Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes

Abstract

Plants grown in distinct soils typically harbor distinct microbial communities, but the degree of the soil microbiome influence on plant microbiome assembly remains largely undetermined. We also know that the microbes associated with seeds can contribute to the plant microbiome, but the magnitude of this contribution is likely variable. We quantified the influence of soil and seed microbiomes on the bacterial community composition of seedlings by independently inoculating seeds from a single cultivar of wheat (Triticum aestivum) with 219 unique soil slurries while holding other environmental factors constant, determining the composition of the seed, soil, and seedling bacterial communities via cultivationindependent methods. Soil bacterial communities exert a strong, but variable, influence on seedling bacterial community structure, with the extent of the soil bacterial contribution dependent on the soil in question. By testing a wide range of soils, we were able to show that the specific composition of the seedling microbiome is predictable from knowing which bacterial taxa are found in soil. Although the most ubiquitous taxa associated with the seedlings were seed derived, the contributions of the seed microbiome to the seedling microbiome were variable and dependent on soil bacterial community composition. Together this work improves our predictive understanding of how the plant microbiome assembles and how the seedling microbiome could be directly or indirectly manipulated to improve plant health.

Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

“…On the contrary, our results show that seeds of all plants tested are able to transmit microbes to their roots (a core set of seed-transmitted Proteobacteria, Fusarium, and Pseudozyma), and in most cases, these microbes go on to dominate the endosphere despite being grown in microbe-rich soil. Other publications corroborate the importance of vertical transmission in establishing root microbiomes: we have shown twice before that seed-derived bacteria are the dominant members of juvenile maize root microbiomes (Johnston-Monje et al, 2014, 2016, with similar observations having been made in wheat (Walsh et al, 2021), rice (Hardoim et al, 2012), Arabidopsis (Truyens et al, 2016), common bean (López-López et al, 2010, barley (Yang et al, 2017;Rahman et al, 2018), sunflower (Leff et al, 2017), and diverse crops (Barret et al, 2015). It has also been noted that these seed-transmitted microbiomes may change in abundance over time, first increasing during germination (Barret et al, 2015) and later being displaced by soil-derived microbes as plants age (Yang et al, 2017).…”

Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities

“…The seed-associated bacterial communities are generally simpler in terms of composition and diversity than communities from soils, seedlings and adult plant tissues ( Chesneau et al, 2020 ; Rochefort et al, 2021 ; Walsh et al, 2021 ). Bacteria within phylum Proteobacteria, including members from Pantoea spp.…”

Seed microbiota revealed by a large-scale meta-analysis including 50 plant species

“…These taxa are also adapted to the seed habitat but generally harbor lower abundances and prevalence. This fraction should not be neglected as it represents an important diversity reservoir that can be transmitted to seedlings 57,58 and provide microbial taxa that are adapted to specific local constraints 8,53 . This meta-analysis provides new insights on seed microbiota diversity and composition but also highlights key knowledge gaps.…”