Legal full-text access ladder (Unpaywall/CORE/author-request) for #183 (#189)

* Add legal full-text access ladder (Unpaywall/CORE/author-request) for #183

scripts/fulltext_access.py: given a PMID/DOI, tries in order of legality+cost —
Europe PMC OA (fullTextXML) -> Unpaywall best OA location (free) -> CORE (needs
$CORE_API_KEY, free for public-research orgs) -> and if none, prints an
author-request email draft. No gray-area sources (Sci-Hub excluded by design).
Verified: OA paper -> europepmc_oa URL; closed-access paper -> NO_LEGAL_OA +
author-request draft.

Wires into the add-growth-conditions skill workflow (step 3) so closed-access
records (the #183 residual) get a legal access attempt + a ready author-request
instead of just "paywalled, skip". Directly informed by the deep-research report
on nonprofit OA access.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* Run full-text access ladder over the #183 residual + CrossRef author fallback

Ran scripts/fulltext_access.py over the 52 records lacking growth conditions:
- 30/52 have a legal OA copy — 17 NEWLY accessible via Unpaywall (green/gold OA
  the earlier Europe-PMC-only sweep never checked), 13 already-seen europepmc_oa
  (natural/endosymbiont/computational — no cultivation conditions to gain).
- 22 have no legal OA -> author-request email drafts in reports/author_requests/.
Summary + lists in reports/fulltext_access_183.md.

Also: add a CrossRef title/author fallback to the author-request draft so DOI-only
records not in Europe PMC (e.g. older or in-press DOIs) still get a populated,
send-ready request instead of an empty template.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* Enrich 6 records from OA copies recovered via the access ladder (#183)

Applied the access ladder to the 9 cultivable records among the 17 Unpaywall
hits; 6 gained real growth conditions from OA full text the earlier
Europe-PMC-only sweep had missed:
- 000144 Altered Schaedler Flora — BHI/Schaedler's+serum, anaerobic, gnotobiotic (OUP PDF)
- 000147 Trichodesmium/Alteromonas — YBC-II seawater, 26C, 14:10 light (PMC mirror)
- 000098 Watermelon SynCom8 — NB medium, 37C, 170 rpm, greenhouse pots (BMC PDF)
- 000139 Aalborg EBPR — wastewater sludge + CONTINUOUS BioDenipho plant (OUP mirror)
- 000043 Maize root — 1/2 MS agar gnotobiotic, 30C, pH 6.0, 16:8 light (PMC mirror)
- 000075 Trichoderma lactate — Mandels medium + FED_BATCH membrane bioreactor (EPFL PDF)
All source-backed with verbatim evidence snippets; validate + validate-terms pass.
3 no-change (278/284/292): Unpaywall "OA" was a false positive (DOI resolver /
repository metadata page, not real full text).

Also harden try_unpaywall: reject a best_oa_location that is just the doi.org
resolver (Unpaywall marks some Elsevier bronze/hybrid records is_oa but the
location redirects to the paywall) — verified it now returns NO_LEGAL_OA for
those instead of a false ACCESS.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* Deep legal access sweep + author-request package for the 22 paywalled residuals

scripts/access_sweep.py — goes one layer past the per-record ladder for the
NO_LEGAL_OA residuals: queries OpenAlex (ALL oa locations, not just Unpaywall's
single best_oa_location) + the bioRxiv/medRxiv API (catches 2025+ 10.64898-prefix
preprints OpenAlex still lags on) + CORE when $CORE_API_KEY is set. Emits
reports/missing_pdfs.md: recovered OA URLs where any exist, else the publisher
landing URL as a last-resort pointer for a curator with institutional access.
Result: 1/22 recovered (000281 bioRxiv preprint — OA but Cloudflare-gated to
bots), 21/22 genuinely paywalled with landing URLs listed. Sci-Hub and other
gray-area mirrors deliberately excluded (sibling CultureMech gates them off too).

scripts/author_request_index.py — consolidates the 22 author-request drafts into
reports/author_requests_index.md with resolved title/journal/likely-corresponding
author/landing URL. Corresponding-author emails are NOT machine-resolvable (they
live only in the paywalled full text; CrossRef/EPMC don't expose them), so the
package is built for a human to open each landing URL, grab the email, and send.
Nothing is sent by this script.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* Enrich 000281 (Infant-gut Prebiotic-response SynCom) from bioRxiv OA full text

