Soil ammonia-oxidizing archaea (AOA) play a crucial role in converting ammonia to nitrite, thereby mobilizing reactive nitrogen species into their soluble form, with a significant impact on nitrogen losses from terrestrial soils. Yet, our knowledge regarding their diversity and functions remains limited. In this study, we reconstructed 97 high-quality AOA metagenome-assembled genomes (MAGs) from 180 soil samples collected in Central Germany during 2014–2019 summers. These MAGs were affiliated with the order Nitrososphaerales (NS) and clustered into four family-level clades (NS-α/γ/δ/ε). Among these MAGs, 75 belonged to the most abundant but least understood δ-clade. Within the δ-clade, the amoA genes in three MAGs from neutral soils showed a 99.5% similarity to the fosmid clone 54d9, which has served as representative of the δ-clade for the past two decades since even today no cultivated representatives are available. 72 MAGs constituted a distinct δ sub-clade, and their abundance and expression activity were more than twice that of other MAGs in slightly acidic soils. Unlike the less abundant clades (α, γ, and ε), the δ-MAGs possessed multiple highly expressed intracellular and extracellular carbohydrate-active enzymes responsible for carbohydrate binding (CBM32) and degradation (GH5), along with highly expressed genes involved in ammonia oxidation. Together, these results suggest metabolic versatility of uncultured soil AOA and a potential mixotrophic or chemolithoheterotrophic lifestyle among 54d9-like AOA.

中文翻译：

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亚硝化球菌相关进化枝的代谢潜力

土壤氨氧化古菌（AOA）在将氨转化为亚硝酸盐的过程中发挥着至关重要的作用，从而将活性氮物质转化为可溶形式，对陆地土壤的氮损失产生重大影响。然而，我们对它们的多样性和功能的了解仍然有限。在这项研究中，我们从 2014 年至 2019 年夏季在德国中部收集的 180 个土壤样本中重建了 97 个高质量 AOA 宏基因组组装基因组 (MAG)。这些 MAG 属于亚硝化球目 (NS)，并分为四个科级进化枝 (NS-α/γ/δ/ε)。在这些 MAG 中，75 个属于最丰富但了解最少的 δ 分支。在δ-进化枝中，来自中性土壤的三个MAG中的amoA基因与fosmid克隆54d9有99.5%的相似性，该克隆54d9在过去二十年中一直作为δ-进化枝的代表，因为即使在今天也没有栽培的代表。 72个MAGs构成了一个独特的δ亚支，其丰度和表达活性在微酸性土壤中是其他MAGs的两倍以上。与不太丰富的进化枝（α、γ和ε）不同，δ-MAG拥有多种高表达的细胞内和细胞外碳水化合物活性酶，负责碳水化合物结合（CBM32）和降解（GH5），以及与氨有关的高表达基因氧化。总之，这些结果表明未培养土壤 AOA 的代谢多功能性以及 54d9 样 AOA 中潜在的混合营养或化学异养生活方式。