Towards a more concise understanding of different environmental DNA states in soils: Common challenges and future perspectives

Answering questions regarding soil microbial abundance and diversity is commonly associated with the extraction and analysis of the total environmental DNA (eDNA). However, eDNA is composed of both intracellular DNA (iDNA) and extracellular DNA (exDNA), revealing even more profound insights into microbial assemblages. Although the potential to improve the temporal or spatial resolution of eDNA-based studies is widely acknowledged, the separation and differential analysis of both eDNA states across various soils has revealed quite contrasting results so far. In this review, we therefore address these deviations and discuss common pitfalls and concomitant implications for the occurrence and ecological relevance of the different eDNA states in soils. While the turnover rates and hence the presence of both exDNA and iDNA are shaped by physicochemical and microbiological soil properties, the methodological separation and downstream processing of the different eDNA states determines whether these patterns are reflected properly. Thus, the induction of cross-contaminations or the over−/underrepresentation of certain taxonomic groups can severely obscure the obtained results. Importantly, we also propose future perspectives on how these aspects could be addressed to achieve more profound insights into the potential and limitations related to the separation and differential analysis of exDNA and iDNA in soils. • Extra- and intracellular DNA can reveal distinct microbial community patterns. • The dynamics of environmental DNA states are determined by soil properties. • In state-specific extraction of environmental DNA, cross-contamination can occur. • PCR-induced biases can inflate microbial abundance and diversity.