Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.
USDA-ARS Sunflower Improvement Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, USA.
Appl Environ Microbiol. 2024 Nov 20;90(11):e0163524. doi: 10.1128/aem.01635-24. Epub 2024 Oct 24.
Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower () at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.
土壤微生物的关联对植物的整体健康和功能至关重要。虽然已经做了很多工作来了解根际微生物组结构和功能的驱动因素，但地理、气候、土壤特性和植物遗传的相对重要性仍不清楚，因为结果参差不齐，而且在许多地点和基因型上进行的综合研究也很有限。根际微生物组对于作物抵抗病原体、耐受胁迫、养分可用性以及最终产量至关重要。在这里，我们使用美国大平原 15 个地点的 10 个栽培向日葵基因型的根际土壤的 16S 和 ITS 基因测序，量化了植物基因型、环境及其相互作用在塑造土壤根际群落中的相对作用。虽然就影响古菌、细菌和真菌丰富度、群落组成和分类群相对丰度而言，地点总体上总体上超过基因型，但也存在显著的相互作用，使得基因型在某些地点对古菌、细菌和真菌微生物组产生了显著影响。地点的影响归因于空间距离和气候及土壤特性的差异的组合。以前与真菌坏死病原体抗性相关的微生物分类群存在于大多数地点，但在不同地点的相对丰度上存在显著差异。我们的研究结果对不同地理区域的农业改良中的植物育种和农业微生物组操作具有重要意义。
