Table 1.
Sediment characteristics.
Fig 1.
Synthetic workflow for the LM DNA extraction method.
Concentrations in parentheses are final concentrations. CTAB: hexadecyltrimethylammonium bromide. PPS: Protein Precipitation Solution. SDS: Sodium dodecyl sulfate. Na Ac. 3 M: Sodium acetate 3 M pH 5.2.
Fig 2.
DNA extraction yield of LM, PSP and PM across sediments.
Yield expressed in µg of DNA extracted per gram of sediment (dry weight, dw). Statistical significance was assessed using a t-test. LM: Laboratory-made method. PSP: PowerSoil Pro. PM: PowerMax Soil. * p < 0.05. ** p < 0.01.
Fig 3.
Mean peak DNA size of LM, PSP and PM across sediments.
“+” indicates that one replicate was above size limit of 60,000 bp. “NA” indicates that the size analysis could not be performed due to insufficient DNA concentration. Statistical significance was assessed using a t-test. LM: Laboratory-made method. PSP: PowerSoil Pro. PM: PowerMax Soil. * p < 0.05. ** p < 0.01. *** p < 0.001.
Table 2.
PCR amplification results on 16S rRNA and 18S rRNA genes.
Fig 4.
Interindividual variability in community structure across sediments.
Phylogenetic distances between samples relates to interindividual variability in community composition. (A) Weighted UniFrac distances of prokaryotic taxa. (B) Unweighted UniFrac distances of eukaryotic taxa. Grey stars indicate significant differences between average within-method and between-method interindividual distances. Red stars indicate significant differences in average within-method interindividual distances across methods. Statistical significance was assessed using a t-test. LM: Laboratory-made method. PSP: PowerSoil Pro. PM: PowerMax Soil. * p < 0.05. ** p < 0.01. *** p < 0.001.
Fig 5.
Heat trees of enriched or depleted taxa by LM for prokaryotes and eukaryotes.
Median difference in proportion between Laboratory-made method (LM) and the other two methods (PowerSoil Pro and PowerMax Soil) of prokaryotic taxa (A) and eukaryotic taxa (B) at the genus level across all sediments. Selected ASVs by LEfSe (LDA > 2, p < 0.05) are either enriched (red) or depleted (blue) in LM. The eukaryotic data from sediment EstCS was unique to the LM method and therefore excluded from the LEfSe analysis.
Table 3.
Costs for each method based on reagents and tubes as of May 2025.