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Xia J, Liu H, Nie Z, Fan X, Zhang D, Zheng X, Liu L, Pan X, Zhou Y. Taking insights into phenomics of microbe-mineral interaction in bioleaching and acid mine drainage: Concepts and methodology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:139005. [PMID: 32361456 DOI: 10.1016/j.scitotenv.2020.139005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/24/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
Phenomics is originally a biological concept. In the most recent years, the studies of plant and human phenomics have started, and show a strong momentum and trend of development. In this paper, based on the related research on bioleaching/acid mine drainage (AMD), we put forward the relevant concepts and methodology of phenomics of microbe-mineral interaction (MMI) in bioleaching/AMD environments. It refers to the systematic study on phenotypes of MMI on both levels of microbiome and mineralome under various environmental conditions, by which it gives the relationship between microbial/mineral genome and phenome of MMI responding to the varying environmental conditions. The pertinent methodology is of mainly (meta)-omics, synchrotron radiation-based techniques and supercomputing-based density function theory (DFT) calculation.
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Affiliation(s)
- Jinlan Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China.
| | - Hongchang Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China
| | - Zhenyuan Nie
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key Laboratory of Biometallurgy of Ministry of Education of China, Central South University, Changsha 410083, China
| | - Xiaolu Fan
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Duorui Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Xingfu Zheng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Lizhu Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Xuan Pan
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Yuhang Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
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Liu LZ, Nie ZY, Yang Y, Pan X, Xia X, Zhou YH, Xia JL, Zhang LJ, Zhen XJ, Yang HY. In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25. Res Microbiol 2018; 169:590-597. [PMID: 30179696 DOI: 10.1016/j.resmic.2018.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/10/2018] [Accepted: 08/24/2018] [Indexed: 01/21/2023]
Abstract
For the first time, synchrotron radiation (SR) -based carbon K-edge X-ray absorption near edge structure (XANES) spectroscopy in-situ characterization was conducted to evaluate the evolution of superficial (about 10 nm) organic components of extracellular polymeric substances (EPS) of thermoacidophilic archaeon Acidianus manzaensis YN-25 acclimated with different energy substrates (FeS2, CuFeS2, S0, FeSO4). The atomic force microscopy (AFM) morphology scanning showed that the strain acclimated with different energy substrates varied a lot in EPS amount. XANES results showed clear associations between the energy substrates and the changes in organic composition in terms of typical function groups (CO, CO and CN). The chalcopyrite- and pyrite-acclimated cells contained higher proportion of proteins but less proportion of polysaccharides than the S0-acclimated cells. The FeSO4-acclimated cells contained the highest proportion of proteins, while the S0-acclimated cells contained more lipids and polysaccharides. The results of linear-combination and peak fitting of the K-edge XANES for the extracellular superficial organic component C is consistent with the trend in comparison with the results of FTIR and spectrophotometric determination, but there are significant differences in the values. These differences are caused by the inconsistencies of measurement depth between XANES and the latter two characterization methods.
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Affiliation(s)
- Li-Zhu Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Zhen-Yuan Nie
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Lab of Biometallurgy of the Ministry of Education of China, Central South University, Changsha, 410083, China.
| | - Yi Yang
- CSIRO Mineral Resources, Clayton South, Vic, 3169, Australia
| | - Xuan Pan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Xu Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Yu-Hang Zhou
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Jin-Lan Xia
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Lab of Biometallurgy of the Ministry of Education of China, Central South University, Changsha, 410083, China.
| | - Li-Juan Zhang
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Xiang-Jun Zhen
- Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Hong-Ying Yang
- School of Metallurgy, Northeastern University, Shenyang, 110819, China
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Combined DFT and XPS Investigation of Cysteine Adsorption on the Pyrite (1 0 0) Surface. MINERALS 2018. [DOI: 10.3390/min8090366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The adsorption of cysteine on the pyrite (1 0 0) surface was evaluated by using first-principles-based density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) measurements. The frontier orbitals analyses indicate that the interaction of cysteine and pyrite mainly occurs between HOMO of cysteine and LUMO of pyrite. The adsorption energy calculation shows that the configuration of the -OH of -COOH adsorbed on the Fe site is the thermodynamically preferred adsorption configuration, and it is the strongest ionic bond according to the Mulliken bond populations. As for Fe site mode, the electrons are found transferred from cysteine to Fe of pyrite (1 0 0) surface, while there is little or no electron transfer for S site mode. Projected density of states (PDOS) is analyzed further in order to clarify the interaction mechanism between cysteine and the pyrite (1 0 0) surface. After that, the presence of cysteine adsorption on the pyrite (1 0 0) surface is indicated by the qualitative results of the XPS spectra. This study provides an alternative way to enhance the knowledge of microbe–mineral interactions and find a route to improve the rate of bioleaching.
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