Table 1.
All the lysing tubes used in the experiments.
Fig 1.
Results based on Qubit quantification after DNA extraction expressed as ng/μl.
(A) Comparison of three commercial products with and without G2. (B) Comparison of three different bead sizes and the two tube types, without added G2. Values shown are averages of n = 3 independent measurements on n = 5 biological replicates. Error bars are calculated from the standard deviation for each series. There was a statistical significance (Scheffe’s score > 27.612) for the three comparisons with and without G2 in test A, while for test B, it occurred in the comparisons between mixed vs. 1.4 mm beads and mixed vs. 0.1 mm beads, but not between 1.4 mm vs. 0.1 mm beads or between the two tube suppliers (S2 Table).
Fig 2.
16S rRNA gene copy number variation after qPCR expressed as genes/μl.
A comparison between three commercial products with and without G2. Values shown are averages of n = 3 technical replicates for n = 3 biological replicates for each series. Error bars are calculated from the standard deviation for each series. (*) Significantly relevant comparison (Scheffe’s score > 26.117). (**) Not statistically relevant (Scheffe’s score < 26.117) (S5 Table).
Fig 3.
Visualisation of the average score of the Scheffe’s test.
Visualisation of the average score of the Scheffe’s test of categories a, b and e, according to S5 Table, visualising the impact of G2 compared with the effect of plastics and beads. The values on which this visualisation is based are reported in S6 Table.
Fig 4.
Alpha diversity analyses on G2 and bead impact on richness and evenness.
(a) Boxplot based on the Faith-pd index and comparing all the samples with G2 (n = 7) and without G2 (n = 9). (b) Boxplot based on the Pielou-S score for evenness between samples obtained with G2 (n = 7) and without G2 (n = 9). (c) Boxplot based on the Faith-pd index and comparing all the samples with 0.1 mm (n = 5), 1.4 mm (n = 5) and mixed (n = 6) beads. (d) Boxplot based on the Pielou-S score for evenness on samples obtained with 0.1 mm (n = 5), 1.4 mm (n = 5) and mixed (n = 6) beads.
Fig 5.
PCoA plots obtained from the UniFrac distance matrix of the sequenced samples from the different tube preparations.
(A) Comparison of data obtained from samples with G2 (blue dots) and without G2 (red dots). (B) Comparison of data obtained from samples using 0.1 mm beads (green dots), 1.4 mm beads (blue dots) and mixed beads (red dots).
Table 2.
Results of the PERMANOVA analyses.
Fig 6.
Heatmap at phylum level of the sequencing dataset.
The logarithmic scale in which colour intensity determines the abundance of the taxa can be seen in the bottom right-hand corner. The top heatmap represents the samples grouped by presence/absence of G2, the middle one refers to the different bead sizes used, while the bottom one is related to the two different tube suppliers. The names of the samples are given on the right, while the names of the phylum are stated below. On the left the dendrogram of similarity between all the samples is presented.