Implications of Seed Vault Storage Strategies for Conservation of Seed Bacterial Microbiomes

Abstract

Global seed vaults are important, as they conserve plant genetic resources for future breeding to improve crop yield and quality and to overcome biotic and abiotic stresses. However, little is known about the impact of standard storage procedures, such as seed drying and cold storage on the seed bacterial community, and the ability to recover seed-associated bacteria after storage. In this study, soybean [Glycine max (L.) Merr.] seeds were analyzed to characterize changes in the bacterial community composition and culturability under varying storage conditions. The G. max bacterial microbiome was analyzed from undried seed, dried seed, and seed stored for 0, 3, 6, and 14months. Storage temperatures consisted of −20°C, 4°C, and room temperature (RT), with −20°C being commonly used in seed storage vaults globally. The seed microbiome of G. max was dominated by Gammaproteobacteria under all conditions. Undried seed was dominated by Pantoea (33.9%) and Pseudomonas (51.1%); however, following drying, the abundance of Pseudomonas declined significantly (0.9%), Pantoea increased significantly (73.6%), and four genera previously identified including Pajaroellobacter, Nesterenkonia, env.OPS_17, and Acidibacter were undetectable. Subsequent storage at RT, 4, or −20°C maintained high-abundance Genera at the majority of time points, although RT caused greater fluctuations in abundances. For many of the low-abundance Genera, storage at −20°C resulted in their gradual disappearance, whereas storage at 4°C or RT resulted in their more rapid disappearance. The changes in seed bacterial composition were reflected by cultured bacterial taxa obtained from the stored G. max seed. The main taxa were largely culturable and had similar relative abundance, while many, but not all, of the low-abundance taxa were also culturable. Overall, these results indicate that the initial seed drying affects the seed bacterial composition, suggesting that microbial isolation prior to seed drying is recommended to conserve these microbes. The standard seed storage condition of −20°C is most suitable for conservation of the bacterial seed microbiome, as this storage temperature slows down the loss of seed bacterial diversity over longer time periods, particularly low-abundance taxa.

Australian native Glycine clandestina seed microbiota hosts a more diverse bacterial community than the domesticated soybean Glycine max

“…In general, the Glycine seed microbiota was occupied by Gammaproteobacteria, Alphaproteobacteria, Bacilli, Bacteroidia and Actinobacteria, which is consistent with previous studies concerning domesticated soybean seeds (Glycine max) [59], ryegrass (Lolium perenne) [60], red sage (Salvia miltiorrhiza) [61], rice (Oryza sp.) [7,62], bean (Phaseolus vulgaris) [63] and Brassicaceae family plants [64], suggesting a commonality between seed microbial communities of Glycine and numerous other plants species (Fig.…”

The Effects of Grass Silage Additive Type and Barley Grain Preservation Method on Rumen Function, Microbial Ecology, and Energy Metabolism of Dairy Cows

“…Barley grain preservation method affected barley associated microbiota. The bacterial composition of fresh crimped barley in our previous study [9] was dominated by Proteobacteria (77%), Actinobacteriota (10%), Firmicutes (9%), and Bacteroidota (3%), which are phyla commonly detected in various seeds [35,36]. The bacterial composition of dried barley in this study resembled the composition of fresh barley and was dominated by Proteobacteria, especially members from Pantoea and Pseudomonas genera.…”

“…Drying of seeds has been demonstrated to alter the seed bacterial abundances. For example, a significant decrease in abundance of Pseudomonas, Sphingomonas, Massilia, or Curtobacterium, and a significant increase in Pantoea was observed in soybean seeds after drying [35]. Pseudomonas is a common epiphyte of wheat [37] and barley [38] seeds and together with Pantoea have demonstrated plant growth promotion or plant resistance characteristics [39].…”

Temporal Dynamics of Endogenous Bacterial Composition in Rice Seeds During Maturation and Storage, and Spatial Dynamics of the Bacteria During Seedling Growth

“…The number of endophytic bacteria gradually decreased with different fates at different storage temperatures. Although Chandel et al (2021) reported the effect of storage temperature on seed microbiomes of soybean, to the best of our knowledge, this is the first study to track the dynamics of bacterial populations during rice seed storage. All bacterial genera that were dominant during the maturation of rice seeds were abundantly recovered in the seed remains after germination.…”

“…The changes in water, oxygen, and nutrient content of the stored seeds might also influence the residing endophytes. In recent reports, the bacterial communities in soybean seeds were altered by storage temperatures, and the genera with low abundance rapidly disappeared from seeds stored at room temperature and 4 • C compared to seeds stored at −20 • C (Chandel et al, 2021). In this study, the decrease in culturable bacteria at 6 mas was significantly higher when the rice seeds were stored at 15 • C than when stored at 4 • C. This might be due to the changes in water and nutrient conditions in the seeds as storage time increased.…”