The access sweep recovered this record's source as an OA bioRxiv preprint
(doi:10.64898/2026.05.29.728681); added a growth_media block from the Methods:
- eGAM (enhanced Gifu Anaerobic Medium) for routine culturing, adjusted M9
  minimal medium for metabolic labelling; 37 C; anaerobic (5% CO2, 5% H2, N2
  balance) in a Coy anaerobic vinyl chamber; 48 h strain cultures pooled into
  the six-member SynCom (P. vulgatus, B. breve, B. infantis, E. coli,
  L. gasseri, R. gnavus), abundance-equalised to OD 0.2 at 5 h.
Three verbatim IN_VITRO evidence snippets. Schema + terms validation pass.

Clears the one open item from reports/missing_pdfs.md (the sole OA-recovered
residual); the remaining 21 stay genuinely paywalled.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

* Add undefined-communities tracking log (excluded from KB, logged separately)

Policy: kb/communities/ holds only defined communities. Undefined ones
(donor-derived faecal/environmental inocula, enrichments, unresolved consortia)
are not added to the resource but tracked in reports/undefined_communities.md so
the observation + cultivation conditions are preserved.

First entry: the donor-derived infant faecal fermentation from the 000281 paper
(Cryptobiotix bioreactors, M0017 medium, 5 g/L prebiotics, 37 C / 24 h anaerobic)
— the undefined backdrop to the defined SynCom already curated as 000281.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

Author: realmarcin

.claude/skills/add-growth-conditions/skill.md

@@ -49,9 +49,15 @@ numerics are floats.
 2. Fetch the abstract — Europe PMC core:
    `…/webservices/rest/search?query=EXT_ID:<pmid>%20AND%20SRC:MED&format=json&resultType=core`
    (DOI: `query=DOI:"<doi>"`).
-3. If open-access, fetch Methods from full text: get `pmcid` from the core
-   result, then `…/webservices/rest/<PMCID>/fullTextXML` (`curl --compressed`).
-   Optionally WebSearch/WebFetch for the Methods if not OA.
+3. Locate legal full text via the access ladder — `scripts/fulltext_access.py
+   --pmid <pmid>` (or `--doi <doi>`). It tries, in order: **Europe PMC OA**
+   (`fullTextXML`) → **Unpaywall** best OA location (free) → **CORE** (set
+   `CORE_API_KEY`) → and if none, prints an **author-request email draft**.
+   - `ACCESS <method> <url>` → fetch that URL for the Methods (`curl --compressed`
+     for the EPMC XML).
+   - `NO_LEGAL_OA` → the paper is closed-access with no legal OA copy; use only
+     abstract-level conditions, and surface the author-request draft to the
+     curator. **Never** use Sci-Hub or other gray-area sources.
 4. Extract conditions → one `growth_media` entry (+ `cultivation_setup` if a
    defined reactor). Insert as new top-level keys (append near end of file);
    keep existing content byte-for-byte.

kb/communities/Aalborg_East_Full_Scale_EBPR_Community.yaml

@@ -293,3 +293,46 @@ associated_datasets:
       The set of nonredundant contigs was uploaded to the MG-RAST v2 server
       (accession number: 4463936.3) and used in local database searches.
     explanation: Links this community record to the public MG-RAST metagenome resource.
+growth_media:
+- name: domestic wastewater (full-scale EBPR activated sludge)
+  inoculum_source: activated sludge from the aeration tank at Aalborg East WWTP, Denmark
+  preparation_notes: Municipal EBPR plant fed mainly domestic wastewater; influent phosphorus
+    10-20 mg P/L with >95% removal and effluent below 0.5 mg P/L. No incubation temperature,
+    pH, or defined atmosphere reported for this full-scale in situ community.
+  evidence:
+  - reference: PMID:22170425
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: Activated sludge was taken from the aeration tank at Aalborg East WWTP, Denmark
+      (57.044565° N, 10.047598° E) on 4 August 2009.
+    explanation: Identifies the wastewater medium and sampling of activated sludge from the
+      aeration tank.
+  - reference: PMID:22170425
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: The plant had stable EBPR performance for several years prior to the time of sampling
+      removing >95% of the incoming P (10-20 mg P l-1) resulting in effluent concentrations
+      below 0.5 mg P l-1.
+    explanation: Reports the influent and effluent phosphorus concentrations of the treated
+      wastewater.
+cultivation_setup:
+- cultivation_mode: CONTINUOUS
+  system_type: BIOREACTOR_UNSPECIFIED
+  instrument_detail: Full-scale BioDenipho activated sludge plant with an anaerobic tank and
+    a tank alternating between denitrifying anoxic and nitrifying oxic conditions.
+  notes: Full-scale municipal EBPR wastewater treatment plant serving 100 000 person equivalents;
+    no temperature, HRT, SRT, pH, or dissolved-oxygen setpoints are reported in the source.
+  evidence:
+  - reference: PMID:22170425
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: The plant has a biodenipho configuration, which includes an anaerobic tank and a
+      tank with alternating denitrifying anoxic and nitrifying oxic conditions.
+    explanation: Describes the reactor configuration and alternating process zones of the
+      full-scale system.
+  - reference: PMID:22170425
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: The plant treats mainly domestic wastewater and serves 100 000 person equivalents
+      with an average load of 45 000 person equivalents.
+    explanation: Establishes the full-scale continuous municipal wastewater treatment operation.

