Spatiotemporal Profiling of Seed-Associated Microbes of an Aquatic, Intermediate Recalcitrant Species, Zizania palustris L. and the Impact of Anti-Microbial Seed Treatments

Northern wild rice (NWR; Zizania palustris var. interior) (NWR) is an ecologically important, annual, aquatic species native to North America, that is also cultivated in irrigated paddies in Minnesota and California. NWR seeds are desiccation-sensitive and must be kept in hydrated conditions, in which viability can decline rapidly within the first two years of storage. During this period, microbial growth is rampant and the relationship between these communities and the viability of NWR seed is unclear. In this study, we cultured and identified bacteria and fungi found in 27 NWR seed stocks, collected over a five-year period from three locations and four NWR genotypes. Results revealed that microbial communities were heavily dependent on seed viability and communities began shifting after one year of seed storage. Fungi became more prominent as years in storage increased suggesting that fungi begin to outcompete bacteria. Spatial analysis of locations and genotypes revealed a core set of microbes found across locations and genotypes. Penicillium and Pseudomonas were ubiquitous in NWR hydrated seed storage. We also evaluated the efficacy of four antimicrobial treatments at reducing microbial growth in hydrated NWR seed storage. These treatments did not reduce or drastically change microbial growth or seed viability. However, previously undetected microbes were identified after treatments, which suggested a disruption to the major constituents of the microbiome. Overall, this study identified common microbial constituents found in an aquatic, recalcitrant species, adapted for a cold climate, during seed storage and provides a foundation for future studies to evaluate the effect of microbial communities on NWR seed viability during hydrated storage.