Geng integrity report: 'Micronutrient deficiency reshapes plant-microbe interaction networks' (BMC Plant Biology, 2025)

Academic fraud report · Geng Detector

Summary

This is a translated integrity assessment of the article by Jie Wu et al. published in BMC Plant Biology (DOI: 10.1186/s12870-025-06966-0). The overall verdict is highly suspicious (orange). Multiple serious methodological inconsistencies and internal contradictions are documented. First, the PCR amplification protocol is incoherent: the text cites Phusion High-Fidelity PCR Master Mix and Easy Taq polymerase with 10× Easy Taq Buffer in the same 30 μL reaction, an incompatible combination whose component volumes already exceed practical limits. Second, the abstract and results directly contradict each other regarding Mn and B deficiencies: the abstract claims a 15–30% Chao1 increase, whereas the results section reports significantly lower Chao1 and Simpson indices for fungal communities under Mn and B deficiency. Third, CuSO₄ reagent forms are inconsistently described (monohydrate vs pentahydrate). Fourth, the reported recovery of millions of 16S/ITS reads from a claimed sterile tissue-culture system, using a soil DNA kit without blank controls, raises contamination concerns. Image-level forensics were not feasible. Confidence is high for textual contradictions, moderate for the contamination inference.

Verdict

Highly suspicious. The manuscript contains multiple internal contradictions spanning the abstract, results, and methods that go beyond ordinary copy-editing errors and point to careless drafting, template reuse, or generated text not checked by the authors. A formal retraction request and a demand for raw data are warranted.

Key findings

Incompatible PCR recipe (Critical). Materials and methods simultaneously invoke Phusion® High-Fidelity PCR Master Mix and Easy Taq polymerase with 10× Easy Taq Buffer in one 30 μL reaction. The two systems are not interchangeable, and the listed component volumes (15 μL Master Mix + 3 μL buffer + 2.4 μL dNTPs + 2.4 μL primers + 0.3 μL Taq) already reach 23.1 μL before template and water, which is internally inconsistent.
Abstract–results contradiction (High). The abstract states that Mn, Mo, and B deficiencies increased microbial richness (Chao1 rise of 15–30%). The results section states that significantly lower Chao1 and Simpson values were observed for fungal communities under Mn and B deficiency. The two sections cannot both be true.
Reagent-description inconsistency (Moderate). The control treatment lists 0.10 µM CuSO₄·H₂O (monohydrate), whereas the Cu-deficient treatment mentions omission of CuSO₄·5H₂O (pentahydrate). The hydration state is inconsistent within the same paragraph.
"Sterile" system yields millions of microbial reads (Moderate–High). The authors claim a sterile tissue-culture system yet report 3,180,867 bacterial 16S and 3,462,115 fungal ITS high-quality reads, extracted with the DNeasy PowerSoil Kit (a kit designed for soil), with no presentation of negative/blank controls. The plausibility of these numbers, given a supposedly axenic system, is questionable and consistent with reagent or kit contamination.
Image forensics not applicable. The study is dominated by amplicon-sequencing and network analyses; no Western blots or microscopy images with raw pixel data are provided, so pixel-level duplication checks could not be performed. The risk of selective thresholding or OTU filtering is noted but unverified.

Evidence highlights

PCR volume arithmetic (as reported): 15 + 3 + 2.4 + 2.4 + 0.3 = 23.1 μL of reagents before template and nuclease-free water in a nominal 30 μL reaction.
Abstract claim (verbatim paraphrase): Mn, Mo, and B deficiencies enhanced microbial richness (Chao1 increase of 15–30%).
Results claim (verbatim paraphrase): Significantly lower Simpson and Chao1 indices in Mn- and B-deficient seedlings for fungal communities.
Sequence totals reported: 3,180,867 bacterial 16S rRNA reads; 3,462,115 fungal ITS reads; extracted with DNeasy PowerSoil Kit.
DOI of concern: 10.1186/s12870-025-06966-0.

Notes

These findings are based on text and figure-level description; raw FASTQ files, bench PCR worksheets, and negative-control sequences were not examined. Author rebuttal and editorial investigation may resolve some items (particularly the abstract/results mismatch, which could in principle be a mislabeled figure or swapped legend).
The report does not constitute a formal finding of misconduct. Recommended actions in the original assessment include requesting raw data from the authors, posting on PubPeer, and notifying the journal editorial office. Reporting to the authors' institutional committee is held in reserve pending the editorial response.
Uncertainty remains for the contamination claim because no kit blanks or process controls were reported; conversely, the PCR and CuSO₄ inconsistencies are textual facts independent of biology.