Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation, and availability to improve the rigor of future studies.

通过标记基因扩增子测序进行微生物群落分析已成为土壤研究领域的常规方法。从这个角度来看，我们讨论了扩增子测序的技术挑战和局限性，并提出了有助于解决土壤时空复杂性和其中生物高度多样性的统计和实验方法。我们说明了组成对相对丰度数据解释的影响，并讨论了样本复制对土壤群落分析统计功效的影响。此外，我们认为需要提高研究的可重复性和数据可用性，以及补充技术，以产生对微生物作用的更深入的生态洞察以及我们在土壤生态系统中的理解。在这个阶段，