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Yang G, Li S, Niu R, Hu M, Huang G, Pan D, Yan S, Liu T, Li X, Li F. Insights into nitrate-reducing Fe(II) oxidation by Diaphorobacter caeni LI3 T through kinetic, nitrogen isotope fractionation, and genome analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168720. [PMID: 38008321 DOI: 10.1016/j.scitotenv.2023.168720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
Nitrate (NO3-)-reducing Fe(II) oxidation (NRFO) is prevalent in anoxic environments. However, it is uncertain in which step(s) the biological Fe(II) oxidation is coupled with denitrification during NRFO. In this study, a heterotrophic NRFO bacterium, Diaphorobacter caeni LI3T, was isolated from paddy soil and used to investigate the transformation of Fe(II) and nitrogen as well as nitrogen isotopic fractionation (δ15N-N2O) during NRFO. Fe(II) oxidation was observed in the Cell+NO3- +Fe(II), Cell+NO2- + Fe(II), and NO2- + Fe(II) treatments, resulting in precipitation of amorphous Fe(III) minerals and lepidocrocite on the surface and in the periplasm of cells. The presence of Fe(II) slightly accelerated microbial NO3- reduction in the Cell+NO3- + Fe(II) treatment relative to the Cell+NO3- treatment, but slowed down the NO2- reduction in the Cell+NO2- + Fe(II) treatment relative to the Cell+NO2- treatment likely due to cell encrustation that blocking microbial NO2- reduction in the periplasm. The δ15N-N2O results in the Cell+NO3- + Fe(II) treatment were close to those in the Cell+NO3- and Cell+NO2- treatments, indicating that the accumulative N2O is primarily of biological origin during NRFO. The genome analysis found a complete set of denitrification and oxidative phosphorylation genes in strain LI3T, the metabolic pathways of which were closely related with cyc2 and cytc as indicated by protein-protein interactions network analysis. It is proposed that Fe(II) oxidation is catalyzed by the outer membrane protein Cyc2, with the resulting electrons being transferred to the nitrite reductase NirS via CytC in the periplasm, and the CytC can also accept electrons from the oxidative phosphorylation in the cytoplasmic membrane. Overall, our findings provide new insights into the potential pathways of biological Fe(II) oxidation coupled with nitrate reduction in heterotrophic NRFO bacteria.
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Affiliation(s)
- Guang Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Shuang Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Rumiao Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Min Hu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guoyong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Dandan Pan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Siyao Yan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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2
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Hribovšek P, Olesin Denny E, Dahle H, Mall A, Øfstegaard Viflot T, Boonnawa C, Reeves EP, Steen IH, Stokke R. Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field. mSystems 2023; 8:e0054323. [PMID: 37921472 PMCID: PMC10734525 DOI: 10.1128/msystems.00543-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/02/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
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Affiliation(s)
- Petra Hribovšek
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Emily Olesin Denny
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Håkon Dahle
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Berge, Bergen, Norway
| | - Achim Mall
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Thomas Øfstegaard Viflot
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Chanakan Boonnawa
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Eoghan P. Reeves
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Runar Stokke
- Centre for Deep Sea Research, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
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3
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Malakar A, Ray C, D'Alessio M, Shields J, Adams C, Stange M, Weber KA, Snow DD. Interplay of legacy irrigation and nitrogen fertilizer inputs to spatial variability of arsenic and uranium within the deep vadose zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165299. [PMID: 37419358 DOI: 10.1016/j.scitotenv.2023.165299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/01/2023] [Accepted: 07/01/2023] [Indexed: 07/09/2023]
Abstract
The vadose zone is a reservoir for geogenic and anthropogenic contaminants. Nitrogen and water infiltration can affect biogeochemical processes in this zone, ultimately affecting groundwater quality. In this large-scale field study, we evaluated the input and occurrence of water and nitrogen species in the vadose zone of a public water supply wellhead protection (WHP) area (defined by a 50-year travel time to groundwater for public supply wells) and potential transport of nitrate, ammonium, arsenic, and uranium. Thirty-two deep cores were collected and grouped by irrigation practices: pivot (n = 20), gravity (n = 4) irrigated using groundwater, and non-irrigated (n = 8) sites. Beneath pivot-irrigated sites, sediment nitrate concentrations were significantly (p < 0.05) lower, while ammonium concentrations were significantly (p < 0.05) higher than under gravity sites. The spatial distribution of sediment arsenic and uranium was evaluated against estimated nitrogen and water loading beneath cropland. Irrigation practices were randomly distributed throughout the WHP area and presented a contrasting pattern of sediment arsenic and uranium occurrence. Sediment arsenic correlated with iron (r = 0.32, p < 0.05), uranium negatively correlated to sediment nitrate (r = -0.23, p < 0.05), and ammonium (r = -0.19 p < 0.05). This study reveals that irrigation water and nitrogen influx influence vadose zone geochemistry and mobilization of geogenic contaminants affecting groundwater quality beneath intensive agricultural systems.
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Affiliation(s)
- Arindam Malakar
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute and School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0844, USA.
| | - Chittaranjan Ray
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute, 2021 Transformation Drive, University of Nebraska, Lincoln, NE 68588-6204, USA
| | - Matteo D'Alessio
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute, University of Nebraska, Lincoln, NE 68583-0915, USA
| | - Jordan Shields
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute and School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0844, USA
| | - Craig Adams
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute and School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0844, USA
| | - Marty Stange
- Hastings Utilities, 1228 N. Denver Avenue, Hastings, NE 68901, USA
| | - Karrie A Weber
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute, 2021 Transformation Drive, University of Nebraska, Lincoln, NE 68588-6204, USA; School of Biological Sciences, University of Nebraska, Lincoln, Lincoln, NE, USA; Earth and Atmospheric Sciences, University of Nebraska, Lincoln, Lincoln, NE 68588, USA
| | - Daniel D Snow
- Nebraska Water Center, part of the Robert B. Daugherty Water for Food Global Institute and School of Natural Resources, University of Nebraska, Lincoln, NE 68583-0844, USA.
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Ding C, Chen LB, Yu LP, Wang R, Yuan LJ, Wang L, Deng LW. Applying sheet iron to enhance the treatment efficiency of digested effluent with continuous flow and the corresponding mechanism. CHEMOSPHERE 2023; 340:139912. [PMID: 37611761 DOI: 10.1016/j.chemosphere.2023.139912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/25/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Because of the unstable wastewater quantity and quality, the biological treatment efficiency of digested effluent was not as expected. A convenient and effective way was eagerly required to improve the efficiency of biological treatment. By sheet iron addition (R1), the COD and TN removal efficiencies under continuous flow condition increased by 59% and 37% respectively. The bulk pH maintained at around 7.5 which benefited most bacteria, while in the control (R0, without sheet iron addition) the pH decreased to 5.0. Both chemical and bio-removal of COD existed in R1, but the chemical removal dominated (63.71%). The enhanced COD removal efficiency came from the chemical oxidation by Fe3+ (47.43%) and Fe0 (10.86%). For the TN removal, the enhancement mainly came from the improvement of anammox activity by Fe3+ (14.87%), the bio-oxidation of ammonium with Fe3+ as electron acceptor (8.78%), and the bio-reduction of nitrate/nitrite with Fe2+ and H2 as electron donor (35.76%). By the first-order kinetic fitting analysis, the COD and TN removal rate in R1 was higher than that in R0. Thus, for a quick and high COD and TN removal from digested effluent, the addition of Fe0/Fe2+/Fe3+ was suggested, and the best form should be Fe0 (e.g., sheet iron). The addition of sheet iron reduces the cost of nitrogen removal and improves the efficiency of COD and TN removal. Comparing with the combined processes, this novel approach has potential advantages with simple operation and high efficiency. It endows the biological process much broader application in digested effluent treatment.
