Catching change in microbial diversity indicators under different soil organic matter managements: Higher taxonomic resolution, better discrimination?

Recent advances in molecular ecology have dramatically improved our knowledge of soil microbial diversity and offers new indicators of soil quality. The usefulness of diversity indices has never been greater as the astronomical amounts of data generated in the literature needs to be synthesized. Despite technical guidelines have been proposed to characterize soil microbiomes using high throughput sequencing, the effect of taxonomic resolution on diversity indices is still largely unknown. Here, we explored how downscaling to higher taxonomic resolution levels may affect alpha-and beta-diversity indices of bacterial communities exposed to different soil organic matter management. To this aim, we collected soil samples in a long-term experimental site (Ultuna, Sweden) where different mineral and organic fertilizers have been applied for since 1956. We used both massive amplicon sequencing from phylum to species (OTU) and molecular fingerprints (PLFA, DGGE and T-RFLP). Our results showed that the discrimination potential increased at finer taxonomic resolution for beta-diversity but not for alpha-diversity indices such as richness and evenness. Also, the relative importance of hierarchical drivers of soil microbial communities such as C, N and pH varied depending on the taxonomic resolution. This study also demonstrated that indicators generated by molecular fingerprints such as PLFA, DGGE and T-RFLP are still consistent to monitor the effect of agricultural management on beta-diversity but not on alpha-diversity, which is useful information as it allows for a better use of results in past literature. We encourage performing such comparative studies on wider surveys, including different contexts and other indicators, in order to increase the efficiency and the robustness of the use of sequencing data in soil biodiversity monitoring.

Automated summary

Recent advances in molecular ecology have improved our understanding of soil microbial diversity and provided new indicators of soil quality. This study investigated the effect of taxonomic resolution on alpha- and beta-diversity indices of bacterial communities in response to different soil organic matter management. The results showed that higher taxonomic resolution increased the discrimination potential for beta-diversity but not for alpha-diversity indices. The relative importance of hierarchical drivers of soil microbial communities also varied depending on the taxonomic resolution. Molecular fingerprints were consistent indicators for monitoring the effect of agricultural management on beta-diversity but not on alpha-diversity. These findings contribute to the efficiency and robustness of using sequencing data in soil biodiversity monitoring.