kb/communities/Altered_Schaedler_Flora_Gnotobiotic_Mouse_Community.yaml

@@ -204,3 +204,39 @@ associated_datasets:
     evidence_source: COMPUTATIONAL
     snippet: GenBank accession no.
     explanation: Supports the table of genome accessions for the ASF members.
+growth_media:
+- name: brain heart infusion medium or Schaedler's medium supplemented with bovine serum
+  atmosphere: ANAEROBIC
+  inoculum_source: mouse-derived bacteria maintained in gnotobiotic mice bred in isolator facilities
+  preparation_notes: The eight ASF members are cultivated in vitro in complex media (BHI plus serum
+    or Schaedler's medium plus serum); only the two lactobacilli grow aerobically, while the
+    remaining members are obligate anaerobes, and no defined medium exists for the EOS members
+    (ASF356, 492, 500, 502). In vivo the community is maintained in gnotobiotic mice continually
+    bred in isolator facilities.
+  evidence:
+  - reference: PMID:26323627
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: each of the ASF is cultivable in complex media including brain heart infusion medium
+      or Schaedler's medium supplemented with bovine serum
+    explanation: Names the complex media (BHI and Schaedler's medium, serum-supplemented) used to
+      culture the ASF members in vitro.
+  - reference: PMID:26323627
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: consisted of eight anaerobic bacteria of which only the two lactobacilli could grow
+      aerobically
+    explanation: Supports the anaerobic cultivation atmosphere for the ASF members.
+  - reference: PMID:26323627
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: all members of the ASF community can be cultivated in vitro (e.g., BHI plus serum or
+      Schaedler's medium plus serum)
+    explanation: Confirms all members are serum-supplemented complex-media cultivable with no defined
+      medium for the EOS members.
+  - reference: PMID:26323627
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: stably passed through multiple generations (at least 15 years or more by the authors)
+      in gnotobiotic mice continually bred in isolator facilities
+    explanation: Supports gnotobiotic isolator husbandry of the host that maintains the community.

