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ENIGMA CORAL

enigma_coral

Tenant: ENIGMA · Snapshot 2026-04-29T21:35:53.838483+00:00

Domain

Schema status

discovered

Curation status

curated

Source

berdl-spark-connect://metrics.berdl.kbase.us:443

Philosophy

Understand subsurface microbial ecology at contaminated sites. Study how microbial community composition (ASVs) varies in space and time and correlates with geochemical parameters (metals, nitrate, etc.) across the Oak Ridge Reservation watershed.

Data sources: ENIGMA SFA

Citation & Attribution

Provider: ENIGMA SFA, LBNL

Website: https://enigma.lbl.gov/

Scale

596

locations

4,346

samples

213,044

asvs

3,154

strains

6,705

genomes

tables

Schema Browser

Tables (350)

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ddt_brick0001195 ddt_brick0001196 ddt_brick0001197 ddt_brick0001198 ddt_brick0001199 ddt_brick0001200 ddt_brick0001201 ddt_brick0001202 ddt_brick0001203 ddt_brick0001204 ddt_brick0001205 ddt_brick0001206 ddt_brick0001207 ddt_brick0001208 ddt_brick0001209 ddt_brick0001210 ddt_brick0001211 ddt_brick0001212 ddt_brick0001213 ddt_brick0001214 ddt_brick0001215 ddt_brick0001216 ddt_brick0001217 ddt_brick0001218 ddt_brick0001219 ddt_brick0001220 ddt_brick0001221 ddt_brick0001222 ddt_brick0001223 ddt_brick0001224 ddt_brick0001225 ddt_brick0001226 ddt_brick0001227 ddt_brick0001228 ddt_brick0001229 ddt_brick0001230 ddt_ndarray sdt_assembly sdt_asv sdt_bin sdt_community sdt_condition sdt_dubseq_library sdt_enigma sdt_gene sdt_genome sdt_image sdt_location sdt_protocol sdt_reads sdt_sample sdt_strain sdt_taxon sdt_tnseq_library sys_ddt_typedef sys_oterm sys_process sys_process_input sys_process_output sys_typedef

`ddt_brick0000989`

Column	Type	Description

Sample Queries

Get SSO community ASV profiles

SELECT ab.sdt_community_name, ab.sdt_asv_name,
       tax.taxonomic_level_sys_oterm_name, tax.sdt_taxon_name,
       ab.count_count_unit
FROM enigma_coral.ddt_brick0000459 ab
JOIN enigma_coral.ddt_brick0000454 tax
  ON ab.sdt_asv_name = tax.sdt_asv_name
WHERE ab.sdt_community_name LIKE 'SSO%'
  AND ab.count_count_unit > 0
  AND tax.taxonomic_level_sys_oterm_name = 'Genus'
ORDER BY ab.sdt_community_name, ab.count_count_unit DESC

Get SSO geochemistry

SELECT sdt_sample_name, molecule_from_list_sys_oterm_name,
       concentration_micromolar, physiochemical_state
FROM enigma_coral.ddt_brick0000010
WHERE sdt_sample_name LIKE 'SSO%'
ORDER BY sdt_sample_name, concentration_micromolar DESC

Get samples with location metadata

SELECT s.sdt_sample_name, s.date, s.depth_meter,
       l.latitude_degree, l.longitude_degree, l.region,
       l.feature_sys_oterm_name
FROM enigma_coral.sdt_sample s
JOIN enigma_coral.sdt_location l
  ON s.sdt_location_name = l.sdt_location_name
WHERE s.sdt_location_name LIKE 'SSO%'
ORDER BY s.date, s.sdt_location_name

Get high-quality genomes

SELECT q.sdt_strain_name,
       q.genome_completeness_method_checkm_percent,
       q.genome_contamination_method_checkm_percent,
       q.genome_n50_method_checkm_count_unit
FROM enigma_coral.ddt_brick0000521 q
WHERE q.genome_completeness_method_checkm_percent >= 95
  AND q.genome_contamination_method_checkm_percent <= 5
ORDER BY q.genome_completeness_method_checkm_percent DESC

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Atlas Pages

claim

Lab fitness can predict field ecology

Several projects suggest that lab-measured fitness signals can align with environmental abundance or isolation context when validation data are available.

claim

AMR mechanism composition is environment-structured

AMR mechanisms differ by environment, making resistance ecology a field and context problem rather than only a clinical annotation problem.

conflict

Lab fitness signals versus field ecology

Lab-derived fitness or tolerance scores can predict ecology in some settings, but metadata quality and field complexity limit broad generalization.

conflict

Metal-AMR co-selection readiness

BERIL has the pieces to test metal-AMR co-selection, but the current evidence is a strong opportunity rather than a resolved result.

meta

BERDL Data Atlas

Entry point for BERDL tenants, collections, data types, derived products, join recipes, reuse patterns, and missing complementary data.

data tenant

ENIGMA Tenant and Contaminated-Site Context

ENIGMA CORAL and related contaminated-site data that connect microbial genomics and communities to DOE field environments.

data type

Environment, Geochemistry, and Ecology

Environmental samples, coordinates, geochemistry, sample metadata, and ecology-facing observations used to validate laboratory predictions in the field.

data type

Multi-Omics, Embeddings, and Molecular Profiles

Metabolomics, proteomics, trait profiles, embeddings, and other matrix-style summaries that create reusable sample or organism representations.

derived product

Metal Tolerance Scores

Reusable species and gene-level metal tolerance signals derived from metal fitness projects and environmental validation work.

derived product

Environment Harmonization Labels

Reusable environment category and coordinate-quality labels that make cross-collection ecology joins safer.

data gap

Missing SSO Geochemistry

ENIGMA SSO registered sample tubes exist, but linked geochemistry measurements are missing from the lakehouse.

data collection

ENIGMA CORAL

Environmental microbiology data from the ENIGMA SFA (samples, genomes, communities, strains)

meta

Research Directions

Entry point for high-value research opportunities synthesized from existing BERIL evidence, data products, and gaps.

direction

Metal-AMR co-selection at contaminated sites

Test whether metal contamination selects for AMR genes, mechanisms, or support networks across DOE-relevant environments.

hypothesis

Metal contamination co-selects AMR mechanisms

Metal-contaminated environments carry higher AMR burden or different AMR mechanism composition after controlling for taxonomy and site context.

hypothesis

Metal tolerance scores predict field isolation context

Species with higher metal tolerance scores are enriched in metal-associated isolation or contaminated-site contexts.

hypothesis

SSO geochemistry closes the plume model

Ingested SSO geochemistry will align microbial community gradients with measured metal, redox, and nutrient chemistry.

meta

Atlas Review Queue

Maintainer queue for deepening flagship topics, promoting reusable products, and resolving Atlas tensions.

opportunity

Metal-AMR Site Co-Selection Analysis

Test whether metal contamination at BER-relevant sites co-selects antibiotic resistance mechanisms using metal fitness, AMR profiles, and environmental metadata.

opportunity