Conserved beta diversity pattern in sorted cells population of microbial phototrophs and fungi in response to soil fertilization

Monitoring changes in community composition of environmental microbes is mainly achieve through molecular analysis of total soil DNA only, thus mixing up intra- and extra-cellular DNA, while ignoring all cellular properties of soil microbes. In this study, we compared high-throughput sequencing of microbial phototrophs and fungi from mineral and organic (farmyard manure) fertilized soils, which were (i) directly extracted from soil and (ii) extracted after a cell density centrifugation step followed by a cell sorting procedure. Flow cytometry cell sorting was found to reduce the OTU richness and Shannon diversity in both fertilization treatments as compared to sequencing from soil DNA extracts. However, a similar and significant effect of fertilization on community composition was observed in both the soil and the sorted cells fractions. Cyanobacteria and sordariomycetes were the dominant groups for both soils in their respective dataset but were significantly more abundant in the organic fertilized soil. Although some discrepancies were observed, we found that the effect of fertilization on phototrophs and fungi community composition could be similarly well described with the sorted cell and soil derived libraries. The presented workflow allows the monitoring of phototrophic and fungal taxonomic variation even at the genus level for the most abundant genera, but also opens avenues for further single cell genomic analysis of uncultivated soil micro-eukaryotes.