diff --git a/kb/communities/Mercury_SFA_EFPC_Sediment_Community.yaml b/kb/communities/Mercury_SFA_EFPC_Sediment_Community.yaml new file mode 100644 index 000000000..79c5745db --- /dev/null +++ b/kb/communities/Mercury_SFA_EFPC_Sediment_Community.yaml @@ -0,0 +1,318 @@ +name: Mercury SFA East Fork Poplar Creek Sediment Community +description: > + A sediment microbial community from East Fork Poplar Creek (EFPC) in Oak Ridge, Tennessee, + contaminated with mercury from historical weapons production at the Y-12 National Security Complex. + 28 metagenome-assembled genomes (MAGs) were reconstructed from two sediment core sections (0-3 cm + and 9-12 cm depth), with 27 representing novel prokaryotic species. 27 of 28 MAGs contained + putative heavy metal resistance genes or ATPase efflux pump genes, reflecting strong selective + pressure from chronic mercury contamination. 17 of 28 MAGs contained selenium assimilatory + metabolism traits. The community includes both bacterial and archaeal members, with several + lineages carrying hgcA/hgcB genes for mercury methylation, a process that converts inorganic + mercury to the more bioavailable and toxic methylmercury. Methanogenic archaea in similar + contaminated environments have been shown to methylate mercury at rates rivaling those of + sulfate- and iron-reducing bacteria. +ecological_state: PERTURBED +community_origin: NATURAL +community_category: BIOREMEDIATION +environment_term: + preferred_term: Mercury-contaminated creek sediment + term: + id: ENVO:00002007 + label: sediment + notes: > + Sediment from East Fork Poplar Creek, Oak Ridge Reservation, Oak Ridge, TN. The creek has been + contaminated with mercury from upstream sources associated with historical weapons production at + the Y-12 National Security Complex. Samples collected from two sediment core depths: 0-3 cm + (surface) and 9-12 cm (subsurface). +taxonomy: +- taxon_term: + preferred_term: Proteobacteria + term: + id: NCBITaxon:1224 + label: Pseudomonadota + notes: > + Multiple MAGs representing Proteobacteria were reconstructed from EFPC sediment metagenomes. + Several contained heavy metal resistance genes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents MAG reconstruction from EFPC sediment metagenomes +- taxon_term: + preferred_term: Acidobacteriota + term: + id: NCBITaxon:57723 + label: Acidobacteriota + notes: MAGs from this phylum were recovered from EFPC sediment metagenomes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents MAG reconstruction including Acidobacteriota from EFPC sediment +- taxon_term: + preferred_term: Actinobacteriota + term: + id: NCBITaxon:201174 + label: Actinomycetota + notes: MAGs from this phylum were recovered from EFPC sediment metagenomes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents MAG reconstruction including Actinobacteriota from EFPC sediment +- taxon_term: + preferred_term: Gemmatimonadota + term: + id: NCBITaxon:142998 + label: Gemmatimonadota + notes: MAGs from this phylum were recovered from EFPC sediment metagenomes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents MAG reconstruction including Gemmatimonadota from EFPC sediment +- taxon_term: + preferred_term: Eisenbacteria + term: + id: NCBITaxon:1930587 + label: Eisenbacteria + notes: > + MAGs from this candidate phylum were recovered from EFPC sediment. Notable for containing + selenium assimilatory metabolism traits. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: 17 of the 28 MAGs contained traits for Se-assimilatory metabolism + explanation: Documents Eisenbacteria MAGs with selenium metabolism traits in EFPC sediment +- taxon_term: + preferred_term: Myxococcota + term: + id: NCBITaxon:2818505 + label: Myxococcota + notes: MAGs from this phylum were recovered from EFPC sediment metagenomes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents MAG reconstruction including Myxococcota from EFPC sediment +- taxon_term: + preferred_term: Thermoproteota + term: + id: NCBITaxon:2283796 + label: Thermoproteota + notes: Archaeal MAGs recovered from EFPC sediment metagenomes. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents archaeal MAG reconstruction from EFPC sediment +- taxon_term: + preferred_term: Methanocella paludicola + term: + id: NCBITaxon:304371 + label: Methanocella paludicola + notes: > + Confirmed hgcAB+ mercury methylator. Demonstrated robust methylmercury production in pure + culture under methanogenic conditions. + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + methylation rates vary inherently among hgcAB+ methanogens but that several species are + capable of MeHg production at rates that rival those of the better-know Hg-methylating + sulfate- and iron-reducing bacteria + explanation: Documents mercury methylation capability of Methanocella paludicola +- taxon_term: + preferred_term: Methanocorpusculum bavaricum + term: + id: NCBITaxon:2188 + label: Methanocorpusculum bavaricum + notes: > + Confirmed hgcAB+ mercury methylator. Demonstrated methylmercury production in pure culture. + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + methylation rates vary inherently among hgcAB+ methanogens but that several species are + capable of MeHg production at rates that rival those of the better-know Hg-methylating + sulfate- and iron-reducing bacteria + explanation: Documents mercury methylation capability of Methanocorpusculum bavaricum +- taxon_term: + preferred_term: Methanofollis liminatans + term: + id: NCBITaxon:43625 + label: Methanofollis liminatans + notes: > + Confirmed hgcAB+ mercury