then to advance our knowledge about the link between microbial communities and plant disease incidence and crop productivity. We observed that the science of microbial ecology is exploding in terms of the ability of scientists to characterize whole communities and to analyze the links between communities and ecosystem services (e.g. plant disease suppression, N-Cycling; C-Cycling etc) through the emergence of new and complex statistical tools and bioinformatics software. We systematically sampled conventional tillage, no-tillage and successional ‘farming’ systems initiated in the spring of 1999 and assessed physical, chemical and biological soil properties. Soybean yields were also assessed at soil sampling in the fall of 2007. Culture-based methods were used to count the density of Burkholderia, Pythium and Fusarium species. DNA was also extracted from soils and analyzed for diversity of these same species – linking culture-based and molecular-based approaches to assessing microbial diversity of soils. DNA was also extracted and is currently being analyzed based on GeoChip Analysis using a novel comprehensive microarray design that has ~25,000 probes and covers ~47,000 sequences for 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation. The outcome of this data is forthcoming. We anticipate that we will be able to take the biological, physical and chemical parameters and advance the understanding of the complex inter-relationships of plant pathogens, soil microbes, disease incidence and soybean yield using tools that employ random matrix theory applications and other types of statistical tools. Although this work is more fundamental, the project generated applied talks at conferences to enable growers to think about the role of microbial communities in soil. Likewise, the project enabled us to engage scientists at the national and international level – particularly on the importance of microbial ecology in sustainable agricultural systems. For example, Dr. Louws attended a series of international microbial ecology meetings in Europe to present data from this work and interact with scientists about driving questions, methods and outcomes of microbial ecology research in sustainable farming systems.

Further analysis is forthcoming and will be added in the report. A few key points are highlighted above.

Project Objectives:

(1) to utilize micro-array technology to assess microbial diversity and structure as impacted by long-term farming systems structure with emphasis on microbial communities associated with nutrient cycling and disease suppression.

(2) To elucidate mechanisms of disease suppression in long term SARE organic and farming systems projects. Soils from the different farming systems will be sampled, analyzed, and manipulated to discover components that contribute to disease suppression (primarily plant pathogen invasion and colonization).

3) To develop functional plant assay(s) to assess plant disease suppressive mechanisms and plant growth promoting effects.

These three objectives seek to link knowledge about the soils, microbial communities, soil borne pathogen fitness, and plant response as impacted by long-term farming systems and management of “soil health”.


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  • Shuijin Hu
  • Paul Mueller


Participation Summary
Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.