Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere
Meta-exoproteomics identifies active plant-microbe interactions operating in the rhizosphere
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DOI：
10.1101/2021.09.01.458574
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发表时间：
2021-09
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通讯作者：
I. Lidbury;S. Raguideau;Senlin Liu;Andrew R. J. Murphy;R. Stark;C. Borsetto;T. Fraser;Andrew Goodall;A. Bottrill;Alex Jones;G. Bending;Mark Tibbet;J. Hammond;C. Quince;D. Scanlan;J. Pandhal;E. Wellington
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作者：
I. Lidbury;S. Raguideau;Senlin Liu;Andrew R. J. Murphy;R. Stark;C. Borsetto;T. Fraser;Andrew Goodall;A. Bottrill;Alex Jones;G. Bending;Mark Tibbet;J. Hammond;C. Quince;D. Scanlan;J. Pandhal;E. Wellington
DNA测序技术的进步极大地改变了我们对植物微生物组的复杂性和结构及其在增强植物健康方面的作用的看法。相比之下，我们准确识别土壤微生物群代谢活性组分及其特定功能作用的能力相对有限。在这里，我们结合了我们最近开发的蛋白质提取方法和迭代生物信息学管道，以捕获和鉴定在芸苔属植物根际表达的胞外蛋白质（元外蛋白质组学）。首先，我们在实验室中通过成功鉴定与宿主植物（芜菁）和细菌接种物恶臭假单胞菌BIRD-1相关的蛋白质来验证我们的方法，揭示了后者表达了许多与植物源营养素获取相关的根际特异性蛋白质。接下来，我们分析了与甘蓝型油菜（油菜）相关的自然田间土壤微生物群落。通过将深度测序宏基因组学与元外蛋白质组学相结合，在散装和根际样品中总共鉴定了1882种蛋白质。重要的是，元外蛋白质组学鉴定了响应于B存在的土壤微生物群的代谢活性部分的明显变化（p<0.001）。在总微生物群落（宏基因组）的组成中不明显的油菜根。这种代谢转变与刺激根际专门的细菌，如γ-变形菌，β-变形菌和黄杆菌和上调植物有益功能有关的磷和氮矿化。通过提供第一个元蛋白质组水平评估的“活性”植物微生物组在现场规模，这项研究表明，过去的植物微生物组的基因组评估，以确定生态重要的植物：微生物相互作用驱动植物生长的重要性。
The advance of DNA sequencing technologies has drastically changed our perception of the complexity and structure of the plant microbiome and its role in augmenting plant health. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and their specific functional role is relatively limited. Here, we combined our recently developed protein extraction method and an iterative bioinformatics pipeline to enable the capture and identification of extracellular proteins (meta-exoproteomics) expressed in the rhizosphere of Brassica spp. First, we validated our method in the laboratory by successfully identifying proteins related to the host plant (Brassica rapa) and a bacterial inoculant, Pseudomonas putida BIRD-1, revealing the latter expressed numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients. Next, we analysed natural field-soil microbial communities associated with Brassica napus L (Oil Seed rape). By combining deep-sequencing metagenomics with meta-exoproteomics, a total of 1882 proteins were identified in bulk and rhizosphere samples. Importantly, meta-exoproteomics identified a clear shift (p<0.001) 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 metabolic shift was associated with the stimulation of rhizosphere-specialised bacteria, such as Gammaproteobacteria, Betaproteobacteria and Flavobacteriia and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralisation. By providing the first meta-proteomic level assessment of the ‘active’ plant microbiome at the field-scale, this study demonstrates the importance of moving past a genomic assessment of the plant microbiome in order to determine ecologically important plant: microbe interactions driving plant growth.