ISME | 土壤和种子相关细菌群落对幼苗微生物群里组装的影响

文献信息：

Walsh Corinne M.*, Becker-Uncapher Isadore, Carlson Madeline, Fierer Noah. Variable influences of soil and seed-associated bacterial communities on the assembly of seedling microbiomes[J]. The ISME Journal, 2021. DOI: 10.1038/s41396-021-00967-1

The ISME Journal最新影响因子：9.180

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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 cultivation-independent 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.

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Fig. 1 Experimental design. A Soil samples (n =219) were collected from across the continental United States. B Soil slurries were created from each soil by mixing 5 g soil with 10 mL PBS, and slowly centrifuging to remove particulates. C Eight seeds were inoculated with each soil slurry, and grown on sterilized germination paper in a growth chamber. D After 1 week, all eight seedlings from one plate were combined and destructively sampled. In panels B–D, the stars indicate soil, seed, and seedling samples were analyzed with 16S rRNA gene sequencing to determine microbial community composition. Created with BioRender.com.

Fig. 2 Community composition and richness of soil slurries, wheat seedlings, and wheat seeds. A, B NMDS ordination plots (first two of three dimensions) of bacterial community structure in soil slurries, soil slurry-treated seedlings (“treated plant”), PBS buffer control-treated seedlings (“control plant”), and seeds. Panel B includes the same samples as panel A with the soil slurry samples excluded. Panel A stress: 0.11; Panel B stress: 0.18. PERMANOVA R²= 0.09, p< 0.001; homogeneity of dispersions test, ANOVA p= 171, p< 0.001. C Bacterial richness per sample type calculated as number of distinct ASVs out of 1000 bacterial reads per sample. D The proportion of reads from “seed-associated” taxa (ASVs detected in >3 seed samples) across different sample types.

Fig. 3 Bacterial diversity in soil slurries, seedlings, and seeds. A A maximum-likelihood phylogenetic tree of the top 533 most abundant bacterial ASVs detected in this study. Colored bar height indicates prevalence (number of samples) in which each ASV was detected in seedlings (green), and soil slurries (blue); red bars indicate seed-associated taxa (ASVs detected in >3 seed samples). B Relative abundances of bacterial classes shown for seed, seedling, and soil samples. Bacterial classes that were detected in seedlings are highlighted in green shades, all other classes are colored gray. C Relative abundance of ASVs in the five plant-associating classes shown for seed, seedling, and soil samples.

Fig. 4 The relationship between the rank abundance of plantassociating bacterial taxa in soil slurry inocula and in seedlings across different levels of taxonomic resolution. A Common plantassociating orders, B families within the orders from panel A directly above, C genera within families from panel B directly above, D ASVs within genera from panel C directly above. Asterisks indicate Spearman correlation values significant at ***p< 0.001, **p< 0.01, *p<0.05.

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