Wire 2 more orphan caches into existing communities (Stordalen, CPR) (#61)

* Wire 2 more orphan caches into existing communities

- Stordalen_Mire_Methylotrophic_Methanogenesis_Community: add the
  Singleton/Tyson 2018 Nature permafrost paper (PMID:30013118) as
  orthogonal supporting evidence. Same Stordalen Mire thaw gradient,
  same site, and the 1,529-MAG genome-resolved catalog directly
  backs the genome-resolved-microbiome framing of this community,
  plus the abstract's mention of "novel syntrophic relationships"
  supports the SYNTROPHY interaction.
- Episymbiotic_CPR_DPANN_Groundwater_Community: add Tian et al. 2020
  Microbiome ("Small and mighty: adaptation of superphylum
  Patescibacteria to groundwater environment", PMID:32252814) as
  orthogonal CPR taxonomic backing. Genome-resolved characterization
  of the same Patescibacteria superphylum this community describes,
  also in groundwater.

Both papers were orphan caches not cited by any community before.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* Address Copilot review on PR #61

- Stordalen_Mire: fix two attribution + scope errors flagged by
  Copilot.
  - "Singleton/Tyson 2018" -> "Woodcroft et al. 2018" (Woodcroft is
    first author; Tyson is last/PI).
  - Drop the "same Stordalen Mire" claim in both explanations - the
    abstract describes the thaw gradient generically and does not
    name Stordalen Mire (that's in the paper body). Downgrade to
    PARTIAL and explicitly note the gap in scope.
- Episymbiotic_CPR_DPANN_Groundwater: replace the over-short
  "superphylum Patescibacteria" snippet with a longer verbatim
  excerpt that links Patescibacteria to groundwater wells via 16S
  amplicon + metagenomic sequencing: "wells over time, we sequenced
  the 16S rRNA gene of 214 samples as well as the metagenomes of 12
  representative wells to identify features unique to the
  Patescibacteria". Explanation rewritten to match what the snippet
  actually supports.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: realmarcin

kb/communities/Episymbiotic_CPR_DPANN_Groundwater_Community.yaml

@@ -40,6 +40,15 @@ taxonomy:
     snippet: The pristine sites, which serve as local sources of drinking water,
       contained up to 31% CPR bacteria
     explanation: Supports CPR membership and high relative abundance.
+  - reference: PMID:32252814
+    supports: SUPPORT
+    evidence_source: COMPUTATIONAL
+    snippet: wells over time, we sequenced the 16S rRNA gene of 214 samples as well
+      as the metagenomes of 12 representative wells to identify features unique to
+      the Patescibacteria
+    explanation: Tian et al. 2020 ("Small and mighty") characterize Patescibacteria
+      via 16S amplicon + metagenomic sequencing of groundwater wells - directly anchors
+      the groundwater Patescibacteria/CPR framing of this community.
 - taxon_term:
     preferred_term: groundwater DPANN archaea
     term:

kb/communities/Stordalen_Mire_Methylotrophic_Methanogenesis_Community.yaml

@@ -46,6 +46,15 @@ taxonomy:
     evidence_source: IN_VIVO
     snippet: across all stages of a permafrost thaw gradient in Stordalen
     explanation: Supports the palsa-bog-fen thaw-gradient sampling context.
+  - reference: PMID:30013118
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: metagenomic sequencing of 214 samples from a permafrost thaw gradient
+      to recover 1,529 metagenome-assembled genomes
+    explanation: Woodcroft et al. 2018 Nature paper establishes a 1,529-MAG genome-resolved
+      catalog from a permafrost thaw gradient. Partial because the abstract describes
+      the gradient generically rather than naming Stordalen Mire specifically - that site
+      identification is in the paper body, not the abstract.
 - taxon_term:
     preferred_term: Stordalen Mire methanogenic archaea
     term:
@@ -129,6 +138,15 @@ ecological_interactions:
     evidence_source: COMPUTATIONAL
     snippet: co-occurrence of methylotrophy throughout
     explanation: Supports methylotrophy as a co-occurring methanogenesis mode.
+  - reference: PMID:30013118
+    supports: PARTIAL
+    evidence_source: COMPUTATIONAL
+    snippet: Microbial and geochemical data highlight lineages that correlate with
+      the production of greenhouse gases and indicate novel syntrophic relationships
+    explanation: Woodcroft et al. 2018 establish novel syntrophic relationships and
+      lineage-greenhouse-gas correlations in a permafrost thaw gradient, supporting
+      the SYNTROPHY framing of methanogenic methylotrophy at the community level.
+      Partial because the abstract does not name Stordalen Mire specifically.
 - name: Bacterial Anaerobic Methylotrophy
   description: Bacterial MAGs encode and express anaerobic methylotrophic
     potential across Stordalen Mire, indicating a bacterial route for processing