Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger

Yingjie Chen; Yuyuan Duan; Tingfang Xue; Xinhui Deng

doi:doi:10.11648/j.ajese.20261001.11

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Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger

Yingjie Chen, Yuyuan Duan, Tingfang Xue, Xinhui Deng^*

Published in American Journal of Environmental Science and Engineering (Volume 10, Issue 1)

Received: 30 December 2025 Accepted: 15 January 2026 Published: 11 February 2026

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Abstract

Aspergillus niger shows resistance to Zn and Cu; however, limited studies have evaluated the genetic mechanisms underlying metal tolerance in the species. In this study, comparative transcriptome analyses of A. niger F2 under Zn (4000 mg/L) and Cu (3000 mg/L) stress for 15 days were performed to identify genes involved in the response to heavy metal stress. There were more upregulated than downregulated genes under both Cu and Zn stress; however, more genes were differentially expre ssed under Cu than under Zn stress. Downregulated genes under Zn stress were enriched mainly in the membrane part of the cellular component category and for catalytic activity of ribonucleases in the molecular function category. Downregulated genes under Cu stress were enriched for import of Cu ions in the biological process category, intrinsic membrane in the cellula r component category, and reductase and oxidoreductase activity in the molecular function category. Differentially express ed genes under Zn and Cu stress were enriched for different functional domains based on Gene Ontology and Kyoto Ency clopedia of Genes and Genomes analyses. These findings indicated that under heavy metal stress, downregulated genes are mainly involved in ion transport and cell membrane-related functions. Furthermore, energy consumption was higher under Cu stress than under Zn stress, contributing to differences in tolerance levels for A. niger. These findings provide a b asis for genetic engineering for efficient bioremediation.

Published in	American Journal of Environmental Science and Engineering (Volume 10, Issue 1)
DOI	10.11648/j.ajese.20261001.11
Page(s)	1-20
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2026. Published by Science Publishing Group

Keywords

Aspergillus, Differential Gene Expression, Heavy Metal Stress, Microbial Transcriptome

References

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APA Style

Chen, Y., Duan, Y., Xue, T., Deng, X. (2026). Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. American Journal of Environmental Science and Engineering, 10(1), 1-20. https://doi.org/10.11648/j.ajese.20261001.11

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ACS Style

Chen, Y.; Duan, Y.; Xue, T.; Deng, X. Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. Am. J. Environ. Sci. Eng. 2026, 10(1), 1-20. doi: 10.11648/j.ajese.20261001.11

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AMA Style

Chen Y, Duan Y, Xue T, Deng X. Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. Am J Environ Sci Eng. 2026;10(1):1-20. doi: 10.11648/j.ajese.20261001.11

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@article{10.11648/j.ajese.20261001.11,
  author = {Yingjie Chen and Yuyuan Duan and Tingfang Xue and Xinhui Deng},
  title = {Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger},
  journal = {American Journal of Environmental Science and Engineering},
  volume = {10},
  number = {1},
  pages = {1-20},
  doi = {10.11648/j.ajese.20261001.11},
  url = {https://doi.org/10.11648/j.ajese.20261001.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajese.20261001.11},
  abstract = {Aspergillus niger shows resistance to Zn and Cu; however, limited studies have evaluated the genetic mechanisms underlying metal tolerance in the species. In this study, comparative transcriptome analyses of A. niger F2 under Zn (4000 mg/L) and Cu (3000 mg/L) stress for 15 days were performed to identify genes involved in the response to heavy metal stress. There were more upregulated than downregulated genes under both Cu and Zn stress; however, more genes were differentially expre ssed under Cu than under Zn stress. Downregulated genes under Zn stress were enriched mainly in the membrane part of the cellular component category and for catalytic activity of ribonucleases in the molecular function category. Downregulated genes under Cu stress were enriched for import of Cu ions in the biological process category, intrinsic membrane in the cellula r component category, and reductase and oxidoreductase activity in the molecular function category. Differentially express ed genes under Zn and Cu stress were enriched for different functional domains based on Gene Ontology and Kyoto Ency clopedia of Genes and Genomes analyses. These findings indicated that under heavy metal stress, downregulated genes are mainly involved in ion transport and cell membrane-related functions. Furthermore, energy consumption was higher under Cu stress than under Zn stress, contributing to differences in tolerance levels for A. niger. These findings provide a b asis for genetic engineering for efficient bioremediation.},
 year = {2026}
}

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TY  - JOUR
T1  - Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger
AU  - Yingjie Chen
AU  - Yuyuan Duan
AU  - Tingfang Xue
AU  - Xinhui Deng
Y1  - 2026/02/11
PY  - 2026
N1  - https://doi.org/10.11648/j.ajese.20261001.11
DO  - 10.11648/j.ajese.20261001.11
T2  - American Journal of Environmental Science and Engineering
JF  - American Journal of Environmental Science and Engineering
JO  - American Journal of Environmental Science and Engineering
SP  - 1
EP  - 20
PB  - Science Publishing Group
SN  - 2578-7993
UR  - https://doi.org/10.11648/j.ajese.20261001.11
AB  - Aspergillus niger shows resistance to Zn and Cu; however, limited studies have evaluated the genetic mechanisms underlying metal tolerance in the species. In this study, comparative transcriptome analyses of A. niger F2 under Zn (4000 mg/L) and Cu (3000 mg/L) stress for 15 days were performed to identify genes involved in the response to heavy metal stress. There were more upregulated than downregulated genes under both Cu and Zn stress; however, more genes were differentially expre ssed under Cu than under Zn stress. Downregulated genes under Zn stress were enriched mainly in the membrane part of the cellular component category and for catalytic activity of ribonucleases in the molecular function category. Downregulated genes under Cu stress were enriched for import of Cu ions in the biological process category, intrinsic membrane in the cellula r component category, and reductase and oxidoreductase activity in the molecular function category. Differentially express ed genes under Zn and Cu stress were enriched for different functional domains based on Gene Ontology and Kyoto Ency clopedia of Genes and Genomes analyses. These findings indicated that under heavy metal stress, downregulated genes are mainly involved in ion transport and cell membrane-related functions. Furthermore, energy consumption was higher under Cu stress than under Zn stress, contributing to differences in tolerance levels for A. niger. These findings provide a b asis for genetic engineering for efficient bioremediation.
VL  - 10
IS  - 1
ER  -