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Affiliation(s)
- Cong Ding
- Department of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Li-Bin Chen
- Shaanxi Land Engineering Construction Group Co. Ltd., Xi'an, 710075, PR China.
| | - Li-Ping Yu
- Shuifa Technology Group Co. Ltp, Jinan, 250000, PR China.
| | - Ru Wang
- Department of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Lin-Jiang Yuan
- Department of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Lan Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, PR China.
| | - Liang-Wei Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, PR China.
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5
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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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6
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Pan Y, Fu YY, Zhou K, Tian T, Li YS, Yu HQ. Microbial mixotrophic denitrification using iron(II) as an assisted electron donor. WATER RESEARCH X 2023; 19:100176. [PMID: 37020531 PMCID: PMC10068250 DOI: 10.1016/j.wroa.2023.100176] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Mixotrophic denitrification processes have a great potential in nitrogen removal in biological wastewater treatment processes. However, so far, few studies have focused on the mixotrophic denitrification system using Fe(II) as an exclusively assisted electron donors and the underlying mechanisms in such a process remain unclear. Furthermore, the mechanisms by which microorganisms cover carbon, nitrogen, phosphorus and iron in an iron-assisted mixotrophic system remain unrevealed. In this work, we explore the feasibility of using Fe(II) as an assisted electron donor for enhancing simultaneous nitrogen and phosphorus removal via long-term reactor operation and batch tests. The results show that Fe(II) could provide electrons for efficient nitrate reduction and that biological reactions played a predominant role in these systems. In these systems Thermomonas, a strain of nitrate-reduction Fe(II)-oxidation bacterium, was enriched and accounted for a maximum abundance of 60.2%. These findings indicate a great potential of the Fe(II)-assisted mixotrophic denitrification system for practical use as an efficient simultaneous nitrogen and phosphorus removal process.
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Affiliation(s)
- Yuan Pan
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei 230026, China
| | - Ying-Ying Fu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Ke Zhou
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Tian Tian
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yu-Sheng Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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7
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Wang Y, Ren S, Wang P, Wang B, Hu K, Li J, Wang Y, Li Z, Li S, Li W, Peng Y. Autotrophic denitrification using Fe(II) as an electron donor: A novel prospective denitrification process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159721. [PMID: 36306837 DOI: 10.1016/j.scitotenv.2022.159721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
As a newly identified nitrogen loss pathway, the nitrate-dependent ferrous oxidation (NDFO) process is emerging as a research hotspot in the field of low carbon to nitrogen ratio (C/N) wastewater treatment. This review article provides an overview of the NDFO process and summarizes the functional microorganisms associated with NDFO from different perspectives. The potential mechanisms by which external factors such as influent pH, influent Fe(II)/N (mol), organic carbon, and chelating agents affect NDFO performance are also thoroughly discussed. As the electron-transfer mechanism of the NDFO process is still largely unknown, the extensive chemical Fe(II)-oxidizing nitrite-reducing pathway (NDFOchem) of the NDFO process is described here, and the potential enzymatic electron transfer mechanisms involved are summarized. On this basis, a three-stage electron transfer pathway applicable to low C/N wastewater is proposed. Furthermore, the impact of Fe(III) mineral products on the NDFO process is revisited, and existing crusting prevention strategies are summarized. Finally, future challenges facing the NDFO process and new research directions are discussed, with the aim of further promoting the development and application of the NDFO process in the field of nitrogen removal.
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Affiliation(s)
- Yaning Wang
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Shuang Ren
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Peng Wang
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China.
| | - Bo Wang
- School of Geosciences, China University of Petroleum, Qingdao 266580, China
| | - Kaiyao Hu
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Jie Li
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China; Gansu membrane science and technology research institute Co.,Ltd., Lanzhou 730020, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Lanzhou 730020, China
| | - Yae Wang
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Zongxing Li
- Key Laboratory of Ecohydrology of Inland River Basin/Gansu Qilian Mountains Ecology Research Center, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Sumei Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Wang Li
- Taiyuan university of technology, Taiyuan 030024, China; State Key Laboratory of Clean and Efficient Coal Utilization, Taiyuan 030024, China
| | - Yuzhuo Peng
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
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8
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Zhu Y, Di Capua F, Li D, Li H. Enhancement and mechanisms of micron-pyrite driven autotrophic denitrification with different pretreatments for treating organic-limited waters. CHEMOSPHERE 2022; 308:136306. [PMID: 36067811 DOI: 10.1016/j.chemosphere.2022.136306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pyrite-driven autotrophic denitrification (PAD) represents a cheap and promising way for nitrogen removal from organic-limited wastewater, which has obtained increasing attention in recent years. However, the limited denitrification rate and unclear mechanism underlying the process have hindered the engineered application of PAD. This study aims to shed light on the impacts of different pretreatments (i.e., ultrasonication, acid-washing and calcination) on micron-pyrite surface characteristics, denitrification performance and biofilm formation during PAD in batch reactors. A series of solid-phase analyses revealed that all pretreatments could significantly promote biofilm attachment on pyrite granules, but impacted the proportion, distribution and chemical oxidation state of sulfur (S) and iron (Fe) at varying degrees. Batch tests showed that ultrasonication and acid-washing could enhance the total nitrogen reduction rate by 14% and 99%, and decrease the sulfate production rate by 51% and 42%, respectively, when compared with untreated pyrite. Microbial community analysis indicated that Thiobacillus and Rhodanobacter dominated in PAD systems. Two types of indirect mechanisms (i.e., contact and non-contact) for pyrite leaching may co-occur in PAD system, resulting in ferrous iron (Fe2+), thiosulfate (S2O32-) and sulfide (S2-) as the main electron donors for denitrification. A PAD mechanism model was proposed to describe the PAD electron transfer pathway with the aim to optimize the engineered application of PAD for nitrogen removal.
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Affiliation(s)
- Yingjie Zhu
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Francesco Di Capua
- Department of Civil Environmental Land Construction and Chemistry (DICATECh), Polytechnic University of Bari, 70125, Bari, Italy
| | - Duanxin Li
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China
| | - Huaizheng Li
- College of Environmental Science and Engineering, Tongji University, 200092, Shanghai, China.
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9
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Visser AN, Wankel SD, Frey C, Kappler A, Lehmann MF. Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation. Front Microbiol 2022; 13:927475. [PMID: 36118224 PMCID: PMC9478938 DOI: 10.3389/fmicb.2022.927475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Natural-abundance measurements of nitrate and nitrite (NOx) isotope ratios (δ15N and δ18O) can be a valuable tool to study the biogeochemical fate of NOx species in the environment. A prerequisite for using NOx isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (15ε, 18ε) associated with the biotic and abiotic NOx transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NOx reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO3–) and nitrite (NO2–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that 15ε and 18ε values obtained for heterotrophic (15ε-NO3–: 17.6 ± 2.8‰, 18ε-NO3–:18.1 ± 2.5‰; 15ε-NO2–: 14.4 ± 3.2‰) vs. mixotrophic (15ε-NO3–: 20.2 ± 1.4‰, 18ε-NO3–: 19.5 ± 1.5‰; 15ε-NO2–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NOx reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (15ε-NO2–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NOx reduction. The similar isotope effects detected during mixotrophic and heterotrophic NOx reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NOx reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.
