Amplicon sequencing is and will remain a valuable approach for investigating the structure of microbial communities in soils. However, the complex nature of soils and high diversity of organisms therein necessitate careful considerations, from sampling strategies to statistical analyses, to avoid mis- or over-interpretation of the data. Amplicon sequencing as a standalone approach should primarily serve as a hypothesis-generation tool that is highly descriptive in nature, mainly allowing one to catalogue nucleic acids of organisms present in a given sample. As one key goal of soil microbial ecology is to link organisms to environmental processes, sequencing-based studies need to be complemented with other data types, in addition to appropriate normalization and statistical approaches. Understanding the nature of amplicon data and the role of sequencing as a valuable tool for soil scientists will further expand our understanding of microbial community diversity and structure in the immensely complex soil environment.
Declaration of competing interests
The authors declare no conflict of interest.
Acknowledgements
We thank Petra Pjevac for helpful comments on the manuscript. Figures 2 and 4 were created with the help of BioRender.com. RA was supported by the Czech Science Foundation (Junior Grant No. 19-24309Y) and MEYS (EF16_013/0001782 - SoWa Ecosystems Research). JS was supported by the Austrian Science Fund (FWF) DK+ program 'Microbial Nitrogen Cycling' (W1257-B20). JJ was supported by the Czech Science Foundation (21-07275S). LA, KS and CK have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 819446).
Supplementary Material