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Liu H, Liu T, Chen S, Liu X, Li N, Huang T, Ma B, Liu X, Pan S, Zhang H. Biogeochemical cycles of iron: Processes, mechanisms, and environmental implications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175722. [PMID: 39187081 DOI: 10.1016/j.scitotenv.2024.175722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/29/2024] [Accepted: 08/08/2024] [Indexed: 08/28/2024]
Abstract
The iron (Fe) biogeochemical cycle is critical for abiotic and biological environmental processes that overlap spatially and may compete with each other. The development of modern molecular biology technologies promoted the understanding of the electron transport mechanisms of Fe-cycling-related microorganisms. Recent studies have revealed a novel pathway for microaerophilic ferrous iron (Fe(II))-oxidizers in extracellular Fe(II) oxidation. In addition, OmcS, OmcZ, and OmcE nanowires on the cell surface have been shown to promote electron transfer between microorganisms and their environment. These processes affect the fate of pollutants in directly or indirectly ways, such as greenhouse gas emissions. In this review, these advances and the environmental implications of the Fe cycle process were discussed, with a particular focus on the mechanisms of intracellular or extracellular electron transport in microorganisms.
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Affiliation(s)
- Huan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tao Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Shengnan Chen
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiaoyan Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Nan Li
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Tinglin Huang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Ben Ma
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiang Liu
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Sixuan Pan
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Haihan Zhang
- Collaborative Innovation Center of Water Pollution Control and Water Quality Security Assurance of Shaanxi Province, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Provincial Field Scientific Observation and Research Station of Water Quality in Qinling Mountains, Xi'an University of Architecture and Technology, Xi'an 710055, China; School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
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Li L, Liu Z, Meng D, Liu Y, Liu T, Jiang C, Yin H. Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation. mSystems 2023; 8:e0072023. [PMID: 37768051 PMCID: PMC10654088 DOI: 10.1128/msystems.00720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Yongjun Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Tianbo Liu
- Hunan Tobacco Science Institute, Changsha, China
| | - Chengying Jiang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Luo D, Li Y, Yao H, Chapman SJ. Effects of different carbon sources on methane production and the methanogenic communities in iron rich flooded paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153636. [PMID: 35124061 DOI: 10.1016/j.scitotenv.2022.153636] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Various carbon sources as substrates and electron donors can produce methane via different metabolic pathways. In particular, the methane produced by rice cultivation has a severe impact on climate change. However, how Fe3+, the most abundant oxide in paddy soil, mediates the methanogenesis of different carbon sources is unknown. In this study, we investigated the effect of four carbon sources with different chain lengths (acetate, glucose, nonanoate, and starch) on CH4 production and associated methanogens in iron-rich paddy soil over 90 days of anaerobic incubation. We found that glucose and starch were the more preferential substrates for liberating methane compared to acetate, and the rate was also faster. Nonanoate was unable to support methane production. Methanosarcinales and Methanobacteriales were the most predominant methanogenic archaea as shown by 16S rRNA gene sequencing, though their abundance changed over time. Additionally, a significantly higher content of iron-reducing bacteria was observed in the glucose and starch treatments, and it was significantly positively correlated with the copy number of the methanogenic mcrA gene. Together, we confirmed the methanogenic capacity of different carbon sources and their related microorganisms. We also showed that iron oxides play a central role in regulating methane emissions from paddy soils and need more attention to be paid to them.
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Affiliation(s)
- Dan Luo
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China.
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Schmidt M, Byrne JM, Maasilta IJ. Bio-imaging with the helium-ion microscope: A review. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2021; 12:1-23. [PMID: 33489663 PMCID: PMC7801799 DOI: 10.3762/bjnano.12.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/26/2020] [Indexed: 06/01/2023]
Abstract
Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.
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Affiliation(s)
- Matthias Schmidt
- Helmholtz-Centre for Environmental Research GmbH - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, United Kingdom
| | - Ilari J Maasilta
- Nanoscience Center, Department of Physics, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
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Bennett BD, Gralnick JA. Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems. Free Radic Biol Med 2019; 140:167-171. [PMID: 31251977 DOI: 10.1016/j.freeradbiomed.2019.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 06/13/2019] [Accepted: 06/23/2019] [Indexed: 12/24/2022]
Abstract
Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe3+), and ferrous iron, the reduced state (Fe2+). Fe2+ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe2+ toxicity, focusing on molecular mechanistic studies in several model systems.
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Affiliation(s)
- B D Bennett
- Pacific Biosciences Research Center, University of Hawai‛i at Mānoa, Honolulu, HI, 96813, USA
| | - J A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, 55108, USA.
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