Add 7 more Banfield post-2020 community entries (round 3)#39
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- CommunityMech:000239 Thiocyanate Afipia/Thiobacillus bioreactor community (Huddy et al. 2021 Frontiers Microbiol, PMID:33897653) - 790-day SCN- bioreactor enrichments; molasses removal selects autotrophic Afipia variant with novel thiocyanate desulfurase + CBB cycle. - CommunityMech:000240 Infant gut strain persistence and maternal seeding community (Lou et al. 2021 Cell Rep Med, PMID:34622230) - 22 infants over 1 year; 17 mother-infant pairs; maternal Bacteroides/Bifidobacterium strains persist; surface adhesion, Fe acquisition, carbohydrate degradation. - CommunityMech:000241 Rifle aquifer bioanode EET community (Arbour et al. 2020 Frontiers Microbiol, PMID:32849356) - 4-year MXC enrichments; novel Geobacter sp. with 72 multiheme cytochromes dominates; broad EET diversity. - CommunityMech:000242 Groundwater Elusimicrobia diverse-metabolism community (Meheust et al. 2020 ISME J, PMID:32681159) - 94 genomes, 12 clades; groundwater clades show heterotrophic/autotrophic versatility and Rnf acetogenesis; novel nitrogenase paralog with radical SAM cluster. - CommunityMech:000243 Ngawha geothermal acidic-spring Hg cycling community (Gionfriddo et al. 2020 Appl Environ Microbiol, PMID:32414793) - ultrahigh Hg (up to 16,000 ng/L dissolved); diverse S/Fe cyclers, Hg/As-resistant bacteria, thermo/acidophilic archaea drive Hg methylation/demethylation/ reduction. - CommunityMech:000244 Anammox bioreactor DNRA destabilization community (Keren et al. 2020 Microbiome, PMID:31980038) - DNRA bacteria outcompete anammox; core members can be detrimental during destabilization. - CommunityMech:000245 Avena rhizosphere/detritusphere niche-succession community (Nuccio et al. 2020 ISME J, PMID:31953507) - four functional guilds with substrate-specific specialization; functional succession outpaces compositional change. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Pull request overview
Adds 7 curated microbial community YAML records (CommunityMech:000239–000245) and their corresponding PubMed reference cache files, continuing the Banfield post-2020 curation thread from PRs #36 and #37. Records span engineered bioreactors (thiocyanate, anammox, bioanode EET), groundwater Elusimicrobia, geothermal mercury cycling, infant gut strain persistence, and rhizosphere niche succession.
Changes:
- Seven new
kb/communities/*.yamlentries with taxonomy, ecological interactions, environmental factors, and evidence snippets validated against cached PubMed abstracts. - Seven new
references_cache/PMID_*.mdfiles mirroring PubMed abstracts for the cited references. - Continues curation conventions from PRs #36/#37 (snippets are whitespace-normalized substrings of the corresponding cache; ASCII-only).
Reviewed changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
| kb/communities/Thiocyanate_Afipia_Thiobacillus_Bioreactor_Community.yaml | CommunityMech:000239 — SCN- bioreactor selection (PMID:33897653) |
| kb/communities/Infant_Gut_Strain_Persistence_Maternal_Community.yaml | CommunityMech:000240 — infant gut + maternal seeding (PMID:34622230) |
| kb/communities/Rifle_Aquifer_Bioanode_EET_Community.yaml | CommunityMech:000241 — Rifle bioanode EET (PMID:32849356) |
| kb/communities/Groundwater_Elusimicrobia_Diverse_Metabolisms.yaml | CommunityMech:000242 — groundwater Elusimicrobia (PMID:32681159) |
| kb/communities/Ngawha_Geothermal_Mercury_Cycling_Community.yaml | CommunityMech:000243 — geothermal Hg cycling (PMID:32414793) |
| kb/communities/Anammox_Bioreactor_DNRA_Destabilization_Community.yaml | CommunityMech:000244 — anammox/DNRA destabilization (PMID:31980038) |
| kb/communities/Avena_Rhizosphere_Detritusphere_Niche_Succession.yaml | CommunityMech:000245 — Avena rhizo/detritusphere guilds (PMID:31953507) |
| references_cache/PMID_33897653.md, PMID_34622230.md, PMID_32849356.md, PMID_32681159.md, PMID_32414793.md, PMID_31980038.md, PMID_31953507.md | Cached PubMed abstracts backing the snippets in the seven community files |
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- community_category: DIET was misused as "dietary" in the infant-gut curation; the schema enum DIET means "Direct Interspecies Electron Transfer". Switch both infant-gut entries to OTHER (the previously merged Bifidobacterium_Ruminococcus file is corrected in the same commit). - Anammox bioreactor: remove the redundant COMMENSALISM interaction "DNRA Bacteria Associated with Anammox Core" — the negative impact on anammox is already captured by the COMPETITION interaction above it, and COMMENSALISM (+/0) doesn't fit a relationship described as detrimental. - Avena rhizosphere/detritusphere: consolidate the four NCBITaxon:2-mapped guild taxonomy entries (which carried no taxonomic information) into a single decomposer-community taxonomy entry; the four substrate-specific guilds remain documented as community-level interactions. - Schema: extend MetalElementEnum with MERCURY (CHEBI:16793) so mercury- cycling communities can populate metals_present rather than encoding the metal only in free-text metal_notes. Ngawha geothermal community now lists MERCURY and uses metal_relevance: PRIMARY. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
Adds 7 more microbial community records (CommunityMech:000239–000245) curated from the 2020–2021 Banfield-lab post-2020 candidate list, continuing the work in PRs #36 and #37.
Test plan
just validatepasses on all 7 community filesjust validate-termspasses on all 7 community files🤖 Generated with Claude Code