Impact of manure-derived fertilizers on bacterial community and antibiotic resistance genes in Washington red raspberry fields

Washington State is the number one producer of processed red raspberries in the nation. Raspberry growers in Whatcom County rely on dairy manure as a ready source to improve soil health prior to planting. Soil is a dynamic entity harboring billions of microorganisms and plays a crucial role in plant production. The microbial quality of soil is also directly associated with food safety, which is impacted by fertilizer practices. Antibiotic resistant bacteria and antibiotic resistance genes (ARGs) have emerged as important contaminants in soil and produce, posing a serious human health risk. Unfortunately, manure fertilizer application could directly or indirectly alter bacterial community structure by enriching antibiotic resistant bacteria and increasing the risk of spread of ARGs among soil bacteria. However, up to now, knowledge about impacts of manure application on soil microbial ecology and the abundance of ARGs of raspberry fields or other production system is very limited, which leaves a critical knowledge gap.  The objective of this study is to comprehensively investigate the impacts of manure-derived fertilizers use on soil bacterial ecology and ARGs abundance using soil samples from the Raspberry beds.  The abundance of soil bacterial community and the major categories of ARGs will be analyzed using Illumina MiSeq sequencing and quantitative PCR amplification, respectively.  This study will provide information about soil microbial ecology and ARGs profiles related to manure fertilizer application, which will provide critical preliminary data for future federal grant applications to systemically access manure fertilizer applications on microbiological safety, soil microbial ecology and ARGs profiles of red raspberry and other produces.