Soybean and cotton spermosphere soil microbiome shows dominance of soil-borne copiotrophs

Abstract

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds, rich in microbial activity. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but is studied less compared to other plant habitats. Previous studies on spermosphere microbiology were primarily culture-based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in non-sterile soil and investigate factors contributing to changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space (3-10 mm soil around a seed) by constraining the soil sampled with an cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within six hours after seeds were sown. By 12 to 18 hours, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition and the proliferation of copiotroph soil bacteria in the phyla Proteobacteria and Firmicutes. Due to their long history of plant growth promotion, prokaryote OTUs in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable genera enriched in the cotton and soybean spermosphere. There was no consistent evidence that fungal communities changed like prokaryotes. However, fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting other taxa besides the copiotrophic may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs

“…The data files and scripts used for this analysis are available on GitHub ( https://github.com/Noel-Lab-Auburn/SpermosphereMicrobiome2022 ) ( 83 ). Raw sequence reads were deposited to the sequence read archive with BioProject number PRJNA925866 .…”

Endophytic bacterial communities of alpine Rosaceae plants are affected by the plant tissue, collection site and host plant and culturable psychrotolerant isolates contribute to plant freezing stress tolerance

“…Co-occurrence networks were constructed to characterize the relationship between core taxa and the whole community using the NetCoMi v1.1.0 package, as previously described (Olofintila & Noel, 2023; Peschel et al ., 2021), and hub ASVs were identified as those that are significantly more connected within the network than other ASVs on the basis of centrality measures (Banerjee et al ., 2018). To construct the correlation matrix, the SpiecEasi v1.1.2 tool (Kurtz et al ., 2015) was used on nonrarefied count data as SpiecEasi performs centered log-ratio normalisation internally.…”

T6SS-mediated competition byStenotrophomonas rhizophilashapes seed-borne bacterial communities and seed-to-seedling transmission dynamics

“…Like other habitats (i.e. rhizosphere and phyllosphere), the nature and quantities of exudates is an important driver of microbial community composition (10). This is perhaps even more striking within the spermosphere since the plant defense responses appear to be not induced during germination (11,12).…”

“…The former is based on the rapid and efficient use of resources, a strategy used by copiotroph (14). High relative abundance of copiotrophic bacterial taxa have been reported in seedlings (15,16) and spermospheres (10) of different plant species. These observations suggested that this life history strategy is important for seed to seedling transmission.…”