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Affiliation(s)
- Anna-Neva Visser
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
- *Correspondence: Anna-Neva Visser,
| | - Scott D. Wankel
- Stable Isotope Biogeochemistry, Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Falmouth, MA, United States
| | - Claudia Frey
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, Eberhard Karls University, Tuebingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen, Germany
| | - Moritz F. Lehmann
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
- Moritz F. Lehmann,
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10
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Li MJ, Wei MY, Fan XT, Zhou GW. Underestimation about the Contribution of Nitrate Reducers to Iron Cycling Indicated by Enterobacter Strain. Molecules 2022; 27:molecules27175581. [PMID: 36080348 PMCID: PMC9457790 DOI: 10.3390/molecules27175581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrate-reducing iron(II) oxidation (NRFO) has been intensively reported in various bacteria. Iron(II) oxidation is found to be involved in both enzymatic and chemical reactions in nitrate-reducing Fe(II)-oxidizing microorganisms (NRFOMs). However, little is known about the relative contribution of biotic and abiotic reactions to iron(II) oxidation for the common nitrate reducers during the NRFO process. In this study, the typical nitrate reducers, four Enterobacter strains E. hormaechei, E. tabaci, E. mori and E. asburiae, were utilized as the model microorganisms. The comparison of the kinetics of nitrate, iron(II) and nitrite and N2O production in setups with and without iron(II) indicates a mixture of enzymatic and abiotic oxidation of iron(II) in all four Enterobacter strains. It was estimated that 22−29% of total oxidized iron(II) was coupled to microbial nitrate reduction by E. hormaechei, E. tabaci, E. mori, and E. asburiae. Enterobacter strains displayed an metabolic inactivity with heavy iron(III) encrustation on the cell surface in the NRFOmedium during days of incubation. Moreover, both respiratory and periplasmic nitrate-reducing genes are encoded by genomes of Enterobacter strains, suggesting that cell encrustation may occur with periplasmic iron(III) oxide precipitation as well as the surface iron(II) mineral coating for nitrate reducers. Overall, this study clarified the potential role of nitrate reducers in the biochemical cycling of iron under anoxic conditions, in turn, re-shaping their activity during denitrification because of cell encrustation with iron(III) minerals.
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Affiliation(s)
- Ming-Jun Li
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
| | - Meng-Yun Wei
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiao-Ting Fan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Guo-Wei Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China
- Correspondence:
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11
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Wang P, Li W, Ren S, Peng Y, Wang Y, Feng M, Guo K, Xie H, Li J. Use of sponge iron as an indirect electron donor to provide ferrous iron for nitrate-dependent ferrous oxidation processes: Denitrification performance and mechanism. BIORESOURCE TECHNOLOGY 2022; 357:127318. [PMID: 35609754 DOI: 10.1016/j.biortech.2022.127318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Sponge iron (SI) can serve as an indirect electron donor to provide Fe(II) for the nitrate-dependent ferrous oxidation (NDFO) process, producing OH- and magnetite. The SI-NDFO system mainly uses Fe(OH)2 as an electron donor, achieving a TN reduction rate of 0.42 mg-TN/(gVSS·h) for a period of at least 90 days. The enrichment of iron-oxidizing bacteria and the competition of iron-carbon micro-electrolysis for reaction sites on the surface of SI are the main reasons for the improvement of total nitrogen removal efficiency (TNRE). With an influent NO3--N concentration of 50 mg/L and a SI concentration of 50 g/L (at pH 5.0 and 30 °C), the TNRE reached a maximum level of 38.28%. In addition, reducing the pH environment was found to improve the denitrification efficiency of the SI-NDFO system, although denitrification stability was also reduced as a result. Overall, the SI-mediated NDFO process is a promising technique.
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Affiliation(s)
- Peng Wang
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Wenxuan Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Shuang Ren
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Yuzhuo Peng
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Yaning Wang
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Muyu Feng
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Kehuan Guo
- Key Laboratory of Water Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100123, PR China
| | - Huina Xie
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China
| | - Jie Li
- College of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Yellow River Water Environment in Gansu Province, Lanzhou 730070, China; Gansu Membrane Science and Technology Research Institute Co., Ltd., Lanzhou 730020, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Lanzhou 730020, China.
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12
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Price A, Macey MC, Pearson VK, Schwenzer SP, Ramkissoon NK, Olsson-Francis K. Oligotrophic Growth of Nitrate-Dependent Fe 2+-Oxidising Microorganisms Under Simulated Early Martian Conditions. Front Microbiol 2022; 13:800219. [PMID: 35418959 PMCID: PMC8997339 DOI: 10.3389/fmicb.2022.800219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
Nitrate-dependent Fe2+ oxidation (NDFO) is a microbially mediated process observed in many anaerobic, low-nutrient (oligotrophic) neutral-alkaline environments on Earth, which describes oxidation of Fe2+ to Fe3+ in tandem with microbial nitrate reduction. Evidence suggests that similar environments existed on Mars during the Noachian epoch (4.1-3.7 Ga) and in periodic, localised environments more recently, indicating that NDFO metabolism could have played a role in a potential early martian biosphere. In this paper, three NDFO microorganisms, Acidovorax sp. strain BoFeN1, Pseudogulbenkiania sp. strain 2002 and Paracoccus sp. strain KS1, were assessed for their ability to grow oligotrophically in simulated martian brines and in a minimal medium with olivine as a solid Fe2+ source. These simulant-derived media were developed from modelled fluids based on the geochemistry of Mars sample locations at Rocknest (contemporary Mars soil), Paso Robles (sulphur-rich soil), Haematite Slope (haematite-rich soil) and a Shergottite meteorite (common basalt). The Shergottite medium was able to support growth of all three organisms, while the contemporary Mars medium supported growth of Acidovorax sp. strain BoFeN1 and Pseudogulbenkiania sp. strain 2002; however, growth was not accompanied by significant Fe2+ oxidation. Each of the strains was also able to grow in oligotrophic minimal media with olivine as the sole Fe2+ source. Biomineralised cells of Pseudogulbenkiania sp. strain 2002 were identified on the surface of the olivine, representing a potential biosignature for NDFO microorganisms in martian samples. The results suggest that NDFO microorganisms could have thrived in early martian groundwaters under oligotrophic conditions, depending on the local lithology. This can guide missions in identifying palaeoenvironments of interest for biosignature detection. Indeed, biomineralised cells identified on the olivine surface provide a previously unexplored mechanism for the preservation of morphological biosignatures in the martian geological record.
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Affiliation(s)
- Alex Price
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Michael C. Macey
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K. Pearson
- School of Physical Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P. Schwenzer
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Nisha K. Ramkissoon
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Karen Olsson-Francis
- School of Environment, Earth and Ecosystem Sciences, Faculty of Science, Technology, Engineering, and Mathematics, The Open University, Milton Keynes, United Kingdom
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13
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Huang K, Li Q, Sun H, Zhang XX, Ren H, Ye L. Metagenomic analysis revealed the sulfur- and iron- oxidation capabilities of heterotrophic denitrifying sludge. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1399-1407. [PMID: 33210230 DOI: 10.1007/s10646-020-02307-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
Heterotrophic denitrification is widely applied in wastewater treatment processes to remove nitrate. However, the ability of the heterotrophic denitrifying sludge to use inorganic matter as electron donors to perform autotrophic denitrification has rarely been investigated. In this study, we enriched heterotrophic denitrifying sludge and demonstrated its sulfur- and iron- oxidizing abilities and denitrification performance with batch experiments. Based on high-throughput sequencing of 16S rRNA genes, high diversity and abundance of sulfur-oxidizing bacteria (SOB) (e.g., Sulfuritalea, Thiobacillus, and Thiothrix) and iron (II)-oxidizing bacteria (FeOB) (e.g., Azospira and Thiobacillus) were observed. Metagenomic sequencing and genome binning results further suggested that the SOB in the heterotrophic denitrifying sludge were mainly Alphaproteobacteria and Betaproteobacteria instead of Gammaproteobacteria and Epsilonproteobacteria. The similarities of potential iron-oxidizing genes with known sequences were very low (32-51%), indicating potentially novel FeOB species in this system. The findings of this study suggested that the heterotrophic denitrifying sludge harbors diverse mixotrophic denitrifying bacterial species, and based on this finding, we proposed that organic carbon and inorganic electron donors (e.g., sulfur, thiosulfate, and iron) could be jointly used in engineering practices according to the quality and quantity of wastewater to balance the cost and efficiency of the denitrification process.
