Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
Microbiome. 2024 May 24;12(1):95. doi: 10.1186/s40168-024-01812-1.
Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.
After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).
Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.
生物固氮是支撑地球上所有生命的基本过程。虽然通过大量的固氮酶基因 PCR 扩增子测序已经研究了固氮土壤微生物的分布和多样性，但由于缺乏事实上的扩增子调查标准协议和可能的 PCR 偏差，对其的全面了解受到了阻碍。在这里，我们充分利用土壤宏基因组的行星收集以及最近扩展的培养物收集，评估了陆地固氮微生物组的全球分布和多样性。
在对 1451 个土壤宏基因组样本进行广泛分析后，我们揭示了δ变形菌门中的 Anaeromyxobacteraceae 和 Geobacteraceae 是具有不同地理起源和土地利用类型的土壤中固氮微生物组的普遍存在的群体，特别是在厌氧土壤（稻田土壤和沉积物）中占有特殊优势。
我们的结果表明，δ变形菌是潜在土壤氮固定种群中的核心细菌分类群，特别是在厌氧环境中，这促使人们在理解陆地氮循环时仔细考虑δ变形菌的固氮生物。
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