Contamination Gradient vs Functional Potential in ENIGMA Communities

This project uses ENIGMA CORAL field data to test whether contamination gradients (uranium and co-occurring metals) are associated with shifts in inferred community functional potential. Functional potential is estimated by linking ENIGMA taxa to BERDL pangenome annotations and aggregating stress-relevant functional signals (COG defense/mobilome and related categories) at the site level. The analysis targets community-level ecological filtering rather than gene-level causality.

ENIGMA taxonomy in ddt_brick0000454 is currently available through Genus (no species/strain rows), so higher-resolution analysis is implemented as a species-proxy sensitivity mode using only uniquely resolved genus-to-clade mappings.

NB01 extracted and QC-filtered overlap data to 108 samples with both geochemistry and community composition:
- Geochemistry matrix shape: (108, 49)
- Community taxon rows: 41,711
- Distinct communities: 212
- Distinct genera: 1,392

NB02 built a genus-normalized bridge to pangenome clades:
- GTDB species rows parsed for genus mapping: 27,690
- Mapped genera: 530
- Unmapped genera: 862
- Strict clades: 530, relaxed clades: 7,380
- Species-proxy clades (unique genus->single clade): 150
- Functional features now computed independently for strict, relaxed, and species-proxy mapping modes.

NB03 produced:
- Site functional score rows: 324 (108 samples x 3 mapping modes)
- Model result rows: 12 (4 outcomes x 3 mapping modes)
- Expanded model diagnostics in model_results.tsv: confirmatory/exploratory labels, bootstrap CIs for key effect sizes, adjusted coordinates/depth models, coverage-adjusted models, site-structure models (location_prefix), fraction-aware models (community_fraction_type), within-fraction correlations, high-coverage subset correlations, and global BH-FDR q-values across all reported p-values.
- Additional robustness tables:
- data/contamination_index_sensitivity.tsv (8 confirmatory variant rows)
- data/mapped_coverage_deciles.tsv (30 decile strata rows)
- data/model_family_sample_counts.tsv (96 model-family count rows)

Overall, confirmatory evidence remains null and robust to index definition; exploratory coverage-aware defense associations persist with positive effect estimates, but are attenuated under global multiple-testing control.

Within this ENIGMA subset, contamination gradients did not translate into a robust community-level shift in inferred stress-related functional potential when features are aggregated at genus resolution from broad COG categories. This is compatible with contamination-driven taxonomic turnover that is functionally redundant or too fine-scale (species/strain/pathway level) for the present mapping.

Literature Context

• Directionally aligned with Hemme et al. (2015; PMID: 26583008), which reported strong contamination-linked taxonomic restructuring in Oak Ridge groundwater with reduced functional breadth in stressed communities. Our confirmatory null Spearman results at genus-aggregated score level are consistent with contamination effects that do not collapse into one robust monotonic community-wide proxy.
• Also consistent with Fan et al. (2025), who reported pronounced compositional shifts but only modest functional-diversity decline in a mixed waste-contaminated Oak Ridge aquifer. This matches the pattern here: ecological differentiation is detectable, while broad functional summaries show weaker confirmatory monotonic response.
• Relative to Carlson et al. (2019; PMID: 30523276), this project extends from taxa-abundance association to reproducible bridge-aware functional sensitivity modeling (strict, relaxed, and species-proxy modes), quantifying where inference remains coverage-limited.
• The bridge/annotation stack depends on GTDB and eggNOG conventions (Parks et al. 2022; Cantalapiedra et al. 2021); at genus-level aggregation, broad COG-style signals can dilute pathway-specific metal-response effects.

Novel Contribution

This project contributes a reproducible ENIGMA-to-BERDL functional inference workflow with independent strict-vs-relaxed feature construction, mapped-coverage diagnostics, a species-proxy unique-clade sensitivity mode, and multi-tier modeling beyond basic univariate association tests.

Limitations

• ENIGMA taxonomy table ddt_brick0000454 currently provides labels through Genus (no species/strain labels), so true species-level bridge testing is not directly possible in this dataset slice.
• Genus-level mapping may mask strain-level adaptation.
• 862/1,392 observed genera were unmapped to current pangenome bridge.
• COG-fraction proxies are coarse summaries, not curated resistance pathways.
• Exploratory sensitivity-model significance is concentrated in defense and depends on coverage/covariate specification; broader effect across outcomes is not yet established.
• Site structure is represented by coarse location_prefix effects rather than full hierarchical/random-effects modeling.

1. Replace COG-fraction proxies with curated metal-stress gene sets and pathway-level summaries.
2. Increase taxonomic resolution where possible (species/strain-level bridge from metagenomic or higher-resolution ENIGMA taxonomy) and quantify gains over genus and species-proxy modes.
3. Fit adjusted models with explicit covariates (depth, location cluster, sampling date) and compositional modeling controls.
4. Investigate unmapped genera contribution to contamination gradients and bridge expansion opportunities.
5. Add mixed-effects or hierarchical site models (well/location-level random effects) to test whether defense associations persist under richer structure control.

Sources

Generated Data

• Carlson HK et al. (2019). The selective pressures on the microbial community in a metal-contaminated aquifer. ISME J 13:937-949. PMID: 30523276.
• Hemme CL et al. (2010). Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4:660-672. DOI: 10.1038/ismej.2009.154.
• Hemme CL et al. (2015). Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Front Microbiol 6:1205. PMID: 26583008.
• Fan Y et al. (2025). Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer. Microbiome 13:106. DOI: 10.1186/s40168-025-02105-x.
• Parks DH et al. (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 50:D785-D794.
• Cantalapiedra CP et al. (2021). eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol Biol Evol 38:5825-5829.