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Affiliation(s)
- Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, 210044, Nanjing, China
| | - Qiaoling Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 210023, Nanjing, China.
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14
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Huang YM, Straub D, Blackwell N, Kappler A, Kleindienst S. Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. Appl Environ Microbiol 2021; 87:e0049621. [PMID: 34020935 PMCID: PMC8276803 DOI: 10.1128/aem.00496-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate reduction coupled to Fe(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing Fe(II)-oxidizing bacteria are rare, and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics, and metaproteomics) to the nitrate-reducing Fe(II)-oxidizing enrichment culture KS growing under autotrophic or heterotrophic conditions and originating from freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in Fe(II) oxidation (e.g., mtoAB, cyc2, and mofA), denitrification (e.g., napGHI), and oxidative phosphorylation (e.g., respiratory chain complexes I to V) along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be performed by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3- and aa3-type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and Fe(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments. IMPORTANCE Nitrate-reducing Fe(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing Fe(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of study is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to Fe(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic, and metaproteomic analyses of culture KS and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key Fe(II) oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to Fe(II) oxidation is not performed by an individual strain but is a cooperation of at least two members of the bacterial community in culture KS. These findings serve as a foundation for our understanding of nitrate-reducing Fe(II)-oxidizing bacteria in the environment.
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Affiliation(s)
- Yu-Ming Huang
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
- Cluster of Excellence, EXC 2124, “Controlling Microbes to Fight Infections,” University of Tübingen, Tübingen, Germany
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
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15
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Lui LM, Majumder ELW, Smith HJ, Carlson HK, von Netzer F, Fields MW, Stahl DA, Zhou J, Hazen TC, Baliga NS, Adams PD, Arkin AP. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology. Front Microbiol 2021; 12:642422. [PMID: 33841364 PMCID: PMC8024649 DOI: 10.3389/fmicb.2021.642422] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.
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Affiliation(s)
- Lauren M. Lui
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Erica L.-W. Majumder
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, United States
| | - Heidi J. Smith
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Hans K. Carlson
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Frederick von Netzer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, United States
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology & Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, United States
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Paul D. Adams
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Adam P. Arkin
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
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16
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Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 738:139710. [PMID: 32544704 DOI: 10.1016/j.scitotenv.2020.139710] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO3- occurs in two steps; in the first step, NO3- is reduced to NO2-; and in the second, unlike denitrification, NO2- is reduced to NH4+ without intermediates. There are two sets of NO3-/NO2- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N2O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N2O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO2-/NO3- ratio, and concentrations of ferrous iron (Fe2+) and sulfide (S2-). Under low-redox conditions, a high C/NO3- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO3- are equal, the NO2-/NO3- ratio modulates partitioning of NO3-, and a high NO2-/NO3- ratio favours DNRA. A high S2-/NO3- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO3- to NH4+, it is essential for protecting NO3- from leaching and gaseous (N2O) losses and enriches soils with readily available NH4+-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO3- pollution, enhance soil health and improve environmental quality.
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Affiliation(s)
- C B Pandey
- ICAR-Central Arid Zone Research Institute, Jodhpur 342003, Rajasthan, India.
| | - Upendra Kumar
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India.
| | - Megha Kaviraj
- ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India
| | - K J Minick
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - A K Mishra
- International Rice Research Institute, New Delhi 110012, India
| | - J S Singh
- Ecosystem Analysis Lab, Centre of Advanced Study in Botany, Banaras Hindu University (BHU), Varanasi 221005, India
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17
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Wang R, Wang WY, Liu MY, Zeb BS, Zhao ZG, Wang L. Improvement of ferrous ion-dependent nitrate removal (FeNiR) process with chelating ferrous ion as substrate. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110841. [PMID: 32579513 DOI: 10.1016/j.jenvman.2020.110841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/19/2020] [Accepted: 05/24/2020] [Indexed: 06/11/2023]
Abstract
In order to improve the ferrous ion-dependent nitrate removal (FeNiR) process, hexametaphosphate chelated ferrous ion was used as substrate to replace the free ferrous ion. With hexametaphosphate chelated ferrous ion as substrate, the influent pH was adjusted to 6.8, and as a result a higher effluent pH (7.2) was detected. The volumetric removal rate (VRR) of nitrate kept at 0.42 ± 0.03 kg-N/(m3∙d) for 48 days and the corresponding nitrogen removal efficiency was 94.39 ± 4.57%. After 88 days of cultivation, FeNiR granules became small because of the oligotrophic substrate. The transmission electron microscope (TEM) analysis showed that less iron encrustation was formed on the surface or in the periplasm of FeNiR cells. The linear curve of the living cell percentage versus time showed that the death rate of FeNiR cells with chelated ferrous ion as substrate was much lower than that with free ferrous ion as substrate (0.4210 vs 0.9221). Without iron encrustation, both the FeNiR activity and alkaline phosphatase (ALP) activity of FeNiR cells kept at high level and thus the efficiency of the FeNiR reactor kept stable and high. With hexametaphosphate chelated ferrous ion as substrate, the pH in bulk liquid was high (pH = 7.2) resulting in the high FeNiR rate, and less iron encrustation was formed around cells ensuring the stability of high FeNiR rate. Therefore, using hexametaphosphate chelated ferrous ion as substrate was an efficient way to improve the FeNiR process.
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Affiliation(s)
- Ru Wang
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Wen-Yan Wang
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Meng-Yu Liu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Bibi Saima Zeb
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan.
| | - Zhi-Guo Zhao
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Lan Wang
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu, 610041, PR China; Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610041, PR China.
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18
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Hu Y, Wu G, Li R, Xiao L, Zhan X. Iron sulphides mediated autotrophic denitrification: An emerging bioprocess for nitrate pollution mitigation and sustainable wastewater treatment. WATER RESEARCH 2020; 179:115914. [PMID: 32413614 DOI: 10.1016/j.watres.2020.115914] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/16/2020] [Accepted: 05/02/2020] [Indexed: 05/09/2023]
Abstract
Iron sulphides, mainly in the form of mackinawite (FeS), pyrrhotite (Fe1-xS, x = 0-0.125) and pyrite (FeS2), are the most abundant sulphide minerals and can be oxidized under anoxic and circumneutral pH conditions by chemoautotrophic denitrifying bacteria to reduce nitrate to N2. Iron sulphides mediated autotrophic denitrification (ISAD) represents an important natural attenuation process of nitrate pollution and plays a pivotal role in linking nitrogen, sulphur and iron cycles in a variety of anoxic environments. Recently, it has emerged as a promising bioprocess for nutrient removal from various organic-deficient water and wastewater, due to its specific advantages including high denitrification capacity, simultaneous nitrogen and phosphorus removal, self-buffering properties, and fewer by-products generation (sulphate, waste sludge, N2O, NH4+, etc.). This paper provides a critical overview of fundamental and engineering aspects of ISAD, including the theoretical knowledge (biochemistry, and microbial diversity), its natural occurrence and engineering applications. Its potential and limitations are elucidated by summarizing the key influencing factors including availability of iron sulphides, low denitrification rates, sulphate emission and leaching heavy metals. This review also put forward two key questions in the mechanism of anoxic iron sulphides oxidation, i.e. dissolution of iron sulphides and direct substrates for denitrifiers. Finally, its prospects for future sustainable wastewater treatment are highlighted. An iron sulphides-based biotechnology towards next-generation wastewater treatment (NEO-GREEN) is proposed, which can potentially harness bioenergy in wastewater, incorporate resources (P and Fe) recovery, achieve simultaneous nutrient and emerging contaminants removal, and minimize waste sludge production.
