Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditio
Provisional — an automated or curator check raised a specific concern and points reviewers here. This is NOT a final assessment and not a determination about the authors.
The main results reproduced, with only marginal, non-material deviations.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓The central claim held under reproduction
- 🟡Could not use the authors’ exact input data
- 🟡Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
PARTIAL reproduction of P. mercuritolerans sp. nov. (Robas Mora 2022) genome characterization. Core pipeline conclusions REPRODUCE: (a) novel-species ANI - fastANI 95.68% vs P. iranensis SWRI54 (paper 95.34-95.46%, both <96% threshold); (b) CDS count - Prokka 1.15.6 = 5491 and NCBI PGAP = 5554 vs paper's 5522 (within ~1%); (c) mer operon - merT/merC/merA/merB all present (Prokka, +merP; NCBI PGAP also merR), confirming the paper's central mercury-resistance claim by two independent annotations; (d) GC% 59.92 vs 60.07 (near-match). THREE figures do NOT match: genome length 6.247 vs 6.312 Mb and contigs 54 vs 192 (the public deposit is an NCBI-filtered version; raw reads were NEVER deposited - ENA read_run=0 - so the 192-contig raw SPAdes assembly is unreproducible), and 16S identity 99.61% vs the paper's 96.60% (our value is biologically consistent with ~95.7% ANI; the paper's 96.60% is implausibly low and is flagged as a possible reporting error). NOT attempted (out of scope): dDDH exact values (GGDC/TYGS proprietary web service), AAI, RAST/KEGG subsystems, and all wet-lab results (MALDI-TOF, FAME, plant assays, Hg MIC). All grades provisional; human reviewer signs off in AUDIT.md.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 54assessed: 2026-06-22 ⛓ db6531bf81ff
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-22
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-22no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: sonnetThe study tests whether the mercury-resistant rhizosphere strain SAICEUPSM^T (proposed as a novel species, Pseudomonas mercuritolerans) can protect Lupinus albus from mercury-induced oxidative stress and promote plant growth/phytostabilization in mercury-contaminated soils, while also characterizing the strain taxonomically.
- ★ Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress finding
- ★ SAICEUPSM^T inoculation significantly increases total plant weight, root weight, and leaf number under mercury stress compared to controls finding
- ★ SAICEUPSM^T inoculation significantly reduces mercury accumulation in plant shoots while root accumulation is unchanged finding
- ★ SAICEUPSM^T represents a new species, proposed as Pseudomonas mercuritolerans sp. nov., based on genomic (ANI, dDDH, AAI, TETRA) and phenotypic/chemotaxonomic thresholds below species-delineation cutoffs finding
- ★ SAICEUPSM^T exhibits plant growth promoting traits including siderophore production, IAA production, and ACC deaminase activity finding
- ★ SAICEUPSM^T genome contains a mercury resistance operon (merT, merC, merA, merB) explaining its phenotypic mercury tolerance mechanism
- ★ No virulence genes or transmissible antibiotic resistance mechanisms were identified in the SAICEUPSM^T genome, supporting its safety for agronomic use finding
- SAICEUPSM^T shows high resistance to multiple heavy metals (mercury, copper, chromium, nickel) as measured by minimum bactericidal concentration finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Greenhouse pot growth trial with biometric measurements | Lupinus albus var. Orden Dorado grown in mercury-contaminated Almadén mine soil (1,710 ppm) vs low-mercury control soil | SAICEUPSM^T rhizosphere inoculation vs non-inoculated control | Total weight, shoot weight, root weight, shoot length, root length, leaf number, secondary root number | — |
| Enzymatic activity assays (CAT, APX, SOD, GR) | Lupinus albus plant tissue | SAICEUPSM^T inoculation under mercury stress | Enzymatic activity levels (Kruskal-Wallis analysis) | — |
| Mercury content quantification | Lupinus albus shoot and root tissue | SAICEUPSM^T inoculation vs control, mercury-contaminated soil | Mercury concentration (μg/g) in shoot and root | — |
| Whole genome sequencing and comparative genomics (ANI, AAI, dDDH, TETRA, GBDP phylogeny) | SAICEUPSM^T bacterial isolate genome | none | Species delineation metrics against closest Pseudomonas relatives | — |
| 16S rRNA gene sequencing and similarity analysis | SAICEUPSM^T bacterial isolate | none | Percent sequence identity to closest type strains | — |
| Phenotypic and biochemical characterization (growth conditions, biochemical tests, MIC/MBC) | SAICEUPSM^T bacterial culture | Varying NaCl, pH, temperature, antibiotics, heavy metals | Growth range, biochemical reactions, MIC/MBC values | — |
| Fatty acid methyl ester (FAME) profiling | SAICEUPSM^T bacterial isolate | none | Fatty acid composition percentages | — |
| MALDI-TOF mass spectrometry protein fingerprinting | SAICEUPSM^T bacterial isolate | none | Peptide mass fingerprint compared to database | MALDI-TOF |
