Table 1.
Number of high quality reads and OTUs0.03 identified for each of the samples (quadrants) studied.
Figure 1.
Distribution of phyla in Zodletone spring source sediment for the 4 quadrants studied.
Percentage abundance is shown on the Y-axis for (A) abundant phyla with >1% abundance in each quadrant studied, (B) phyla with % abundance ranging between 0.1 and 1% in quadrant 1, (C) phyla with % abundance ranging between 0.01 and 0.1% in quadrant 1, and (D) phyla with % abundance <0.01% in quadrant 1. Color-coding is as follows: quadrant 1 (blue), quadrant 2 (red), quadrant 3 (green), and quadrant 4 (purple).
Table 2.
Qualitative and quantitative similarity indices at the species level for the rare and abundant members of the community (defined at specific empirical cutoffs) as well as for the totals at both the phylum and the species levels.
Figure 2.
Venn diagrams showing the number of unique and shared OTUs between the 4 quadrants studied for (A) empirical cutoff (n = 1) for defining rare species, (B) empirical cutoff (n≤2) for defining rare species, (C) empirical cutoff (n≤5) for defining rare species, (D) empirical cutoff (n≤10) for defining rare species, (E) empirical cutoff (n>10) for defining abundant species, (F) empirical cutoff (% abundance ≤0.004%) for defining rare species, (G) empirical cutoff (% abundance >1%) for defining abundant species, and (H) the entire datasets.
Color-coding is as follows: quadrant 1 (yellow), quadrant 2 (red), quadrant 3 (green), and quadrant 4 (blue).
Figure 3.
Non-metric multidimensional scaling plots of the 4 quadrants studied.
Pair wise Bray-Curtis similarity indices for each of the quadrants at 4 empirical rare cutoffs (n = 1 (N1), n≤2 (N2), n≤5 (N5), and n≤10 (N10)), one empirical abundant cutoff (n>10 (Ab)), as well as for the entire datasets (All) were used to construct the plot. Grey shapes show rare and abundant members from each quadrant clustering closer together with the whole quadrant. Stress value was close to 0, and most of the variation (65–95.3%) was explained by 2 axes. The addition of a third axis did not improve the model substantially.
Table 3.
Number of OTUs0.03 identified for each quadrant at each of the rare and abundant species definitions used in this study.
Figure 4.
Effect of inadequate sampling on the observed beta diversity in Zodletone spring.
A sub-sampling approach was implemented in which 3 subsamples from quadrant 2 (sub1, sub2, and sub3) were compared to three subsamples, each from a different quadrant (Quad 1_r, Quad 3_r, and Quad 4_r). (A) The percentage unshared OTUs, and the percentage shared OTUs between 2 quadrants, and 3 quadrants for the 3 subsamples from quadrant 2 versus the 3 subsamples from quadrants 1, 3, and 4 (* denotes that the percentage shared/unshared OTUs were significantly different between the 2 groups). Error bars represent standard deviations from 3 pairs of subsamples (2 quads) and 3 subsamples (1 quad). No error bars were obtained for the single 3-quads data point. Color-coding is as follows: the 3 subsamples from quadrant 2 (black), and the 3 subsamples from quadrants 1, 3, and 4 (white). (B) Non-metric multidimensional scaling plot for the 6 subsamples studied. Pair wise Bray-Curtis similarity indices were used to construct the plot. Stress value was close to 0 and most of the variation (77.8%) was explained by 2 axes. (C) Observed and expected number of species (Sobs, and Sexpected, respectively) and singletons for each of the quadrants studied. The numbers were used to construct theoretical Venn diagrams as described in text. (D) The percentage shared OTUs between 4 quadrants, 3 quadrants, 2 quadrants, and the percentage unshared OTUs calculated from the obtained Venn diagram for n = 1 (shown in Figure 2A) (observed data), and the average percentages calculated from the theoretical Venn diagrams (predicted data). Error bars represent standard deviations from 4 data points for each of the observed and predicted unshared OTUs percentages (1 quad), 6 data point for the observed shared OTUs percentages and 4 data points for the predicted shared OTUs percentages between 2 quads, 4 data points for each of the observed and predicted shared OTUs percentages between 3 quads, 4 data points for the predicted shared OTUs percentages between 4 quads. No error bars were obtained for the single 4-quads observed shared OTUs percentage data point. Color-coding is as follows: Observed data (black), and predicted data (white).
Table 4.
Beta diversity measures for the rare biosphere sub-groups across the 4 quadrants compared to the total rare biosphere (n≤5).