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Affiliation(s)
- Yuansheng Hu
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guangxue Wu
- Institute of Environmental Engineering and Management, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Ruihua Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163# Xianlin Avenue, Nanjing, 210023, China
| | - Liwen Xiao
- Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, Dublin 2, Ireland
| | - Xinmin Zhan
- Civil Engineering, College of Engineering and Informatics, National University of Ireland, Galway, Ireland; Ryan Institute, National University of Ireland, Galway, Ireland; MaREI Centre for Marine and Renewable Energy, Ireland.
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Wang R, Xu SY, Zhang M, Ghulam A, Dai CL, Zheng P. Iron as electron donor for denitrification: The efficiency, toxicity and mechanism. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 194:110343. [PMID: 32151862 DOI: 10.1016/j.ecoenv.2020.110343] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 06/10/2023]
Abstract
For the treatment of low C/N wastewaters, methanol or acetate is usually dosed as electron donor for denitrification but such organics makes the process costly. To decrease the cost, iron which is the fourth most abundant element in lithosphere is suggested as the substitution of methanol and acetate. The peak volumetric removal rate (VRR) of nitrate nitrogen in the ferrous iron-dependent nitrate removal (FeNiR) reactor was 0.70 ± 0.04 kg-N/(m3·d), and the corresponding removal efficiency was 98%. Iron showed toxicity to cells by decreasing the live cell amount (dropped 56%) and the live cell activity (dropped 70%). The toxicity of iron was mainly expressed by the formation of iron encrustation. From microbial community data analysis, heterotrophs (Paracocccus, Thauera and Azoarcus) faded away while the facultative chemolithotrophs (Hyphomicrobium and Anaerolineaceae_uncultured) dominated in the reactor after replacing acetate with ferrous iron in the influent. Through scanning electron microscope (SEM) and transmission electron microscope (TEM), two iron oxidation sites in FeNiR cells were observed and accordingly two FeNiR mechanisms were proposed: 1) extracellular FeNiR in which ferrous iron was bio-oxidized extracellularly; and 2) intracellular FeNiR in which ferrous iron was chemically oxidized in periplasm. Bio-oxidation (extracellular FeNiR) and chemical oxidation (intracellular FeNiR) of ferrous iron coexisted in FeNiR reactor, but the former one predominated. Comparing with the control group without electron donor in the influent, FeNiR reactor showed 2 times higher and stable nitrate removal rate, suggesting iron could be used as electron donor for denitrification. However, further research works are still needed for the practical application of FeNiR in wastewater treatment.
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Affiliation(s)
- Ru Wang
- Environmental and Municipal Engineering College, Xi'an Univerisity of Architecture and Technology, Xi'an, 710055, PR China.
| | - Shao-Yi Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
| | - Meng Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment Water Research Institute, Nanyang Technological University, Singapore, 637141, Singapore.
| | - Abbas Ghulam
- Department of Chemical Engineering and Technology, University of Gujrat, Gujrat, 50700, Pakistan.
| | - Chen-Lin Dai
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, PR China.
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Iron Redox Reactions Can Drive Microtopographic Variation in Upland Soil Carbon Dioxide and Nitrous Oxide Emissions. SOIL SYSTEMS 2019. [DOI: 10.3390/soilsystems3030060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Topographic depressions in upland soils experience anaerobic conditions conducive for iron (Fe) reduction following heavy rainfall. These depressional areas can also accumulate reactive Fe compounds, carbon (C), and nitrate, creating potential hot spots of Fe-mediated carbon dioxide (CO2) and nitrous oxide (N2O) production. While there are multiple mechanisms by which Fe redox reactions can facilitate CO2 and N2O production, it is unclear what their cumulative effect is on CO2 and N2O emissions in depressional soils under dynamic redox. We hypothesized that Fe reduction and oxidation facilitate greater CO2 and N2O emissions in depressional compared to upslope soils in response to flooding. To test this, we amended upslope and depressional soils with Fe(II), Fe(III), or labile C and measured CO2 and N2O emissions in response to flooding. We found that depressional soils have greater Fe reduction potential, which can contribute to soil CO2 emissions during flooded conditions when C is not limiting. Additionally, Fe(II) addition stimulated N2O production, suggesting that chemodenitrification may be an important pathway of N2O production in depressions that accumulate Fe(II). As rainfall intensification results in more frequent flooding of depressional upland soils, Fe-mediated CO2 and N2O production may become increasingly important pathways of soil greenhouse gas emissions.
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21
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Zhang Y, Liu X, Fu C, Li X, Yan B, Shi T. Effect of Fe 2+ addition on chemical oxygen demand and nitrogen removal in horizontal subsurface flow constructed wetlands. CHEMOSPHERE 2019; 220:259-265. [PMID: 30590292 DOI: 10.1016/j.chemosphere.2018.12.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
Horizontal subsurface flow constructed wetlands (CWs) planted with Phragmites australis were set up to analyze the effect of external ferrous iron (Fe2+) addition on chemical oxygen demand (COD) and nitrogen removal. The results showed that external Fe2+ addition has no significant effect on COD removal, while the COD removal efficiencies in CWs with Fe2+ addition were slightly lower than those in CWs without Fe2+ addition, since Fe2+ as an electron donor for denitrification may decrease the consumption of organic carbon. However, external Fe2+ addition significantly enhanced the nitrogen removal capability of the CWs. With an increase in external Fe2+ concentration, the removal efficiencies for total nitrogen (TN), nitrate nitrogen (NO3N), and ammonium nitrogen (NH4N) all increased. The removal efficiencies for TN and NH4N were greatest for an influent Fe2+ concentration of 50 mg L-1, while the greatest removal efficiencies for NO3N were observed at an influent Fe2+ concentration of 150 mg L-1. With increasing hydraulic retention time (HRT), the COD and NO3N removal efficiencies in the CWs with external Fe2+ addition increase sharply and then became stable, while the removal efficiency for TN exhibited a continuous increase. The removal efficiency for NH4N was greatest at an HRT of 5 d-7 d with Fe2+ addition. The change in pH with increasing HRT indicated that external Fe2+ addition did not significantly affect the pH value of the effluent water, but that the wetland systems caused an increase in effluent pH. Fe2+ addition remarkably reduced the oxygen-reduction potential of both the influent and effluent water, which was beneficial to denitrification of microorganisms.
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Affiliation(s)
- Yan Zhang
- Poultry Institute, Shangdong Academy of Agricultural Science, Jinan 250023, PR China
| | - Xuelan Liu
- Poultry Institute, Shangdong Academy of Agricultural Science, Jinan 250023, PR China.
| | - Chunyan Fu
- Poultry Institute, Shangdong Academy of Agricultural Science, Jinan 250023, PR China
| | - Xinhua Li
- Shandong Institute of Agricultural Sustainable Development, Jinan 250100, PR China
| | - Baixing Yan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130012, PR China
| | - Tianhong Shi
- Poultry Institute, Shangdong Academy of Agricultural Science, Jinan 250023, PR China
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22
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Liu T, Chen D, Li X, Li F. Microbially mediated coupling of nitrate reduction and Fe(II) oxidation under anoxic conditions. FEMS Microbiol Ecol 2019; 95:5371120. [DOI: 10.1093/femsec/fiz030] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/06/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tongxu Liu
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
| | - Dandan Chen
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaomin Li
- The Environmental Research Institute, MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Fangbai Li
- Guangzhou Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, P. R. China
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Draft Genome Sequences of the Nitrate-Dependent Iron-Oxidizing Proteobacteria Acidovorax sp. Strain BoFeN1 and Paracoccus pantotrophus Strain KS1. Microbiol Resour Announc 2018; 7:MRA01050-18. [PMID: 30533623 PMCID: PMC6256601 DOI: 10.1128/mra.01050-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 08/15/2018] [Indexed: 12/03/2022] Open
Abstract
The draft genomes of the nitrate-dependent iron-oxidizing bacteria Acidovorax sp. strain BoFeN1 and Paracoccus pantotrophus strain KS1 are presented. The draft genomes of the nitrate-dependent iron-oxidizing bacteria Acidovorax sp. strain BoFeN1 and Paracoccus pantotrophus strain KS1 are presented. These genomes supply supporting data to investigations of the mechanisms underlying this anaerobic form of microbial biogeochemical iron cycling.