kb/communities/Infant_Gut_Prebiotic_Response_SynCom.yaml

@@ -184,3 +184,40 @@ ecological_interactions:
     evidence_source: IN_VITRO
     snippet: with lactate exerting species-specific inhibitory effects independent of bulk pH changes
     explanation: Fermentation-product (lactate) driven, species-specific competitive inhibition beyond pH.
+growth_media:
+- name: eGAM (enhanced Gifu Anaerobic Medium); adjusted M9 minimal medium for metabolic labelling
+  temperature: '37'
+  temperature_unit: °C
+  atmosphere: ANAEROBIC
+  headspace_gas: 5% CO2, 5% H2, balanced with N2 (Coy anaerobic vinyl chamber)
+  incubation_time: '48'
+  incubation_time_unit: h
+  vessel_type: Coy anaerobic vinyl chamber; individual 48 h strain cultures pooled into the SynCom
+  inoculum_source: Six-member defined SynCom — Phocaeicola vulgatus, Bifidobacterium breve,
+    B. infantis, Escherichia coli, Lactobacillus gasseri, Ruminococcus gnavus
+  preparation_notes: Enhanced GAM (eGAM) was used for all routine culturing (adjusted M9 minimal
+    medium for metabolic labelling and secondary-metabolite production); exact medium composition
+    is given in the paper's supplementary Excel sheet. For SynCom assembly, baseline growth rates
+    were measured in eGAM+glucose (1:100 dilution from a two-day culture); strains were
+    abundance-equalised to reach OD 0.2 at 5 h, and each 48 h culture was centrifuged (3000 x g,
+    10 min, RT) and resuspended in fresh medium before pooling.
+  evidence:
+  - reference: doi:10.64898/2026.05.29.728681
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: All bacteria were grown under anaerobic conditions (5% CO2, 5% H2, balanced with N2)
+      using an anaerobic vinyl chamber (Coy Laboratory Products) at 37°C.
+    explanation: SynCom cultivation atmosphere (anaerobic gas mix), chamber, and temperature.
+  - reference: doi:10.64898/2026.05.29.728681
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 'As medium either eGAM (enhanced GAM; for all culturing if not indicated differently)
+      or adjusted M9 minimal medium (for metabolic labelling and secondary metabolite production)
+      was used'
+    explanation: Growth medium — eGAM for routine culturing, adjusted M9 minimal for labelling.
+  - reference: doi:10.64898/2026.05.29.728681
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: we constructed a six-member simplified defined microbial community (referred to as
+      SynCom; see Methods) comprising Phocaeicola vulgatus
+    explanation: Establishes the defined six-member SynCom cultured under these conditions.

kb/communities/Maize_Root_Simplified_Community.yaml

@@ -531,3 +531,57 @@ environmental_factors:
 metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements
+growth_media:
+- name: 1/2 Murashige and Skoog (MS) agar gnotobiotic maize-root system (members precultured
+    on 0.1x TSA / tryptic soy broth)
+  temperature: '30'
+  temperature_unit: °C
+  ph: '6.0'
+  light_regime: 16 h light (day) / 8 h dark (night)
+  inoculum_source: Maize root-derived bacterial isolates obtained by host-mediated selection
+  vessel_type: Glass test tube (16 x 150 mm) double-tube gnotobiotic chamber (root assembly);
+    9-cm Petri dish (seed germination); pots in a plant growth chamber (soil-grown plants)
+  preparation_notes: 'Community members were streaked on 0.1x TSA plates (30 °C, 24-48 h)
+    and precultured in tryptic soy broth (TSB) shaken at 30 °C before inoculation. The
+    simplified synthetic community was assembled on the roots of axenic maize seedlings
+    grown in sterile 1/2 MS agar [0.8% (wt/vol), pH adjusted to 6.0 to simulate soil pH]
+    within double-tube gnotobiotic chambers. Surface-sterilized seeds were germinated at
+    30 °C in the dark for ~50-55 h. Soil-grown plants were kept in a plant growth chamber
+    at 25 °C with 54% relative humidity under a 16 h light / 8 h dark cycle.'
+  evidence:
+  - reference: PMID:28275097
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The bacterial strains for inoculation were streaked on 0.1× TSA plates and incubated
+      at 30 °C for 24–48 h. Then, a single colony of each strain was inoculated in 5 mL of
+      tryptic soy broth (TSB) and shaken at 30 °C overnight.
+    explanation: Bacterial member preculture medium (0.1x TSA / TSB) and incubation temperature
+      (30 °C).
+  - reference: PMID:28275097
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: the resulting seedlings were grown in sterile 1/2 Murashige and Skoog (MS) agar
+      [0.8% (wt/vol)] (adjusting the pH to 6.0 to simulate the pH of soil
+    explanation: MS agar cultivation substrate and pH (6.0) for the gnotobiotic root-assembly
+      system.
+  - reference: PMID:28275097
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: A seed inoculated with bacteria was put into a glass test tube (16 × 150 mm) containing
+      20 mL of 1/2 MS agar
+    explanation: Double-tube gnotobiotic chamber vessel used to grow the axenic maize seedlings
+      on which the community assembles.
+  - reference: PMID:28275097
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: 10 seeds, embryo side up, were placed in a Perti dish (9-cm diameter) filled with
+      7 mL of sterile water and incubated at 30 °C in the dark until the seeds germinated (usually
+      after 50–55 h).
+    explanation: Seed germination conditions (30 °C, dark, ~50-55 h) preceding community inoculation.
+  - reference: PMID:28275097
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: 'the pots were placed in a plant growth chamber under the following conditions:
+      16 h of light (day) and 8 h of dark (night), 25 °C, and a relative humidity of 54%.'
+    explanation: Plant (Zea mays) growth chamber photoperiod, temperature, and humidity for
+      soil-grown host plants.