- ▲ Significant increase in total weight, root weight, and leaf number in SAICEUPSM^T-inoculated plants under mercury stress vs control p-value < 0.05
- ▼ Significant reduction in CAT, SOD, APX, and GR enzymatic response with SAICEUPSM^T inoculation p-value ≤ 0.001
- ▼ Significant decrease in mercury accumulation in shoot with inoculation (0.21 to 0.13 μg/g) p-value ≤ 0.001
- – No significant difference in root mercury accumulation between inoculated and control plants (10.06 vs 10.04 μg/g)
- – ANI, AAI, dDDH, and TETRA values against closest relative P. iranensis fall below species-differentiation thresholds ANI 95.34-95.47%, dDDH 61.5-61.9%, AAI 97.04-97.13%, TETRA 0.99%
- – IAA (auxin) production quantified 7.72 μg.ml-1
- – 16S rRNA gene similarity to closest relative P. iranensis SWRI54 96.60%
- – Strain shows high mercury bactericidal resistance 140 ppm MBC
- pvalue p < 0.05 (ANOVA/LSD for biometric parameters (total weight, root weight, leaf number))
- pvalue p ≤ 0.001 (Kruskal-Wallis test for enzymatic content (CAT, SOD, APX, GR))
- pvalue p ≤ 0.001 (Difference in shoot mercury content between inoculated and control plants)
- other ANI 95.34-95.47% (Average nucleotide identity vs P. iranensis SWRI54, below 95-96% species threshold)
- other dDDH 61.5-61.9% (DNA-DNA hybridization in silico vs closest relatives, below 70% species threshold)
- other AAI 97.04-97.13% (Average amino acid identity vs P. iranensis SWRI54)
- other 96.60% (16S rRNA gene identity vs P. iranensis SWRI54)
- other 140 ppm (Minimum bactericidal concentration of mercury for SAICEUPSM^T)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The paper used a greenhouse pot experiment comparing Lupinus albus plants grown with and without inoculation by strain SAICEUPSM^T in mercury-contaminated versus control soils. Biometric parameters (total weight, root weight, number of leaves) were analyzed by ANOVA with least significant difference (LSD) post-hoc comparison, oxidative-stress enzyme levels (CAT, SOD, APX, GR) were analyzed by Kruskal-Wallis, and mercury tissue content was compared between inoculated and non-inoculated conditions with a reported significance threshold. Results are reported as means with standard error bars and significance denoted by p-value thresholds rather than exact values.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| One-way ANOVA | Biometric parameters: total weight, root weight, number of leaves (Figure 2A-C) | — | not stated |
| Least significant difference (LSD) post-hoc test | Pairwise comparisons following ANOVA for biometric parameters (Figure 2 caption) | — | not stated |
| Kruskal-Wallis test | Enzymatic content: CAT, SOD, APX, GR (Figure 3A-D) | — | not stated |
| Statistical comparison (test not named) | Mercury accumulation in shoot/root tissue, inoculated vs. control (Table 5) | — | not stated |
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Biometric parameters were compared across groups using ANOVA followed by the least significant difference (LSD) post-hoc test.↳ Could also: A post-hoc method such as Tukey's HSD or a Bonferroni-adjusted comparison — These alternatives are often preferred over LSD when multiple pairwise comparisons are made, since they more directly control the family-wise error rate across all comparisons.
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Enzymatic response data (CAT, SOD, APX, GR) were analyzed with the Kruskal-Wallis test, a non-parametric approach suitable for small or non-normally distributed samples.↳ Could also: A non-parametric post-hoc test such as Dunn's test with multiplicity adjustment — Following an overall Kruskal-Wallis result, a dedicated post-hoc procedure can identify which specific group pairs differ while accounting for multiple comparisons.
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Significance was reported using threshold notation (e.g., p < 0.05, p ≤ 0.001) rather than exact p-values.↳ Could also: Reporting exact p-values — Exact values let readers evaluate the strength of evidence more precisely and support later meta-analytic use of the data.
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Variability in the figures and tables is presented as standard error (SEM).↳ Could also: Standard deviation (SD) or a 95% confidence interval — SD conveys the spread of the raw data directly, while a CI communicates the precision of the estimated group difference; either can complement SEM depending on the inferential point being emphasized.
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Differences between inoculated and control groups were reported primarily through p-values (e.g., Table 5 mercury content).↳ Could also: Reporting an effect size measure (e.g., mean difference with CI, Cohen's d, or eta-squared for the ANOVA) — Effect sizes provide a magnitude-of-difference metric that complements significance testing, particularly useful when comparing across studies or assessing biological relevance.
