Data_Sheet_1_Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling.PDF

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.

土壤微生物，诸如细菌与古菌，在土壤营养元素的生物地球化学循环中扮演着至关重要的角色，因其既作为分解者，亦或为互利共生或拮抗共生体，从而影响植物的生长与健康。在本研究中，我们探究了瑞士森林中欧洲栎树和橡树物种在石灰岩基岩上土壤元基因组在垂直方向上的分布，深度达1.5米。我们旨在揭示树木属种与土壤深度对遗传库的影响，并深入理解微生物碳氮循环。在域水平上，分配给各类群的序列读数的相对丰度表明，在深层土壤中，古菌的丰度比细菌高出5至10倍，而细菌的丰度随土壤深度的变化未发生显著变化。在深层土壤中，碳水化合物活性酶基因的丰度显著增加，这些酶参与寡糖转移的催化作用，以及壳聚糖或纤维素等碳水化合物的结合。此外，参与氮化合物降解和合成、硝化与反硝化以及硝酸盐还原的氮循环基因（NCyc）在深层土壤中也表现出较高的丰度。因此，我们的研究结果指示，深层土壤中的氮转化受到土壤深度的显著影响，并且氮不仅用于同化作用，还用于能量保存，这表明深层土壤中氧气含量较低。通过使用枪式宏基因组学方法，我们的研究为土壤微生物及其功能遗传潜力提供了初步发现，以及这些潜力如何随土壤特性的变化而变化。因此，我们的数据为土壤“暗物质”提供了新颖且深入的见解。