Organic amendments to potato soils inconsistently enrich yield-associated soil microbiota across growing regions of the continental US

Plant health is regulated by complex consortia of soil microbes with growth-promoting and pathogenic functions. In potato production, various soil management practices are undertaken to boost yields and suppress diseases, but connections between these practices, soil microbiomes, and tuber yields have not been characterized across diverse growing regions. To identify growing practices and microbes associated with increased yields, we established four-year field trials across eight US sites from Oregon to Maine that consisted of controls, fumigations, organic amendments, and mustard incorporations. Amplicon sequencing of 16S ribosomal RNA (rRNA) genes and intergenic transcribed spacer (ITS) regions was used to investigate bacterial and eukaryotic soil microbiomes, respectively. Fumigation and organic amendment treatments increased tuber yields in 23% and 29% of treatments relative to controls. While soil treatments influenced both microbiome types differently across all field sites, eukaryotes were more sensitive than bacteria to all treatments. Across field sites, soil treatments impacted relative abundances of amplicon sequence variants (ASVs) to varying degrees, even among ASVs belonging to the same genus. Associations between ASVs and tuber yields similarly varied within genera, highlighting the lack of consistent yield-associated taxa across US growing regions. Nevertheless, forty-five "target ASVs" across nine bacterial and three fungal phyla were identified as both treatment-impacted and yield-associated within any particular field site. Models identified three of thirteen organic amendment scenarios and one of thirteen fumigation scenarios where increased relative abundances of specific target ASVs accounted for up to a 23% increase in tuber yields compared to control treatments. These ASVs were largely site-specific and not influenced by treatment-associated changes in soil nutrients or organic matter, highlighting complex relationships within field sites that require further study to achieve the goal of implementing sustainable, microbiome-informed potato production techniques.