ENIGMA CORAL

What it is

Canonical name: ENIGMA CORAL. The source uses enigma_coral as the dataset or tenant identifier. No stable external identifier is reported in the document. ₁

Known aliases: ENIGMA CORAL; enigma_coral. ₁

ENIGMA CORAL is a KBase Data Lakehouse field-sample data resource used for environmental and biological observations. ₁ The atlas recommends it for field samples and places it within the broader multi-omics-integration and environmental-resistome integration landscape. ₁ The contamination-gradient study refines this characterization by demonstrating a reproducible workflow linking ENIGMA geochemistry and community composition to kbase-ke-pangenome clades and eggnog-derived functional proxies across 108 samples. ₂

The SSO subsurface ecology analysis supports CORAL’s role as a field-sample resource by using its sediment and groundwater 16S amplicon sequence variant (ASV) observations to resolve community structure across a 3×3 well grid spanning approximately 6 m. ₃ It also refines the integration picture: 221 SSO geochemistry sample tubes are registered in CORAL, but the associated metals, ion chromatography/total organic carbon, isotope, ammonia, and nitrite measurements were not loaded in the analyzed dataset. ₃

The field-versus-lab fitness survey refines expectations about CORAL’s current utility for gene-level ecological analysis: its 47 tables contained field geochemistry and community resources but no Desulfovibrio vulgaris Hildenborough gene-level fitness data. ₄ The survey found one TnSeq library for FW300-N2E2 (Pseudomonas) and DubSeq libraries for Escherichia coli, Pseudomonas putida, and Bacteroides thetaiotaomicron, so CORAL cannot currently bridge DvH Fitness Browser measurements to field observations. ₄

The Oak Ridge field-ecology study supports CORAL’s utility for directly comparing field communities with laboratory phenotypes: it linked 16S amplicon profiles and geochemistry across 108 sites to kescience-fitnessbrowser metal-tolerance scores. ₅ Of 26 Fitness Browser genera, 14 were detected; Sphingomonas, Pseudomonas, and Caulobacter occurred at 93%, 91%, and 82% of sites, respectively. ₅ The aggregate laboratory-tolerance/field-abundance relationship was positive but non-significant (Spearman rho=0.503, p=0.095, n=12), so this result refines the earlier cross-tenant limitation: CORAL can support genus-level field-versus-lab tests, but not yet species- or strain-resolved prediction. ₅

Key facts

• The inventory contains 4,346 ENIGMA SDT samples. ₁
• The inventory contains 579 ENIGMA DDT measurement bricks. ₁
• The inventory contains 218,510 ENIGMA SDT amplicon sequence variants (ASVs). ₁
• ENIGMA contains 36% of the KBase Data Lakehouse tables but appears in 6 of the 66 audited BERIL projects. ₁
• ENIGMA covers 5 biological topics and has a topic-coverage entropy of 0.43. ₁
• The contamination-gradient analysis used a quality-controlled overlap of 108 samples, a geochemistry matrix with shape (108, 49), 41,711 community taxon rows, 212 distinct communities, and 1,392 distinct genera. ₂
• That analysis supports the atlas’s placement of ENIGMA in multi-omics-integration: it integrated geochemistry, community composition, pangenome clades, and eggNOG-derived functional features, while documenting incomplete cross-dataset coverage. ₂
• The genus-level analysis found no robust monotonic association between contamination and broad functional scores in its confirmatory tests; exploratory defense associations were sensitive to coverage, covariate specification, taxonomic resolution, and multiple-testing correction. ₂
• The SSO analysis measured 23,458 sediment ASVs across 37 sediment core samples aggregated per well and found significant spatial distance-decay, while hydrogeological zone explained 27.5% of community variance (F = 4.05, p = 0.0001). ₃
• SSO groundwater communities were sampled from 5 of 9 wells, and their well identity explained 49.9% of variance; date explained 0.8% over the 9-day interval. ₃
• The CORAL survey catalogued 6,705 genomes, 15,015 genes, 4,346 field samples with geochemistry data across 596 Oak Ridge locations, and 213,044 ASVs; these collections support field-context analyses but not DvH gene-level fitness analysis. ₄
• In the new 108-site study, five of 11 tested genera had uranium associations after Benjamini–Hochberg false-discovery-rate correction, with both positive and negative directions; this supports environmental sorting but refines any simple metal-tolerance interpretation because pH, redox, carbon sources, competition, and temporal history were not controlled. ₅

Cross-tenant relevance

The atlas identifies an unused ENIGMA–PhageFoundry bridge with 11 shared schema-level keys for studying subsurface prophages, metal resistance, and the Oak Ridge contamination gradient. ₁ This bridge is schema-level only and had zero realized use at audit time; value-space validity requires live-cluster execution. ₁ The proposed integration connects ENIGMA CORAL with phagefoundry and is relevant to environmental-resistome. ₁

The contamination-gradient workflow supports the environmental-resistome relevance by testing an eight-metal contamination index against inferred community defense and stress potential, but its confirmatory genus-level defense associations were null. ₂ It therefore refines the proposed use of ENIGMA for metal-resistance research: broad COG-category proxies did not establish a contamination-linked functional shift, and finer-resolution species, strain, or curated pathway analyses remain necessary. ₂

The SSO study supports investigating contamination-linked spatial structure in CORAL, but refines the evidence level: its proposed northeast-to-southwest plume, M5 mixing zone, and inferred redox ladder are hypotheses based on 16S composition and taxonomy-to-trait inference, not direct geochemical measurements. ₃ Loading the registered SSO geochemistry and pairing it with metagenomics, isolate genomes, and repeat seasonal sampling would directly test these interpretations. ₃

The new field-ecology study supports using CORAL to test laboratory-to-field transfer, while its non-significant aggregate tolerance result and bidirectional genus-level uranium associations contradict a simple expectation that laboratory metal tolerance alone determines abundance. ₅ Species- or strain-level matching, multivariate CCA or RDA controlling for pH, redox, and carbon sources, temporal sampling, and metal-specific fitness scores are proposed to resolve this limitation. ₅

The absence of DvH fitness data refines the cross-tenant roadmap: CORAL’s field geochemistry and community collections could eventually be linked to Fitness Browser data, but that analysis requires a different ENIGMA organism with both environmental observations and gene-level fitness measurements, or newly loaded DvH data. ₄

Source

• BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies — KBase Data Lakehouse inventory, topic map, cross-tenant bridges, and realized-use audit. ₁
• Contamination Gradient vs Functional Potential in ENIGMA Communities — ENIGMA contamination-gradient analysis linking geochemistry, community composition, pangenome clades, and functional proxies. ₂
• SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers — SSO subsurface ASV ecology, spatial structure, hydrogeological gradients, and missing geochemical validation. ₃
• Field vs Lab Gene Importance in *Desulfovibrio vulgaris* Hildenborough — DvH field-versus-lab fitness analysis and ENIGMA CORAL data-availability survey. ₄
• Lab Fitness Predicts Field Ecology at Oak Ridge — Oak Ridge field ecology linked to Fitness Browser laboratory metal-tolerance measurements. ₅