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Jamieson J, Prommer H, Kaksonen AH, Sun J, Siade AJ, Yusov A, Bostick B. Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5771-5781. [PMID: 29676145 PMCID: PMC6427828 DOI: 10.1021/acs.est.8b01122] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.
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Affiliation(s)
- James Jamieson
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Henning Prommer
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- Corresponding Author: .
| | - Anna H. Kaksonen
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jing Sun
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Adam J. Siade
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Anna Yusov
- Department of Chemistry, Barnard College, 3009 Broadway, New York, New York 10027, United States
| | - Benjamin Bostick
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
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25
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Price A, Pearson VK, Schwenzer SP, Miot J, Olsson-Francis K. Nitrate-Dependent Iron Oxidation: A Potential Mars Metabolism. Front Microbiol 2018; 9:513. [PMID: 29616015 PMCID: PMC5869265 DOI: 10.3389/fmicb.2018.00513] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 03/06/2018] [Indexed: 11/13/2022] Open
Abstract
This work considers the hypothetical viability of microbial nitrate-dependent Fe2+ oxidation (NDFO) for supporting simple life in the context of the early Mars environment. This draws on knowledge built up over several decades of remote and in situ observation, as well as recent discoveries that have shaped current understanding of early Mars. Our current understanding is that certain early martian environments fulfill several of the key requirements for microbes with NDFO metabolism. First, abundant Fe2+ has been identified on Mars and provides evidence of an accessible electron donor; evidence of anoxia suggests that abiotic Fe2+ oxidation by molecular oxygen would not have interfered and competed with microbial iron metabolism in these environments. Second, nitrate, which can be used by some iron oxidizing microorganisms as an electron acceptor, has also been confirmed in modern aeolian and ancient sediment deposits on Mars. In addition to redox substrates, reservoirs of both organic and inorganic carbon are available for biosynthesis, and geochemical evidence suggests that lacustrine systems during the hydrologically active Noachian period (4.1-3.7 Ga) match the circumneutral pH requirements of nitrate-dependent iron-oxidizing microorganisms. As well as potentially acting as a primary producer in early martian lakes and fluvial systems, the light-independent nature of NDFO suggests that such microbes could have persisted in sub-surface aquifers long after the desiccation of the surface, provided that adequate carbon and nitrates sources were prevalent. Traces of NDFO microorganisms may be preserved in the rock record by biomineralization and cellular encrustation in zones of high Fe2+ concentrations. These processes could produce morphological biosignatures, preserve distinctive Fe-isotope variation patterns, and enhance preservation of biological organic compounds. Such biosignatures could be detectable by future missions to Mars with appropriate instrumentation.
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Affiliation(s)
- Alex Price
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Victoria K. Pearson
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Susanne P. Schwenzer
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
| | - Jennyfer Miot
- CNRS, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, UMR 7590, Paris, France
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, United Kingdom
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26
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Thorpe CL, Law GTW, Lloyd JR, Williams HA, Atherton N, Morris K. Quantifying Technetium and Strontium Bioremediation Potential in Flowing Sediment Columns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:12104-12113. [PMID: 28968094 DOI: 10.1021/acs.est.7b02652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The high-yield fission products 99Tc and 90Sr are found as problematic radioactive contaminants in groundwater at nuclear sites. Treatment options for radioactively contaminated land include bioreduction approaches, and this paper explores 99mTc and 90Sr behavior and stability under a range of biogeochemical conditions stimulated by electron donor addition methods. Dynamic column experiments with sediment from the Sellafield nuclear facility, completed at site relevant flow conditions, demonstrated that Fe(III)-reducing conditions had developed by 60 days. Sediment reactivity toward 99Tc was then probed using a 99mTc(VII) tracer at <10-10 mol L-1 and γ camera imaging showed full retention of 99mTc in acetate amended systems. Sediment columns were then exposed to selected treatments to examine the effects of different acetate amendment regimes and reoxidation scenarios over 55 days when they were again imaged with 99mTc. Here, partially oxidized sediments with no further electron donor additions remained reactive toward 99mTc under relevant groundwater O2 and NO3- concentrations over 55 days. Immobilization of 99mTc was highest where continuous acetate amendment had resulted in sulfate-reducing conditions. Interestingly, the sulfate reducing system showed enhanced Sr retention when stable Sr2+ was added continuously as a proxy for 90Sr. Overall, sediment reactivity was nondestructively imaged over an extended period to provide new information about dynamic iron and radionuclide biogeochemistry throughout realistic sediment redox cycling regimes.
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Affiliation(s)
- Clare L Thorpe
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester , Manchester M13 9PL, United Kingdom
| | - Gareth T W Law
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester , Manchester M13 9PL, United Kingdom
- Centre for Radiochemistry Research, School of Chemistry, The University of Manchester , Manchester M13 9PL, United Kingdom
| | - Jonathan R Lloyd
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester , Manchester M13 9PL, United Kingdom
| | - Heather A Williams
- Nuclear Medicine Centre, Manchester Royal Infirmary , Manchester M13 9WL, United Kingdom
| | - Nick Atherton
- Sellafield Ltd. , Land Quality, Sellafield, Seascale, Cumbria CA20 1PG, United Kingdom
| | - Katherine Morris
- Research Centre for Radwaste Disposal and Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester , Manchester M13 9PL, United Kingdom
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Mechanism of H 2S Oxidation by the Dissimilatory Perchlorate-Reducing Microorganism Azospira suillum PS. mBio 2017; 8:mBio.02023-16. [PMID: 28223460 PMCID: PMC5358917 DOI: 10.1128/mbio.02023-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The genetic and biochemical basis of perchlorate-dependent H2S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) Azospira suillum PS (PS). Previously, it was shown that all known DPRMs innately oxidize H2S, producing elemental sulfur (So). Although the process involving PSOX is thermodynamically favorable (ΔG°' = -206 kJ ⋅ mol-1 H2S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H2S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism. Here, we determined that PSOX is due to a combination of enzymatic and abiotic interactions involving reactive intermediates of perchlorate respiration. Using various approaches, including barcode analysis by sequencing (Bar-seq), transcriptome sequencing (RNA-seq), and proteomics, along with targeted mutagenesis and biochemical characterization, we identified all facets of PSOX in PS. In support of our proposed model, deletion of identified upregulated PS genes traditionally known to be involved in sulfur redox cycling (e.g., Sox, sulfide:quinone reductase [SQR]) showed no defect in PSOX activity. Proteomic analysis revealed differential abundances of a variety of stress response metal efflux pumps and divalent heavy-metal transporter proteins, suggesting a general toxicity response. Furthermore, in vitro biochemical studies demonstrated direct PSOX mediated by purified perchlorate reductase (PcrAB) in the absence of other electron transfer proteins. The results of these studies support a model in which H2S oxidation is mediated by electron transport chain short-circuiting in the periplasmic space where the PcrAB directly oxidizes H2S to So The biogenically formed reactive intermediates (ClO2- and O2) subsequently react with additional H2S, producing polysulfide and So as end products.IMPORTANCE Inorganic sulfur compounds are widespread in nature, and microorganisms are central to their transformation, thereby playing a key role in the global sulfur cycle. Sulfur oxidation is mediated by a broad phylogenetic diversity of microorganisms, including anoxygenic phototrophs and either aerobic or anaerobic chemotrophs coupled to oxygen or nitrate respiration, respectively. Recently, perchlorate-respiring microorganisms were demonstrated to be innately capable of sulfur oxidation regardless of their phylogenetic affiliation. As recognition of the prevalence of these organisms intensifies, their role in global geochemical cycles is being queried. This is further highlighted by the recently recognized environmental pervasiveness of perchlorate not only across Earth but also throughout our solar system. The inferred importance of this metabolism not only is that it is a novel and previously unrecognized component of the global sulfur redox cycle but also is because of the recently demonstrated applicability of perchlorate respiration in the control of biogenic sulfide production in engineered environments such as oil reservoirs and wastewater treatment facilities, where excess H2S represents a significant environmental, process, and health risk, with associated costs approximating $90 billion annually.
