Omics from source to sink: microbiome of a stream irrigation system and its potential impact

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Food-borne illnesses associated with consumption of contaminated fresh produce are widely reported in the United States. Despite the recognized importance of irrigation water, a substantial unexplored gap exists in the knowledge of microbial communities present in irrigation systems and their potential roles in pathogen transmission and infection. This proposal addresses the critical need to determine potential microbial risk factors for environmental and human health. Technical advances developed in this project will contribute to the NIH-COBRE mission to use ‘omics’ approaches to define relationships between human health and microbiomes in irrigation water. Soft rot pectinolytic bacterial plant pathogens (SRP) macerate plant tissues of vegetable crops thereby producing a niche for human enteric pathogens and enabling the latter to colonize fresh produce. Our aims are: (I) To determine the composition and structure of the microbiomes of stream irrigation systems and (II) To determine the role of microbes in irrigation water in establishing niches for food-borne pathogens. Application of new technologies will permit more precise identification of microbial communities and results of this study will elucidate the interactions between SRP and enteric pathogens when co-infecting a plant host. The proposed research is creative and original in its genomic approach and provides a sound model for studying associations of enteric pathogens with edible crops grown in many other locations. Knowledge generated by this research will contribute not only to understanding the general ecology of microbial communities, but more specifically to dynamics of food-borne human pathogens and their interactions with plant pathogens. Our projected results are expected to have important positive impacts on environmental policy by providing robust evidence defining the microbial interactions between plant and human pathogens in fresh produce as well as survival and/or growth of pathogens on fresh produce following application of contaminated water.