Global soil metagenomics reveals ubiquitous yet previously-hidden predominance of Deltaproteobacteria in nitrogen-fixing microbiome
Global soil metagenomics reveals ubiquitous yet previously-hidden predominance of Deltaproteobacteria in nitrogen-fixing microbiome
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DOI：
10.1101/2022.12.09.519847
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发表时间：
2022-12
期刊：
影响因子：
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通讯作者：
Yoko Masuda;Kazumori Mise;Zhenxing Xu;Zhengcheng Zhang;Y. Shiratori;K. Senoo;Hideomi Itoh
中科院分区：
文献类型：
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作者：
Yoko Masuda;Kazumori Mise;Zhenxing Xu;Zhengcheng Zhang;Y. Shiratori;K. Senoo;Hideomi Itoh
生物固氮是维持地球上所有生命生存的基本过程。在土壤中，α蛋白细菌、β蛋白细菌和蓝藻传统上被认为是主要的固氮种群。这一常规知识是通过对固氮酶基因进行大量的PCR扩增调查而积累起来的。然而，这种流行的观点似乎与最近不含聚合酶链式反应的荟萃组学研究结果不一致。在这里，我们展示了陆地重氮营养微生物群的全球分布和多样性，通过充分利用土壤元基因组的行星集合以及最近扩大的培养集合进行了更新。通过对1,445个土壤后基因组样本的广泛分析，我们证明了三角洲蛋白细菌中先前被低估的厌氧粘细菌科和地细菌科是土壤中普遍存在的优势类群，它们横跨广泛的环境，具有不同的地理来源和土地利用类型，包括好氧的(农田、草地)和厌氧的(水稻土、沉积物)。我们的结果描绘了一个修改后的土壤固氮方案，它包括传统的重氮菌和迄今为止被低估的三角洲蛋白细菌。
Biological nitrogen fixation is a fundamental process sustaining all life on earth. In the soil, Alphaproteobacteria, Betaproteobacteria, and Cyanobacteria are traditionally considered the major groups of nitrogen fixation population. This conventional knowledge has been accumulated by numerous PCR amplicon surveys for nitrogenase genes. However, this prevalent view appears to be inconsistent with results of recent PCR-free meta-omics investigations. Here, we show the global distribution and diversity of terrestrial diazotrophic microbiome, updated by fully leveraging the planetary collections of soil metagenomes along with recently expanded culture collections. After extensive analysis of 1,445 soil metagenomic samples, we proved that the previously-undervalued Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous and predominant groups of diazotrophic microbiome in the soils, spanning a broad spectrum of environments, with different geographic origins and land usage types, including aerobic (croplands, grasslands) and anaerobic ones (paddy soils, sediments). Our results delineate a revised scheme of soil nitrogen fixation, which is inclusive of both conventional diazotrophs and the so far undervalued Deltaproteobacteria.