Table 1.
Commonly used and commercially available kits for DNA extraction from soil.
Extraction kits in bold were compared. High-throughput equipment refers to available automated solutions for the high-throughput solution.
Fig 1.
Top: Experimental design. Five different soil types were used to benchmark three different HT DNA extraction methods. DNA extractions were evaluated by DNA quality, quantity, length, and observed community profile. The I.DOT One was subsequently used to miniaturize metagenomes and amplicons. Bottom: Hands-on time, total time, and cost associated with each step from DNA extraction to prepared metagenome or amplicon libraries. The time reflects the processing time of a full 96-well plate, whereas costs are calculated per sample. For both sequencing strategies, two 96-well plates can be processed concurrently with only a minor increase in total time.
Fig 2.
Community characteristics for DNA extraction kits.
(A) Heatmap of community profile at phylum level across DNA extraction kits faceted by soil type. (B) PCA on Hellinger transformed relative abundance. (C) PCA on Hellinger transformed relative abundance for the Clay samples only. For all plots: ASVs not exceeding 0.1% relative abundance in at least one sample were filtered out.
Fig 3.
Comparison of community characteristics between standard and miniaturized amplicons.
(A) Heatmap of community profile at the genus level across reaction volume faceted by soil type. (B) Differential relative abundance plot of ASVs. (C) Hellinger transformed relative abundance, PCA. ASVs not exceeding 0.1% relative abundance in at least one sample were filtered out.
Fig 4.
(A) Heatmap of community profile at the genus level across reaction volume faceted by soil type. (B) Differential abundance plot of all genera (C) Hellinger transformed relative abundance, PCA. Genera which did not exceed 0.1% relative abundance in at least one sample were filtered out.