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ORIGINAL RESEARCH article

Front. Microbiol.

Sec. Microbiotechnology

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1674444

This article is part of the Research TopicMicrobial Interactions with Metals/Minerals: From Environmental Aspects to ApplicationsView all 5 articles

Unraveling the Stress Response and Biosorption Mechanisms of Aspergillus niger to Rare Earth Element Cerium(III) Based on Transcriptomics and DNA Methylomics

Provisionally accepted
Jingqi  LiuJingqi Liu1Donghua  TanDonghua Tan1Huangfeng  QiuHuangfeng Qiu1Yuting  LiangYuting Liang1,2Haiyan  WuHaiyan Wu1,2Yu  YangYu Yang1,2,3*Hongbo  ZhaoHongbo Zhao1,2*
  • 1Central South University School of Minerals Processing and Bioengineering, Changsha, China
  • 2Key Lab of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, China
  • 3Hunan Provincial Engineering Research Center for Mineral and Biological Metallurgy, Central South University, Changsha, China

The final, formatted version of the article will be published soon.

Rare earth elements (REEs) represent critical industrial resources, yet conventional extraction methods face substantial environmental and efficiency constraints. Fungal bioleaching emerges as an eco-friendly alternative, leveraging organic acid secretion to facilitate REEs dissolution and adsorption. However, progressive REEs accumulation inhibits microbial activity, with fungal resistance mechanisms remaining incompletely understood. Here, we report the discovery of Aspergillus niger FH1, a highly REEs-tolerant strain exhibiting remarkable Ce(III) tolerance (600 mg/L maximum) and achieving 74.05% adsorption efficiency under optimized conditions. Integrated physicochemical characterization (SEM, FTIR, XPS) revealed dual adsorption mechanisms: physical entrapment evidenced by Ce(III)-induced cellular invagination, and chemical monolayer binding via extracellular functional group coordination (amino, hydroxyl, carboxyl, carbonyl, phosphate), with specific moieties enabling Ce(III) capture through surface complexation. Transcriptomic analysis identified 3,733 differentially expressed genes under Ce(III) stress. Functional annotation (GO/KEGG) demonstrated: (1) Significant repression of oxidative phosphorylation genes; (2) Concomitant upregulation of glycolysis, pentose phosphate pathway, and amino acid metabolism genes indicating metabolic rerouting for energy maintenance; (3) Enhanced expression of antioxidative/chelating metabolite synthesis pathways. Whole-genome bisulfite sequencing revealed conserved global 5mC DNA methylation levels (0.32% vs. 0.36% in controls) with preferential CHH-context targeting. Collectively, these adaptation strategy combines extracellular sequestration, metabolic plasticity, and stress mitigation to confers exceptional resilience against rare earth metal toxicity. The demonstrated adsorption-tolerance synergy positions A. niger FH1 as an important bioagent for sustainable recovery of recalcitrant rare earth resources.

Keywords: Aspergillus niger, REEs adsorption, REEs tolerance mechanisms, metabolic adaptation, Transcriptomics, DNA Methylation, Bioleaching applications

Received: 28 Jul 2025; Accepted: 29 Sep 2025.

Copyright: © 2025 Liu, Tan, Qiu, Liang, Wu, Yang and Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Yu Yang, csuyangyu@csu.edu.cn
Hongbo Zhao, zhbalexander@csu.edu.cn

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