Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions.
Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions.
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DOI：
10.1128/msystems.00025-22
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发表时间：
2022-08-30
期刊：
影响因子：
6.4
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中科院分区：
文献类型：
--
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DNA 测序技术的进步极大地改变了我们对植物微生物组结构和复杂性的看法。相比之下，我们准确识别土壤微生物群的代谢活性部分及其在增强植物健康方面的特定功能作用的能力相对有限。通过分析细胞外蛋白质部分可以研究微生物进行的重要生态相互作用。在这里，我们结合了独特的蛋白质提取方法和迭代生物信息学流程来捕获和鉴定在芸苔属植物根际合成的细胞外蛋白质（宏外蛋白质组学）。我们首先在实验室验证了我们的方法，成功鉴定了与宿主植物（白菜）及其细菌接种物恶臭假单胞菌 BIRD-1 相关的蛋白质。这鉴定出了恶臭假单胞菌中与获取植物源性营养物质相关的许多根际特异性蛋白质。接下来，我们分析了与甘蓝型油菜（Brassica napus L.）（油菜）相关的自然田间土壤微生物群落。通过将宏基因组学与宏外蛋白质组学相结合，在大量样品和根际样品中鉴定出了 1,885 种植物、昆虫和微生物蛋白质。元外蛋白质组学发现，土壤微生物群的代谢活性部分因甘蓝型油菜根的存在而发生显着变化，而这在整个微生物群落（宏基因组）的组成中并不明显。这包括刺激根际特化细菌，例如γ-变形菌、β-变形菌和黄杆菌，以及上调与磷和氮矿化相关的植物有益功能。我们对田间规模“活跃”植物微生物组的宏蛋白质组学评估表明，超越宏基因组学来确定支撑植物健康的生态上重要的植物-微生物相互作用的重要性。重要性 植物与微生物的相互作用对于生态系统功能和作物生产至关重要。尽管在了解植物微生物组的结构方面已经取得了重大进展，但对其完整功能作用的了解仍处于起步阶段。这主要是由于无法完全确定在田间条件下活跃运行的原位植物-微生物相互作用。蛋白质是细胞的功能实体。因此，微生物群落内的鉴定和相对定量为哪些微生物代谢最活跃以及哪些微生物正在驱动重要的植物-微生物相互作用提供了最佳代理。在这里，我们使用田间种植的油菜作为模型作物物种，对植物微生物组进行了首次宏外蛋白质组学评估，确定了负责特定生态相互作用的关键类群。对植物微生物组的机械理解对于开发工程植物微生物组以改善可持续农业方法并减少我们对不可再生资源的依赖至关重要。
Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.
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影响因子：
28.3
作者：
Christie-Oleza JA;Sousoni D;Lloyd M;Armengaud J;Scanlan DJ
通讯作者：
Scanlan DJ
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48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
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影响因子：
15.5
作者：
Heyer, R.;Schallert, K.;Reichl, U.
通讯作者：
Reichl, U.
影响因子：
4.8
作者：
Fierer, Noah;Bradford, Mark A.;Jackson, Robert B.
通讯作者：
Jackson, Robert B.
影响因子：
6.7
作者：
Cordell, Dana;White, Stuart
通讯作者：
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