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Ishii S, Joikai K, Otsuka S, Senoo K, Okabe S. Denitrification and Nitrate-Dependent Fe(II) Oxidation in Various Pseudogulbenkiania Strains. Microbes Environ 2016; 31:293-8. [PMID: 27431373 PMCID: PMC5017806 DOI: 10.1264/jsme2.me16001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/14/2016] [Indexed: 12/05/2022] Open
Abstract
Pseudogulbenkiania is a relatively recently characterized genus within the order Neisseriales, class Betaproteobacteria. This genus contains several strains that are capable of anaerobic, nitrate-dependent Fe(II) oxidation (NDFO), a geochemically important reaction for nitrogen and iron cycles. In the present study, we examined denitrification functional gene diversities within this genus, and clarified whether other Pseudogulbenkiania sp. strains perform denitrification and NDFO. Seventy strains were analyzed, including two type strains, a well-characterized NDFO strain, and 67 denitrifying strains isolated from various rice paddy fields and rice-soybean rotation fields in Japan. We also attempted to identify the genes responsible for NDFO by mutagenesis. Our comprehensive analysis showed that all Pseudogulbenkiania strains tested performed denitrification and NDFO; however, we were unable to obtain NDFO-deficient denitrifying mutants in our mutagenesis experiment. This result suggests that Fe(II) oxidation in these strains is not enzymatic, but is caused by reactive N-species that are formed during nitrate reduction. Based on the results of the comparative genome analysis among Pseudogulbenkiania sp. strains, we identified low sequence similarity within the nos gene as well as different gene arrangements within the nos gene cluster, suggesting that nos genes were horizontally transferred. Since Pseudogulbenkiania sp. strains have been isolated from various locations around the world, their denitrification and NDFO abilities may contribute significantly to nitrogen and iron biogeochemical cycles.
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Affiliation(s)
- Satoshi Ishii
- Department of Soil, Water, and Climate; BioTechnology Institute, University of Minnesota140 Gortner Laboratory, 1479 Gortner Ave., St. Paul, MN 55108–6106USA
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
| | - Kazuki Joikai
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, The University of Tokyo1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, The University of Tokyo1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
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Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS. Appl Environ Microbiol 2016; 82:2656-2668. [PMID: 26896135 DOI: 10.1128/aem.03493-15] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/16/2016] [Indexed: 01/22/2023] Open
Abstract
Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458-1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae, and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochromec system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochromecand multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.
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Mejia J, Roden EE, Ginder-Vogel M. Influence of Oxygen and Nitrate on Fe (Hydr)oxide Mineral Transformation and Soil Microbial Communities during Redox Cycling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3580-8. [PMID: 26949922 PMCID: PMC5066396 DOI: 10.1021/acs.est.5b05519] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Oscillations between reducing and oxidizing conditions are observed at the interface of anaerobic/oxic and anaerobic/anoxic environments, and are often stimulated by an alternating flux of electron donors (e.g., organic carbon) and electron acceptors (e.g., O2 and NO3(-)). In iron (Fe) rich soils and sediments, these oscillations may stimulate the growth of both Fe-reducing bacteria (FeRB) and Fe-oxidizing bacteria (FeOB), and their metabolism may induce cycling between Fe(II) and Fe(III), promoting the transformation of Fe (hydr)oxide minerals. Here, we examine the mineralogical evolution of lepidocrocite and ferrihydrite, and the adaptation of a natural microbial community to alternating Fe-reducing (anaerobic with addition of glucose) and Fe-oxidizing (with addition of nitrate or air) conditions. The growth of FeRB (e.g., Geobacter) is stimulated under anaerobic conditions in the presence of glucose. However, the abundance of these organisms depends on the availability of Fe(III) (hydr)oxides. Redox cycling with nitrate results in decreased Fe(II) oxidation thereby decreasing the availability of Fe(III) for FeRB. Additionally, magnetite is detected as the main product of both lepidocrocite and ferrihydrite reduction. In contrast, introduction of air results in increased Fe(II) oxidation, increasing the availability of Fe(III) and the abundance of Geobacter. In the lepidocrocite reactors, Fe(II) oxidation by dissolved O2 promotes the formation of ferrihydrite and lepidocrocite, whereas in the ferrihydrite reactors we observe a decrease in magnetite stoichiometry (e.g., oxidation). Understanding Fe (hydr)oxide transformation under environmentally relevant redox cycling conditions provides insight into nutrient availability and transport, contaminant mobility, and microbial metabolism in soils and sediments.
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Affiliation(s)
- Jacqueline Mejia
- Environmental Chemistry and Technology Program, Department of Civil and Environmental Engineering, The University of Wisconsin–Madison, 660 North Park Street, Madison, Wisconsin 53706, United States
| | - Eric E. Roden
- Department of Geoscience, The University of Wisconsin–Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, United States
| | - Matthew Ginder-Vogel
- Environmental Chemistry and Technology Program, Department of Civil and Environmental Engineering, The University of Wisconsin–Madison, 660 North Park Street, Madison, Wisconsin 53706, United States
- Corresponding Author, Matthew Ginder-Vogel. . Phone: 608-262-0768. Fax: 608-262-0454
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31
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Liu Y, Feng C, Chen N, Sheng Y, Dong S, Hao C, Lei K. Bioremediation of nitrate and Fe(ii) combined contamination in groundwater by heterotrophic denitrifying bacteria and microbial community analysis. RSC Adv 2016. [DOI: 10.1039/c6ra22687f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The optimal condition range was determined for the simultaneous removal of nitrate and Fe(ii) in groundwater mediated by denitrifying Betaproteobacterial communities.
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Affiliation(s)
- Ying Liu
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Chuanping Feng
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Nan Chen
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Yizhi Sheng
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Shanshan Dong
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Chunbo Hao
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
| | - Kang Lei
- School of Water Resources and Environment
- China University of Geosciences
- Beijing 100083
- China
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32
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White GF, Edwards MJ, Gomez-Perez L, Richardson DJ, Butt JN, Clarke TA. Mechanisms of Bacterial Extracellular Electron Exchange. Adv Microb Physiol 2016; 68:87-138. [PMID: 27134022 DOI: 10.1016/bs.ampbs.2016.02.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The biochemical mechanisms by which microbes interact with extracellular soluble metal ions and insoluble redox-active minerals have been the focus of intense research over the last three decades. The process presents two challenges to the microorganism. Firstly, electrons have to be transported at the cell surface, which in Gram-negative bacteria presents an additional problem of electron transfer across the ~6nm of the outer membrane. Secondly, the electrons must be transferred to or from the terminal electron acceptors or donors. This review covers the known mechanisms that bacteria use to transport electrons across the cell envelope to external electron donors/acceptors. In Gram-negative bacteria, electron transfer across the outer membrane involves the use of an outer membrane β-barrel and cytochrome. These can be in the form of a porin-cytochrome protein, such as Cyc2 of Acidithiobacillus ferrooxidans, or a multiprotein porin-cytochrome complex like MtrCAB of Shewanella oneidensis MR-1. For mineral-respiring organisms, there is the additional challenge of transferring the electrons from the cell to mineral surface. For the strict anaerobe Geobacter sulfurreducens this requires electron transfer through conductive pili to associated cytochrome OmcS that directly reduces Fe(III)oxides, while the facultative anaerobe S. oneidensis MR-1 accomplishes mineral reduction through direct membrane contact, contact through filamentous extensions and soluble flavin shuttles, all of which require the outer membrane cytochromes MtrC and OmcA in addition to secreted flavin.