kb/communities/Trichoderma_Lactate_Platform.yaml

@@ -257,3 +257,66 @@ related_ingredients:
 metals_present: []
 metal_relevance: INCIDENTAL
 metal_notes: Metal/REE detected via environmental factor measurements
+growth_media:
+- name: Mandels medium
+  temperature: '30'
+  temperature_unit: °C
+  ph: '6.0'
+  inoculum_size: '5'
+  inoculum_unit: '% v/v'
+  vessel_type: membrane-aerated bioreactor
+  preparation_notes: >-
+    Reactor autoclaved with microcrystalline cellulose or pretreated beechwood; remaining
+    medium components added at inoculation. Three-step sequential inoculation: T. reesei
+    (5% v/v), then the lactic acid bacteria to OD600 0.5 after 48 h, then the
+    lactate-fermenting anaerobe (5% v/v) after a further 48 h. The membrane was
+    continuously flushed with air (140 mL/min per liter liquid phase), generating an
+    aerobic-to-anaerobic oxygen gradient. pH controlled with 4 N phosphoric acid / 4 M
+    sodium hydroxide.
+  evidence:
+  - reference: PMID:32855308
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The temperature was set to 30°C and the pH to 6.0 using 4 N phosphoric acid
+      and 4 M sodium hydroxide.
+    explanation: Methods specify the reactor setpoints (30°C, pH 6.0) for the lactate-platform
+      coculture.
+  - reference: PMID:32855308
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The remaining medium components were added when the reactor was inoculated
+      with 5% (v/v) T. reesei. After 48 hours, the lactic acid bacteria were inoculated
+      to an optical density (OD600) of 0.5 by centrifuging the cells at 3000 rpm for 10 min
+      and suspending them in fresh Mandels medium.
+    explanation: Identifies Mandels medium as the reactor medium and the sequential inoculum
+      sizes used in the platform.
+cultivation_setup:
+- cultivation_mode: FED_BATCH
+  system_type: MEMBRANE_BIOREACTOR
+  instrument_detail: Stirred-tank fermenter modified with a tubular polydimethylsiloxane
+    (PDMS) gas-transfer membrane for membrane aeration and oxygen-gradient generation.
+  manufacturer_model: Infors HT Multifors 2 / Labfors 5 (Switzerland)
+  working_volume: 2.7
+  working_volume_unit: L
+  operating_temperature: 30.0
+  operating_temperature_unit: °C
+  ph_controlled: true
+  notes: >-
+    Membrane-aerated bioreactor; 0.5 L (Multifors 2) and 2.7 L (Labfors 5) working volumes
+    used. Membrane continuously flushed with air at 140 mL/min per liter liquid phase to
+    create an aerobic-to-anaerobic oxygen gradient. Soluble substrates fed after LAB
+    inoculation (fed-batch).
+  evidence:
+  - reference: PMID:32855308
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The membrane bioreactors were based on Multifors 2 and Labfors 5 bioreactors
+      (Infors HT, Switzerland) with 0.5 and 2.7 liter working volume, respectively. Both
+      reactors were modified with a tubular polydimethylsiloxane (PDMS) membrane.
+    explanation: Defines the reactor hardware, manufacturer/models, and working volumes.
+  - reference: PMID:32855308
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: For fed-batch experiments, the feed solution was sterile filtered and fed at
+      a constant feeding rate.
+    explanation: Establishes fed-batch operating mode with constant-rate feeding.

