Supplementary materials for the doctoral thesis "Soil Microbial Communities and Functional Potential along the Chilean Coastal Cordillera: Insights from DNA-Pool Separation and iDNA Metagenomics"

Supplementary materials for Chapters 2–4 (Appendices A–C) of Xiuling Wang’s doctoral thesis, “Soil Microbial Communities and Functional Potential along the Chilean Coastal Cordillera: Insights from DNA-Pool Separation and iDNA Metagenomics”. Version 1.0.6 synchronizes the public supplements with the accepted thesis V17 and source-paper V16 content. Manuscript version finalization does not imply journal acceptance. Appendix A / Chapter 2: Tables A1–A6 and Figures A1–A12 are unchanged from the previous public release. Appendix B / Chapter 3: Tables B1–B5 and Figures B1–B6 reflect the current archaeal source content, including function-unresolved labels. The reference in Table B2 to the published bacterial paper is correctly retained as that paper’s Supplementary Fig. S1. Protocol B1 is carried forward unchanged from public version 1.0.5 for historical continuity. It is not the pending local protocol revision; the revised extraction description and TE-buffer preparation detail require source verification before a revised protocol can be released. Appendix C / Chapter 4: Tables C1–C4 and Data C1 are byte-identical to the current source-paper V16 workbooks. Data C1 now contains 18 worksheets and is named Data_C1_Metagenomics.xlsx. Both original C03 and C18 are excluded from downstream sample comparisons, without remapping; 15 libraries remain. AZ C01 is descriptive, the replicated SG/LC/NA surface comparison uses n=9, the primary NA depth analysis uses n=8 and the complete-pit sensitivity uses n=6. The fixed gene catalogue and 228-MAG reference remain unchanged. Figures C1–C3 and captions match the current thesis; C2 includes both pages. Internal journal S-numbered worksheet labels are mapped to thesis C numbering in README.md. The convenience ZIP duplicates the four workbooks and file guide. Individual figures, the historical protocol, README and checksums are provided separately. No new statistical analysis is introduced. Previous public records and source manuscripts remain unchanged. Amplicon reads: https://www.ebi.ac.uk/ena/browser/view/PRJEB73502Metagenomic reads (all 17 deposited runs): https://www.ebi.ac.uk/ena/browser/view/PRJEB123235Bacterial code: https://github.com/Xiuling-Wang/chile-soil-bacteriaArchaeal code: https://github.com/Xiuling-Wang/chile-soil-archaeaMetagenomic code: https://github.com/Xiuling-Wang/chile-soil-metagenomics Repository instructions distinguish current and historical code and document required inputs. These result workbooks do not include every raw or intermediate input required for a complete rerun. DNA fractions are operationally defined; DNA representation and gene co-occurrence do not directly establish activity, viability or physiological function. Source-study attribution is retained in References. The existing CC BY 4.0 licence and creator attribution are preserved.