8. Summary and outlook

Amplicon sequencing remains a valuable approach for investigating the structure of microbial communities in soils. However, careful considerations must be taken at each step – from sampling to analyses of Amplicon Sequencing Variants (ASVs) to avoid mis- or over-interpretation of the data. It is important to consider that amplicon sequencing is primarily a hypothesis-generation tool, which may require additional experimental support to unravel microbial community dynamics. Sequencing is highly descriptive in nature, allowing one to catalog the organisms present in a given environment/sample. However, the goal of microbial ecology is to link organisms to dynamic processes observed in the environment. This challenging work must therefore be undertaken in complement to sequence-focused studies. When conducted in combination with more quantitative approaches or the addition of other forms of data, as well as more rigorous normalization and statistical approaches, we as a field can improve the quality of our science and further our understanding of microbial communities in the immensely complex soil environment.