methylator. Demonstrated methylmercury production in pure culture. + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + methylation rates vary inherently among hgcAB+ methanogens but that several species are + capable of MeHg production at rates that rival those of the better-know Hg-methylating + sulfate- and iron-reducing bacteria + explanation: Documents mercury methylation capability of Methanofollis liminatans +- taxon_term: + preferred_term: Methanosphaerula palustris + term: + id: NCBITaxon:521012 + label: Methanosphaerula palustris + notes: > + Confirmed hgcAB+ mercury methylator. Demonstrated methylmercury production in pure culture. + functional_role: + - CROSS_FEEDER + evidence: + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + methylation rates vary inherently among hgcAB+ methanogens but that several species are + capable of MeHg production at rates that rival those of the better-know Hg-methylating + sulfate- and iron-reducing bacteria + explanation: Documents mercury methylation capability of Methanosphaerula palustris +ecological_interactions: +- name: Mercury Methylation by hgcAB+ Organisms + description: > + Both bacterial and archaeal community members carry hgcA/hgcB genes enabling conversion of + inorganic mercury (Hg(II)) to methylmercury (MeHg). Methanogenic archaea have been shown to + methylate mercury at rates rivaling those of the better-known sulfate- and iron-reducing + bacteria. This process is of major environmental concern as methylmercury bioaccumulates + through aquatic food webs. + interaction_type: COMMENSALISM + metabolites: + - preferred_term: methylmercury + term: + id: CHEBI:30785 + label: methylmercury(1+) + notes: Toxic organomercury compound produced by hgcAB+ organisms from inorganic mercury + biological_processes: + - preferred_term: mercury methylation + term: + id: GO:0018636 + label: methylmercury biosynthetic process + evidence: + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + Methanogenesis has been linked to Hg methylation in several natural habitats where + methylmercury production incurs risk to people and ecosystems + explanation: Documents the link between methanogenesis and mercury methylation + - reference: PMID:29636434 + supports: SUPPORT + evidence_source: IN_VITRO + snippet: > + methylation rates vary inherently among hgcAB+ methanogens but that several species are + capable of MeHg production at rates that rival those of the better-know Hg-methylating + sulfate- and iron-reducing bacteria + explanation: Documents mercury methylation rates by methanogenic archaea +- name: Heavy Metal Resistance + description: > + 27 of 28 MAGs from EFPC sediment contained either putative heavy metal resistance genes or + ATPase efflux pump genes, reflecting strong selective pressure from chronic mercury + contamination in the creek. This widespread resistance enables community persistence in a + heavily contaminated environment. + interaction_type: COMMENSALISM + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: 27 of the 28 MAGs contained either putative heavy metal resistance genes or ATPase efflux pump genes + explanation: Documents near-universal heavy metal resistance in EFPC sediment community +- name: Selenium Assimilatory Metabolism + description: > + 17 of 28 MAGs from EFPC sediment contained traits for selenium assimilatory metabolism, + suggesting an important role for selenium cycling in this mercury-contaminated environment. + Selenium can interact with mercury biogeochemistry through formation of mercury-selenium + complexes. + interaction_type: COMMENSALISM + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: 17 of the 28 MAGs contained traits for Se-assimilatory metabolism + explanation: Documents selenium metabolism traits across EFPC sediment MAGs +environmental_factors: +- name: Mercury Contamination + value: elevated + description: > + East Fork Poplar Creek has been contaminated with mercury from upstream sources at the Y-12 + National Security Complex, part of the Oak Ridge Reservation. This represents decades of + chronic mercury contamination from historical weapons production. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents mercury contamination in EFPC +- name: Sediment Depth + value: 0-3 cm and 9-12 cm + unit: cm + description: > + Two sediment core sections were sampled for metagenomic analysis, representing surface (0-3 cm) + and subsurface (9-12 cm) sediment layers with potentially different redox conditions and + microbial community composition. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: IN_VIVO + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents sediment sampling depths for EFPC metagenomics +associated_datasets: +- name: EFPC Sediment Metagenome + dataset_type: METAGENOME + repository: NCBI_BIOPROJECT + accession: PRJNA670906 + url: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA670906 + description: > + Shotgun metagenomic sequencing of two sediment core sections from East Fork Poplar Creek, + yielding 28 metagenome-assembled genomes of novel prokaryotic species. + evidence: + - reference: PMID:33927032 + supports: SUPPORT + evidence_source: COMPUTATIONAL + snippet: > + We sequenced two metagenomes of sediments from the East Fork Poplar Creek in the Oak Ridge + Reservation (Oak Ridge, TN), a natural stream that has been contaminated with Hg from upstream + sources, and we reconstructed 28 metagenome-assembled genomes of novel prokaryotic species + explanation: Documents the metagenome sequencing and MAG reconstruction from EFPC sediment