🪰

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)

ddt_brick0000010 ddt_brick0000072 ddt_brick0000073 ddt_brick0000080 ddt_brick0000452 ddt_brick0000454 ddt_brick0000457 ddt_brick0000458 ddt_brick0000459 ddt_brick0000460 ddt_brick0000461 ddt_brick0000462 ddt_brick0000476 ddt_brick0000477 ddt_brick0000478 ddt_brick0000479 ddt_brick0000510 ddt_brick0000517 ddt_brick0000520 ddt_brick0000521 ddt_brick0000522 ddt_brick0000528 ddt_brick0000529 ddt_brick0000928 ddt_brick0000929 ddt_brick0000930 ddt_brick0000931 ddt_brick0000932 ddt_brick0000933 ddt_brick0000934 ddt_brick0000935 ddt_brick0000936 ddt_brick0000937 ddt_brick0000938 ddt_brick0000939 ddt_brick0000940 ddt_brick0000941 ddt_brick0000942 ddt_brick0000943 ddt_brick0000944 ddt_brick0000945 ddt_brick0000946 ddt_brick0000947 ddt_brick0000948 ddt_brick0000949 ddt_brick0000950 ddt_brick0000951 ddt_brick0000952 ddt_brick0000953 ddt_brick0000954 ddt_brick0000955 ddt_brick0000956 ddt_brick0000957 ddt_brick0000958 ddt_brick0000959 ddt_brick0000960 ddt_brick0000961 ddt_brick0000962 ddt_brick0000963 ddt_brick0000964 ddt_brick0000965 ddt_brick0000966 ddt_brick0000967 ddt_brick0000968 ddt_brick0000969 ddt_brick0000970 ddt_brick0000971 ddt_brick0000972 ddt_brick0000973 ddt_brick0000974 ddt_brick0000975 ddt_brick0000976 ddt_brick0000977 ddt_brick0000978 ddt_brick0000979 ddt_brick0000980 ddt_brick0000981 ddt_brick0000982 ddt_brick0000983 ddt_brick0000984 ddt_brick0000985 ddt_brick0000986 ddt_brick0000987 ddt_brick0000988 ddt_brick0000989 ddt_brick0000990 ddt_brick0000991 ddt_brick0000992 ddt_brick0000993 ddt_brick0000994 ddt_brick0000995 ddt_brick0000996 ddt_brick0000997 ddt_brick0000998 ddt_brick0000999 ddt_brick0001000 ddt_brick0001001 ddt_brick0001002 ddt_brick0001003 ddt_brick0001004 ddt_brick0001005 ddt_brick0001006 ddt_brick0001007 ddt_brick0001008 ddt_brick0001009 ddt_brick0001010 ddt_brick0001011 ddt_brick0001012 ddt_brick0001013 ddt_brick0001014 ddt_brick0001015 ddt_brick0001016 ddt_brick0001017 ddt_brick0001018 ddt_brick0001019 ddt_brick0001020 ddt_brick0001021 ddt_brick0001022 ddt_brick0001023 ddt_brick0001024 ddt_brick0001025 ddt_brick0001026 ddt_brick0001027 ddt_brick0001028 ddt_brick0001029 ddt_brick0001030 ddt_brick0001031 ddt_brick0001032 ddt_brick0001033 ddt_brick0001034 ddt_brick0001035 ddt_brick0001036 ddt_brick0001037 ddt_brick0001038 ddt_brick0001039 ddt_brick0001040 ddt_brick0001041 ddt_brick0001042 ddt_brick0001043 ddt_brick0001044 ddt_brick0001045 ddt_brick0001046 ddt_brick0001047 ddt_brick0001048 ddt_brick0001049 ddt_brick0001050 ddt_brick0001051 ddt_brick0001052 ddt_brick0001053 ddt_brick0001054 ddt_brick0001055 ddt_brick0001056 ddt_brick0001057 ddt_brick0001058 ddt_brick0001059 ddt_brick0001060 ddt_brick0001061 ddt_brick0001062 ddt_brick0001063 ddt_brick0001064 ddt_brick0001065 ddt_brick0001066 ddt_brick0001067 ddt_brick0001068 ddt_brick0001069 ddt_brick0001070 ddt_brick0001071 ddt_brick0001072 ddt_brick0001073 ddt_brick0001074 ddt_brick0001075 ddt_brick0001076 ddt_brick0001077 ddt_brick0001078 ddt_brick0001079 ddt_brick0001080 ddt_brick0001081 ddt_brick0001082 ddt_brick0001083 ddt_brick0001084 ddt_brick0001085 ddt_brick0001086 ddt_brick0001087 ddt_brick0001088 ddt_brick0001089 ddt_brick0001090 ddt_brick0001091 ddt_brick0001092 ddt_brick0001093 ddt_brick0001094 ddt_brick0001095 ddt_brick0001096 ddt_brick0001097 ddt_brick0001098 ddt_brick0001099 ddt_brick0001100 ddt_brick0001101 ddt_brick0001102 ddt_brick0001103 ddt_brick0001104 ddt_brick0001105 ddt_brick0001106 ddt_brick0001107 ddt_brick0001108 ddt_brick0001109 ddt_brick0001110 ddt_brick0001111 ddt_brick0001112 ddt_brick0001113 ddt_brick0001114 ddt_brick0001115 ddt_brick0001116 ddt_brick0001117 ddt_brick0001118 ddt_brick0001119 ddt_brick0001120 ddt_brick0001121 ddt_brick0001122 ddt_brick0001123 ddt_brick0001124 ddt_brick0001125 ddt_brick0001126 ddt_brick0001127 ddt_brick0001128 ddt_brick0001129 ddt_brick0001130 ddt_brick0001131 ddt_brick0001132 ddt_brick0001133 ddt_brick0001134 ddt_brick0001135 ddt_brick0001136 ddt_brick0001137 ddt_brick0001138 ddt_brick0001139 ddt_brick0001140 ddt_brick0001141 ddt_brick0001142 ddt_brick0001143 ddt_brick0001144 ddt_brick0001145 ddt_brick0001146 ddt_brick0001147 ddt_brick0001148 ddt_brick0001149 ddt_brick0001150 ddt_brick0001151 ddt_brick0001152 ddt_brick0001153 ddt_brick0001154 ddt_brick0001155 ddt_brick0001156 ddt_brick0001157 ddt_brick0001158 ddt_brick0001159 ddt_brick0001160 ddt_brick0001161 ddt_brick0001162 ddt_brick0001163 ddt_brick0001164 ddt_brick0001165 ddt_brick0001166 ddt_brick0001167 ddt_brick0001168 ddt_brick0001169 ddt_brick0001170 ddt_brick0001171 ddt_brick0001172 ddt_brick0001173 ddt_brick0001174 ddt_brick0001175 ddt_brick0001176 ddt_brick0001177 ddt_brick0001178 ddt_brick0001179 ddt_brick0001180 ddt_brick0001181 ddt_brick0001182 ddt_brick0001183 ddt_brick0001184 ddt_brick0001185 ddt_brick0001186 ddt_brick0001187 ddt_brick0001188 ddt_brick0001189 ddt_brick0001190 ddt_brick0001191 ddt_brick0001192 ddt_brick0001193 ddt_brick0001194 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_brick0001005`