kb/communities/Trichodesmium_Alteromonas_Marine_Consortium.yaml

@@ -277,4 +277,25 @@ metals_present:
 - IRON
 metal_relevance: SIGNIFICANT
 metal_notes: Iron acquisition is one inferred interaction axis in Trichodesmium-associated bacterial consortia.
+growth_media:
+- name: YBC-II
+  temperature: '26'
+  temperature_unit: °C
+  light_regime: 14:10 light:dark
+  light_intensity: '150'
+  light_intensity_unit: μmol m-2 s-1
+  vessel_type: 2 l polycarbonate baffled flask
+  preparation_notes: YBC-II is an artificial seawater medium for oceanic cyanobacteria (Chen et al.,
+    1996). Trichodesmium erythraeum IMS101 consortium enrichments grown with continuous shaking under
+    fluorescent light to avoid cell sedimentation; associated Alteromonas macleodii epibionts were
+    isolated from these Trichodesmium cultures on soft-agar RMP medium.
+  evidence:
+  - reference: PMID:28440800
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: Enrichments were grown in 1 l of YBC-II media (Chen et al., 1996) in 2 l polycarbonate
+      baffled flasks at 26 °C under a 14:10 light:dark cycle (150 μM m−2 s−1) with fluorescent
+      light. Enrichments were continuously shaken to avoid cell sedimentation.
+    explanation: Reports the seawater medium, temperature, light regime/intensity, vessel, and
+      shaking used to grow the Trichodesmium consortium enrichment.
 

kb/communities/Watermelon_Rhizosphere_Fusarium_SynCom8.yaml

@@ -81,3 +81,45 @@ related_ingredients:
       the SM of these strains, indicating metabolic cross-feeding potential among these species
     explanation: Names N-acetyl-L-serine as a verified cross-feeding metabolite in the simplified
       SynCom centered on Pseudomonas aeruginosa Q6.
+growth_media:
+- name: beef extract peptone broth (NB) medium
+  temperature: '37'
+  temperature_unit: °C
+  shaking_speed: '170'
+  shaking_speed_unit: rpm
+  inoculum_size: '0.1'
+  inoculum_unit: OD600
+  preparation_notes: SynCom members were each grown overnight in NB medium, then centrifuged and
+    re-suspended in sterile water to OD600 0.1 and mixed in equal volume (v/v) to establish the
+    SynCom. The SynCom was applied to ungrafted watermelon seedlings (cultivar Zaojia 8424) in
+    polypropylene pots filled with 600 g of non-sterile soil in a greenhouse (daytime 16 h at 30 °C,
+    night 8 h at 26 °C).
+  evidence:
+  - reference: PMID:38840214
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: each of the 16 core strains was inoculated in beef extract peptone broth (NB) medium
+      and incubated overnight at 37℃ at 170 rpm
+    explanation: Names the growth medium (NB), incubation temperature (37 °C) and shaking speed (170
+      rpm) used to culture the SynCom member strains.
+  - reference: PMID:38840214
+    supports: SUPPORT
+    evidence_source: IN_VITRO
+    snippet: The fermentation broth of each strain was centrifuged at 4000 × g for 5 min and re-suspended
+      in sterile water with OD600 adjusted to 0.1. The suspensions of the 16 strains were mixed in
+      equal volume (v/v) to establish the SynCom.
+    explanation: Gives the inoculum preparation and density (OD600 0.1) used to assemble and apply
+      the SynCom.
+  - reference: PMID:38840214
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: 'The pot experiments were run in a greenhouse (daytime: 16 h long at 30°C, night: 8 h
+      long at 26°C) located in Nanjing Agriculture University.'
+    explanation: Gives the greenhouse day/night temperature and photoperiod regime under which the
+      inoculated watermelon plants (and rhizosphere SynCom) were grown.
+  - reference: PMID:38840214
+    supports: SUPPORT
+    evidence_source: IN_VIVO
+    snippet: Each replicate was run in polypropylene pots filled with 600 g of dry, non-sterile soil
+      with no history of watermelon cultivation.
+    explanation: Describes the pot/soil cultivation vessel for the SynCom-inoculated watermelon plants.

reports/author_requests/000001_AMD_Acidophile_Heterotroph_Network.txt

@@ -0,0 +1,11 @@
+--- author-request draft ---
+To: <corresponding author of: P. L. Wichlacz, R. F. Unz, T. A. Langworthy>
+Subject: Request for Methods details — Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Aci
+
+Dear Author,
+
+I am curating an open, public microbial-community knowledge base and would like to cite your paper "Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Acidiphilium rubrum sp. nov.: Acidophilic Heterotrophic Bacteria Isolated from Acidic Coal Mine Drainage" (doi:10.1099/00207713-36-2-197). The abstract does not include the cultivation / Methods details I need (medium composition, temperature, pH, atmosphere, and the member strain identities). Could you share the relevant Methods/supplementary text, or a PDF? The extracted, source-attributed data would be published openly with full citation to your work.
+
+Thank you,
+CommunityMech curation team
+