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Sample size and replicate structure for the greenhouse comparisons are not detailed in the presented text.↳ Could also: An a priori power analysis or explicit statement of the number of biological/technical replicates per group — Clarifying replicate numbers and power considerations helps readers assess how precisely the observed differences were estimated.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-36560952
Paper: Robas Mora et al. (2022) Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions. Front Microbiol 13:1032901. DOI 10.3389/fmicb.2022.1032901 · PMID 36560952 · PMCID PMC9763275.
Study type: Description of a novel bacterial species, Pseudomonas mercuritolerans sp. nov. (type strain SAICEUPSM / SAICEUPSMT). Combines wet-lab microbiology + chemotaxonomy + plant assays with a whole-genome sequencing + bioinformatic characterization.
Named code artifact (BRIEF): https://github.com/tseemann/prokka — a third-party genome-annotation tool (P16 path: applying an existing tool to the paper's own data is a valid reproduction).
Data availability (CRITICAL FINDING)
- BioProject PRJNA847155, BioSample SAMN28920853.
- Raw reads are NOT deposited. SRA/ENA report ZERO read runs for the
BioProject and for the BioSample (
result=read_run→ only header row; NCBI esearch db=sraPRJNA847155→ 0 hits). The paper states Illumina MiSeq 2×300 WGS but no FASTQ was released. - Only the assembled genome is public:
- GenBank assembly GCA_025706525.1 (ASM2570652v1), WGS prefix JAMSHA01, GenBank accession JAMSHA000000000, assembly level = contig.
- NOTE: NCBI re-annotated the deposit with PGAP, not the authors' Prokka. The FASTA (nucleotide contigs) is what we reproduce annotation on.
IN SCOPE (pipeline-derived, reproducible from the deposited genome)
| # | Reported result | Pipeline | How we reproduce |
|---|---|---|---|
| C1 | Genome length 6,312,264 bp | SPAdes assembly | seqkit stats on deposited GCA_025706525.1 FASTA |
| C2 | 192 contigs | SPAdes assembly | seqkit / count contigs |
| C3 | GC content 60.07% | assembly | seqkit GC% on deposited FASTA |
| C4 | 5,522 CDS | Prokka 1.13 | run Prokka on deposited FASTA, count CDS |
| C5 | ANI vs P. iranensis 95.34–95.46% | ANI | fastANI: target vs GCA_014268585 (SWRI54) |
| C6 | dDDH neighbours 61.5/61.7/60.8/59.7% | dDDH (GGDC) | fastANI as ANI proxy vs all 4 type strains (dDDH itself = web service, see out-of-scope) |
| C7 | 16S rRNA 96.60% identity to P. iranensis SWRI54 | 16S | barrnap extract 16S, blastn vs SWRI54 16S |
| C8 | mer operon genes merT, merC, merA, merB present | annotation | grep Prokka annotation / abricate |
Reference type strains (exact strains named in the paper's dDDH table):
- P. iranensis SWRI54 = GCA_014268585.2
- P. atacamensis M7D1 = GCA_004801935.1
- P. triticicola SWRI88 = GCA_019145375.1
- P. siliginis SWRI31 = GCA_019145195.1
OUT OF SCOPE (not pipeline-reproducible / external / wet-lab)
- SPAdes assembly from raw reads — reads not deposited (
data_unavailablefor the FASTQ layer). We verify the deposited assembly's stats instead and flag the read gap. - dDDH exact values — GGDC/TYGS is a proprietary web service (Genome BLAST Distance Phylogeny formula 2). We report a fastANI proxy and note dDDH itself was not recomputed. AAI (97.04–97.13%) likewise via web service — optional.
- RAST subsystems, KofamKOALA/KEGG, PathogenFinder, GBDP phylogeny tree — external web services / not the named pipeline.
- MALDI-TOF, fatty-acid (FAME) profile, plant growth-promotion assays, oxidative stress / mercury MIC, all wet-lab — out of scope.
Honesty notes
- C4 (CDS) is version-sensitive: Prokka 1.13 (2018) vs a current build can differ by tens–hundreds of CDS; also the deposit's NCBI may differ from authors' contigs only by sub-200bp filtering. Graded with tolerance, human to confirm.
- All grades are PROVISIONAL; a human reviewer decides match/mismatch.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
The two central claims reproduce robustly: ANI 95.68% (<96% species threshold) confirms the novel Pseudomonas species and the merT/merC/merA/merB operon is present by two independent annotations (Prokka + NCBI PGAP), with GC, CDS and ANI all within ~1%. The unreproducible figures — genome length and contig count — sit on the data-availability/preprocessing side: raw reads were never deposited, so only the NCBI-filtered assembly is public. One genuinely suspicious item is the paper's 16S identity of 96.60% vs our 99.61%, which is biologically implausible at ~95.7% ANI and most likely an authors' reporting error, but it does not affect the central conclusion. Overall a solid partial reproduction with explainable, mostly authors'/data-side deviations.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.