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Dissecting the blueberry soil microbiome to assess soil health

J. J. Polashock, P. V. Oudemans
Acta horticulturae 2017 v. no.1180 pp. 405-408
DNA, DNA libraries, Nematoda, Vaccinium, bacteria, barcoding, blueberries, cover crops, databases, fungi, high-throughput nucleotide sequencing, internal transcribed spacers, microbiome, quality control, remediation, rhizosphere, soil quality, soil types
The plant rhizosphere is made up of not only soil, but a myriad of living organisms; these living organisms can both contribute to, and be indicators of, soil health. We explored the possibility of assaying the soil microbiome in areas where blueberry fields are declining, as compared to healthy fields in an effort to extract clues as to what might be causing the decline. To assay the microbiome, soil samples were collected from representative fields and total DNA was extracted. The DNA was amplified using 16S primers for bacteria and ITS primers for fungi. Primers were also designed and tested for nematodes. The resulting amplicons were purified and used to prepare DNA libraries by following the Illumina TruSeq DNA library preparation protocol. Sequencing was performed on a MiSeq next-generation sequencing platform. Sequences were joined and depleted of barcodes. Sequences that failed quality control parameters were deleted. Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity). Final OTUs were taxonomically classified using BLASTn against a curated database derived from GreenGenes, RDPII and NCBI. These data were compared to see if there are biological 'signatures' associated with poor soils. Our preliminary data showed that no single organism or groups of organisms were found associated with a particular soil type (bad vs. good). Thus, it is likely the causal agent(s) vary by location. The ultimate goal is to use these data to develop plans for remediation using, for example, cover crops.