Additional file 1 of Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring
Bibliographic record
Abstract
Additional file 1: Figure S1.a. Photograph of GH-4 primary outlet and downstream channels (July 2019). A fine layer of gypsum coats the area around the springs. b. Location of the Gypsum Hill springs on Axel Heiberg Island, Nunavut, Canada (indicated with red dot). Map generated in QGIS with the Natural Earth dataset. c. Photograph of the Gypsum Hill springs area in which GH-4 is located. Photos: E. Magnuson. Figure S2. Phylogenetic tree of DsrAB sequences. Figure S3. Phylogenetic tree of DsrA sequences. Figure S4. Phylogenetic tree of DsrB sequences. Figure S5. Phylogenetic trees of DsrA and DsrB sequences. Figure S6. Relative abundance of reads in the metagenome and metatranscriptome classified by Kaiju using the NCBI non-redundant database (nr_euk). Relative abundance was averaged between replicates for both the metagenome and metatranscriptome. Figure S7. Level of taxonomic novelty of ASVs (2,885 ASVs in total). Figure S8. Spearman’s rank correlation of the top 50 most abundant taxa in the subset of thirteen 16S rRNA gene sequencing data sets with environmental parameters. Metadata for this plot is located in Table S4. Figure S9. NMDS plot with Bray Curtis dissimilarity matrix for 16S rRNA gene amplicon sequences from GH and comparable environments. Metadata for this plot is located in Table S4. Table S1. Physical and chemical parameters in GH-4. Table S2. Sequencing library statistics. Table S3. Metagenome co-assembly statistics. Table S4. Metadata for amplicon metagenome libraries used in beta diversity analysis. Table S5. Taxonomic count table used for beta diversity analysis. Table S6. List of contigs in each MAG. Table S7. MAG supplemental information. Table S8. Taxonomic classification of genes of interest with mapped transcripts. Table S9. Gene content of MAGs. Table S10. Relative expression of genes of interest in MAGs. Table S11. Total tpm per genome feature product ID. Table S12. Gene counts and relative expression of genes of interest in the metagenome. Table S13. Complete BLAST output of elemental sulfur reduction proteins queried against Desulfuromusa sp. GH17. Table S14. Relative expression of all genes.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.012 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.007 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.892 | 0.216 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".