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A critical perspective on interpreting amplicon sequencing data in soil ecological research
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  • Lauren V. Alteio,
  • Joana Séneca,
  • Alberto Canarini,
  • Roey Angel,
  • Ksenia Guseva,
  • Jan Jansa,
  • Christina Kaiser,
  • Andreas Richter,
  • Hannes Schmidt
Lauren V. Alteio
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Joana Séneca
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Alberto Canarini
Centre for Microbiology and Environmental Systems Science, University of Vienna, Austria
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Roey Angel
Soil and Water Research Infrastructure and Institute of Soil Biology, Biology Centre CAS, České Budějovice, Czechia
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Ksenia Guseva
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Jan Jansa
Institute of Microbiology, Czech Academy of Sciences, Praha, Czechia
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Christina Kaiser
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Andreas Richter
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Hannes Schmidt
Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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Abstract

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 studies in soil 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.