Soil is an extremely complex and dynamic matrix, in part, due to the wide diversity of organisms living within it. Soil organic matter (SOM) is the fundamental substrate on which the delivery of ecosystem services depends, providing the metabolic fuel to drive soil function. As such, studying the soil metabolome (the diversity and concentration of low molecular weight metabolites), as a subset of SOM, holds the potential to greatly expand our understanding of the behaviour, fate, interaction and functional significance of small organic molecules in soil. Encompassing a wide range of chemical classes (including amino acids, peptides, lipids and carbohydrates) and a large number of individual molecules (ca. = 10 to 10), the metabolome is a resultant (indirect) output of several layers of a biological hierarchy, namely the metagenome, metatranscriptome and metaproteome. As such, it may also provide support and validation for these “multi-omics” datasets. We present a case for the increased use of untargeted metabolomics in soil biochemistry, particularly for furthering our fundamental understanding of the functions driving SOM composition and biogeochemical cycling. Further, we discuss the scale of the challenge in terms of metabolite extraction, analysis and interpretation in complex plant-soil-microbial systems. Lastly, we highlight key knowledge gaps which currently limit our use of metabolomic approaches to better understand soil processes, including: (i) interpretation of large untargeted metabolomic datasets; (ii) the source, emission and fate of soil-derived volatile organic compounds (VOCs), (iii) assessing temporal fluxes of metabolites, and (iv) monitoring ecological interactions in the rhizosphere. While the application of metabolomics in ecosystem science is still in its relative infancy, its importance in understanding the biochemical system in relation to regulation, management and underpinning the delivery of ecosystem services is key to further elucidating the complex links between organisms, as well as the fundamental ability of the biological community to process and cycle key nutrients.

中文翻译：

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土壤代谢组学——当前挑战和未来前景

土壤是一个极其复杂和动态的基质，部分原因在于土壤中生活着多种多样的生物。土壤有机质（SOM）是生态系统服务提供所依赖的基本基质，为驱动土壤功能提供代谢燃料。因此，研究土壤代谢组（低分子量代谢物的多样性和浓度）作为 SOM 的一个子集，有可能极大地扩展我们对土壤中有机小分子的行为、命运、相互作用和功能意义的理解。代谢组包含广泛的化学类别（包括氨基酸、肽、脂质和碳水化合物）和大量单个分子（大约 10 到 10），是生物层次结构的多个层的合成（间接）输出，即宏基因组、宏转录组和宏蛋白质组。因此，它还可以为这些“多组学”数据集提供支持和验证。我们提出了在土壤生物化学中增加使用非靶向代谢组学的案例，特别是为了进一步加深我们对驱动 SOM 组成和生物地球化学循环的功能的基本理解。此外，我们讨论了复杂植物-土壤-微生物系统中代谢物提取、分析和解释方面的挑战规模。最后，我们强调目前限制我们使用代谢组学方法来更好地了解土壤过程的关键知识差距，包括：（i）大型非目标代谢组数据集的解释； (ii) 土壤来源的挥发性有机化合物 (VOC) 的来源、排放和归宿，(iii) 评估代谢物的时间通量，以及 (iv) 监测根际生态相互作用。虽然代谢组学在生态系统科学中的应用仍处于相对起步阶段，但其在理解与调节、管理和支持生态系统服务提供有关的生化系统方面的重要性是进一步阐明生物体之间复杂联系的关键，以及生物群落处理和循环关键营养物质的基本能力。