Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation

IF 20.5 1区生物学 Q1 MICROBIOLOGY

Nature Microbiology Pub Date : 2025-03-26 DOI:10.1038/s41564-025-01973-1

Daniel Garrido-Sanz, Christoph Keel

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Abstract

Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.

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种传细菌通过生态位分配和促进作用驱动小麦根际微生物组组装

微生物群落在支持植物健康和生产力方面发挥着关键作用。可再生的，天然的植物相关微生物组可以帮助解开跨越时间和空间的微生物动力学。本研究采用序列繁殖策略，建立了一个复杂的可繁殖小麦根际微生物群（RhizCom），以研究微观环境下土壤与可遗传根际微生物群（SbRB）的演替动态和相互作用。利用16S rRNA测序和基因组解析霰弹枪宏基因组学，我们发现SbRB超越了原生土壤微生物，成为根际相关微生物组的主要来源。SbRB基因组富含宿主相关性状，包括关键糖的降解（生态位分配）和支持伴侣菌株的交叉取食相互作用（生态位促进）。体外共培养实验证实，辅助性SbRB菌株以双糖为唯一碳源，促进伴侣菌的生长。这些结果揭示了种子微生物群动态在微生物演替和群落组装中的重要性，这可以为作物微生物群的控制策略提供信息。

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来源期刊

Nature Microbiology Immunology and Microbiology-Microbiology

CiteScore

44.40

自引率

1.10%

发文量

226

期刊介绍： Nature Microbiology aims to cover a comprehensive range of topics related to microorganisms. This includes: Evolution: The journal is interested in exploring the evolutionary aspects of microorganisms. This may include research on their genetic diversity, adaptation, and speciation over time. Physiology and cell biology: Nature Microbiology seeks to understand the functions and characteristics of microorganisms at the cellular and physiological levels. This may involve studying their metabolism, growth patterns, and cellular processes. Interactions: The journal focuses on the interactions microorganisms have with each other, as well as their interactions with hosts or the environment. This encompasses investigations into microbial communities, symbiotic relationships, and microbial responses to different environments. Societal significance: Nature Microbiology recognizes the societal impact of microorganisms and welcomes studies that explore their practical applications. This may include research on microbial diseases, biotechnology, or environmental remediation. In summary, Nature Microbiology is interested in research related to the evolution, physiology and cell biology of microorganisms, their interactions, and their societal relevance.