The use of different 16S rRNA gene variable regions in biogeographical studies

• Published in: Environmental Microbiology Reports
• Main Authors: Varliero, Gilda, Lebre, Pedro H., Stevens, Mark I., Czechowski, Paul, Makhalanyane, Thulani Peter, Cowan, Don A.
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2023
• Subjects: 16S rRNA gene amplicon sequencing; Online sequence data repositories; 16S rRNA gene variable regions; Biogeographical studies; Composite datasets; Prince Charles Mountains
• Online Access: http://hdl.handle.net/2263/92438; https://doi.org/10.1111/1758-2229.13145

DATA AVAILABILITY STATEMENT : All Illumina sequences generated and analyzed in this study were deposited into the European Nucleotide Archive (accession number PRJEB55051). SUPPORTING INFORMATION 1 : FIGURE S1. Samples located in four inland areas of the Prince Charles Mountains (ME1 from Mount Rubin, ME2 and ME3 from Mawson Escarpment, MM1 and MM2 from Mount Menzies, LT1 and LT2 from Lake Terrasovoje), in the Reinbolt Hills (RH1), and in coastal sites in proximity of the Prince Charles Mountains (C1 and C2; see Table S1). Map was produced using MODIS mosaic (125 m) imagery distributed by Quantarctica (https://cmr.earthdata.nasa.gov/; https://www.npolar.no/quantarctica/). FIGURE S2. Pearson's pairwise correlations between Bray–Curtis dissimilarity matrices calculated on relative abundance taxonomic dataset (genus level; A), and between Jaccard dissimilarity matrices calculated on presence/absence taxonomic dataset (genus level; B). Correlations were calculated for all the variable region datasets (V1–V3, V3–V4, V4, V4–V5 and V8–V9), and the mixed datasets (Mix 1, Mix 2 and Mix 3) constituted by randomly picked samples from V1–V3, V3–V4, V4, V4–V5 and V8–V9 (Table S4). Pearson's correlation coefficients (r) are reported only in case of significant correlation (p < 0.05). SUPPORTING INFORMATION 2 : TABLE S1. Sample specifics. TABLE S2. Geochemical data. TABLE S3. Relative abundance (%) of the taxonomic domains Bacteria and Archaea in sample (i.e., ME1, ME2, ME3, MM1, MM2, LT1, LT2, RH1, C1 and C2) for each variable region dataset (i.e., V1–V3, V3–V4, V4, V4–V5 and V8–V9). TABLE S4. Composition of mixed communities. TABLE S5. Number of reads at each step of the 16S rRNA gene processing pipeline. *counts reported as read pairs. TABLE S6. Number and percentage of unknown amplicon sequence variants (ASVs) at genus level for each phylum. TABLE S7. Relative abundance associated to unknown amplicon sequence variants at genus-level for each phylum. TABLE S8. Pearson's correlations from pairwise comparisons of ...