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Yingjie Chen

School of Resource & Environment, Hunan University of Technology and Business, Changsha, China

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Yuyuan Duan

School of Resource & Environment, Hunan University of Technology and Business, Changsha, China

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Tingfang Xue

School of Resource & Environment, Hunan University of Technology and Business, Changsha, China

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Xinhui Deng

School of Resource & Environment, Hunan University of Technology and Business, Changsha, China

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http://orcid.org/0000-0002-7873-355X

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APA Style

Chen, Y., Duan, Y., Xue, T., Deng, X. (2026). Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. American Journal of Environmental Science and Engineering, 10(1), 1-20. https://doi.org/10.11648/j.ajese.20261001.11

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ACS Style

Chen, Y.; Duan, Y.; Xue, T.; Deng, X. Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. Am. J. Environ. Sci. Eng. 2026, 10(1), 1-20. doi: 10.11648/j.ajese.20261001.11

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AMA Style

Chen Y, Duan Y, Xue T, Deng X. Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger. Am J Environ Sci Eng. 2026;10(1):1-20. doi: 10.11648/j.ajese.20261001.11

Copy | Download

@article{10.11648/j.ajese.20261001.11,
  author = {Yingjie Chen and Yuyuan Duan and Tingfang Xue and Xinhui Deng},
  title = {Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger},
  journal = {American Journal of Environmental Science and Engineering},
  volume = {10},
  number = {1},
  pages = {1-20},
  doi = {10.11648/j.ajese.20261001.11},
  url = {https://doi.org/10.11648/j.ajese.20261001.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajese.20261001.11},
  abstract = {Aspergillus niger shows resistance to Zn and Cu; however, limited studies have evaluated the genetic mechanisms underlying metal tolerance in the species. In this study, comparative transcriptome analyses of A. niger F2 under Zn (4000 mg/L) and Cu (3000 mg/L) stress for 15 days were performed to identify genes involved in the response to heavy metal stress. There were more upregulated than downregulated genes under both Cu and Zn stress; however, more genes were differentially expre ssed under Cu than under Zn stress. Downregulated genes under Zn stress were enriched mainly in the membrane part of the cellular component category and for catalytic activity of ribonucleases in the molecular function category. Downregulated genes under Cu stress were enriched for import of Cu ions in the biological process category, intrinsic membrane in the cellula r component category, and reductase and oxidoreductase activity in the molecular function category. Differentially express ed genes under Zn and Cu stress were enriched for different functional domains based on Gene Ontology and Kyoto Ency clopedia of Genes and Genomes analyses. These findings indicated that under heavy metal stress, downregulated genes are mainly involved in ion transport and cell membrane-related functions. Furthermore, energy consumption was higher under Cu stress than under Zn stress, contributing to differences in tolerance levels for A. niger. These findings provide a b asis for genetic engineering for efficient bioremediation.},
 year = {2026}
}

Copy | Download

TY  - JOUR
T1  - Comparative Transcriptomics Reveals the Molecular Mechanism Underlying Heavy Metal Detoxification in Aspergillus Niger
AU  - Yingjie Chen
AU  - Yuyuan Duan
AU  - Tingfang Xue
AU  - Xinhui Deng
Y1  - 2026/02/11
PY  - 2026
N1  - https://doi.org/10.11648/j.ajese.20261001.11
DO  - 10.11648/j.ajese.20261001.11
T2  - American Journal of Environmental Science and Engineering
JF  - American Journal of Environmental Science and Engineering
JO  - American Journal of Environmental Science and Engineering
SP  - 1
EP  - 20
PB  - Science Publishing Group
SN  - 2578-7993
UR  - https://doi.org/10.11648/j.ajese.20261001.11
AB  - Aspergillus niger shows resistance to Zn and Cu; however, limited studies have evaluated the genetic mechanisms underlying metal tolerance in the species. In this study, comparative transcriptome analyses of A. niger F2 under Zn (4000 mg/L) and Cu (3000 mg/L) stress for 15 days were performed to identify genes involved in the response to heavy metal stress. There were more upregulated than downregulated genes under both Cu and Zn stress; however, more genes were differentially expre ssed under Cu than under Zn stress. Downregulated genes under Zn stress were enriched mainly in the membrane part of the cellular component category and for catalytic activity of ribonucleases in the molecular function category. Downregulated genes under Cu stress were enriched for import of Cu ions in the biological process category, intrinsic membrane in the cellula r component category, and reductase and oxidoreductase activity in the molecular function category. Differentially express ed genes under Zn and Cu stress were enriched for different functional domains based on Gene Ontology and Kyoto Ency clopedia of Genes and Genomes analyses. These findings indicated that under heavy metal stress, downregulated genes are mainly involved in ion transport and cell membrane-related functions. Furthermore, energy consumption was higher under Cu stress than under Zn stress, contributing to differences in tolerance levels for A. niger. These findings provide a b asis for genetic engineering for efficient bioremediation.
VL  - 10
IS  - 1
ER  -

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