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

Related Collections

🧬

Pangenome Collection

Pangenome data for 293,059 genomes across 27,690 microbial species derived from ...

📊

Fitness Browser

Gene fitness data from transposon mutant experiments across 40+ bacterial organi...

Projects Using This Collection

ENIGMA Carbon Census 1

For 83 groundwater- and necromass-derived carbon compounds proposed for community enrichment and isolate phenotyping, wh...

BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies

What data is available in BERDL (across tenants, agencies, and programs), what biological topics does it cover, and wher...

Genotype × Condition → Phenotype Prediction from ENIGMA Growth Curves

Can we predict bacterial growth phenotype — at multiple resolutions from binary growth through continuous kinetics to co...

SSO Subsurface Community Ecology — Spatial Structure, Functional Gradients, and Hydrogeological Drivers

Does 16S community similarity across the 9 ENIGMA SSO wells (3x3 grid, ~4 m span at Oak Ridge) recapitulate the spatial ...

Field vs Lab Gene Importance in Desulfovibrio vulgaris Hildenborough

Which genes matter for survival under environmentally-realistic conditions but appear dispensable in the lab, and vice v...

Contamination Gradient vs Functional Potential in ENIGMA Communities

Do high-contamination Oak Ridge groundwater communities show enrichment for taxa with higher inferred stress-related fun...

Lab Fitness Predicts Field Ecology at Oak Ridge

Do lab-measured fitness effects under contaminant stress predict the field abundance of Fitness Browser organisms across...

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