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Affiliation(s)
- G F White
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - M J Edwards
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - L Gomez-Perez
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - D J Richardson
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - J N Butt
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - T A Clarke
- School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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33
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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Bennett BD, Brutinel ED, Gralnick JA. A Ferrous Iron Exporter Mediates Iron Resistance in Shewanella oneidensis MR-1. Appl Environ Microbiol 2015; 81:7938-44. [PMID: 26341213 PMCID: PMC4616933 DOI: 10.1128/aem.02835-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022] Open
Abstract
Shewanella oneidensis strain MR-1 is a dissimilatory metal-reducing bacterium frequently found in aquatic sediments. In the absence of oxygen, S. oneidensis can respire extracellular, insoluble oxidized metals, such as iron (hydr)oxides, making it intimately involved in environmental metal and nutrient cycling. The reduction of ferric iron (Fe(3+)) results in the production of ferrous iron (Fe(2+)) ions, which remain soluble under certain conditions and are toxic to cells at higher concentrations. We have identified an inner membrane protein in S. oneidensis, encoded by the gene SO_4475 and here called FeoE, which is important for survival during anaerobic iron respiration. FeoE, a member of the cation diffusion facilitator (CDF) protein family, functions to export excess Fe(2+) from the MR-1 cytoplasm. Mutants lacking feoE exhibit an increased sensitivity to Fe(2+). The export function of FeoE is specific for Fe(2+), as an feoE mutant is equally sensitive to other metal ions known to be substrates of other CDF proteins (Cd(2+), Co(2+), Cu(2+), Mn(2+), Ni(2+), or Zn(2+)). The substrate specificity of FeoE differs from that of FieF, the Escherichia coli homolog of FeoE, which has been reported to be a Cd(2+)/Zn(2+) or Fe(2+)/Zn(2+) exporter. A complemented feoE mutant has an increased growth rate in the presence of excess Fe(2+) compared to that of the ΔfeoE mutant complemented with fieF. It is possible that FeoE has evolved to become an efficient and specific Fe(2+) exporter in response to the high levels of iron often present in the types of environmental niches in which Shewanella species can be found.
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Affiliation(s)
- Brittany D Bennett
- BioTechnology Institute and Department of Microbiology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Evan D Brutinel
- BioTechnology Institute and Department of Microbiology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Microbiology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
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Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer. Front Microbiol 2015; 6:879. [PMID: 26441847 PMCID: PMC4562303 DOI: 10.3389/fmicb.2015.00879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.
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Affiliation(s)
- Jennyfer Miot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Adriana Gonzalez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Sylvain Pont
- Département des Collections, Muséum National d’Histoire NaturelleParis, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
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36
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Gregoire P, Engelbrektson A, Hubbard CG, Metlagel Z, Csencsits R, Auer M, Conrad ME, Thieme J, Northrup P, Coates JD. Control of sulfidogenesis through bio-oxidation of H2S coupled to (per)chlorate reduction. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:558-564. [PMID: 25756108 DOI: 10.1111/1758-2229.12156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We investigated H2S attenuation by dissimilatory perchlorate-reducing bacteria (DPRB). All DPRB tested oxidized H2S coupled to (per)chlorate reduction without sustaining growth. H2S was preferentially utilized over organic electron donors resulting in an enriched (34S)-elemental sulfur product. Electron microscopy revealed elemental sulfur production in the cytoplasm and on the cell surface of the DPRB Azospira suillum. Based on our results, we propose a novel hybrid enzymatic-abiotic mechanism for H2S oxidation similar to that recently proposed for nitrate-dependent Fe(II) oxidation. The results of this study have implications for the control of biosouring and biocorrosion in a range of industrial environments.
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37
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The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon. Appl Environ Microbiol 2014; 81:1003-12. [PMID: 25416759 DOI: 10.1128/aem.02705-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genus Geoglobus is their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds, n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multiheme c-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds and n-alkanes, although an ability of G. acetivorans to grow on these substrates was not observed in laboratory experiments. Overall, our results suggest that Geoglobus species could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.
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38
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Melton ED, Swanner ED, Behrens S, Schmidt C, Kappler A. The interplay of microbially mediated and abiotic reactions in the biogeochemical Fe cycle. Nat Rev Microbiol 2014; 12:797-808. [DOI: 10.1038/nrmicro3347] [Citation(s) in RCA: 503] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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39
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Schmid G, Zeitvogel F, Hao L, Ingino P, Floetenmeyer M, Stierhof YD, Schroeppel B, Burkhardt CJ, Kappler A, Obst M. 3-D analysis of bacterial cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using complementary microscopy tomography approaches. GEOBIOLOGY 2014; 12:340-361. [PMID: 24828365 DOI: 10.1111/gbi.12088] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
The formation of cell-(iron)mineral aggregates as a consequence of bacterial iron oxidation is an environmentally widespread process with a number of implications for processes such as sorption and coprecipitation of contaminants and nutrients. Whereas the overall appearance of such aggregates is easily accessible using 2-D microscopy techniques, the 3-D and internal structure remain obscure. In this study, we examined the 3-D structure of cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using a combination of advanced 3-D microscopy techniques. We obtained 3-D structural and chemical information on different cellular encrustation patterns at high spatial resolution (4-200 nm, depending on the method): more specifically, (1) cells free of iron minerals, (2) periplasm filled with iron minerals, (3) spike- or platelet-shaped iron mineral structures, (4) bulky structures on the cell surface, (5) extracellular iron mineral shell structures, (6) cells with iron mineral filled cytoplasm, and (7) agglomerations of extracellular globular structures. In addition to structural information, chemical nanotomography suggests a dominant role of extracellular polymeric substances (EPS) in controlling the formation of cell-(iron)mineral aggregates. Furthermore, samples in their hydrated state showed cell-(iron)mineral aggregates in pristine conditions free of preparation (i.e., drying/dehydration) artifacts. All these results were obtained using 3-D microscopy techniques such as focused ion beam (FIB)/scanning electron microscopy (SEM) tomography, transmission electron microscopy (TEM) tomography, scanning transmission (soft) X-ray microscopy (STXM) tomography, and confocal laser scanning microscopy (CLSM). It turned out that, due to the various different contrast mechanisms of the individual approaches, and due to the required sample preparation steps, only the combination of these techniques was able to provide a comprehensive understanding of structure and composition of the various Fe-precipitates and their association with bacterial cells and EPS.
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Affiliation(s)
- G Schmid
- Center for Applied Geoscience, University of Tuebingen, Tuebingen, Germany
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40
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Dubinina GA, Sorokina AY. Neutrophilic lithotrophic iron-oxidizing prokaryotes and their role in the biogeochemical processes of the iron cycle. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714020052] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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41
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Beller HR, Zhou P, Legler TC, Chakicherla A, Kane S, Letain TE, A O'Day P. Genome-enabled studies of anaerobic, nitrate-dependent iron oxidation in the chemolithoautotrophic bacterium Thiobacillus denitrificans. Front Microbiol 2013; 4:249. [PMID: 24065960 PMCID: PMC3753534 DOI: 10.3389/fmicb.2013.00249] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 08/06/2013] [Indexed: 01/15/2023] Open
Abstract
Thiobacillus denitrificans is a chemolithoautotrophic bacterium capable of anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, both of which can strongly influence the long-term efficacy of in situ reductive immobilization of uranium in contaminated aquifers. We previously identified two c-type cytochromes involved in nitrate-dependent U(IV) oxidation in T. denitrificans and hypothesized that c-type cytochromes would also catalyze Fe(II) oxidation, as they have been found to play this role in anaerobic phototrophic Fe(II)-oxidizing bacteria. Here we report on efforts to identify genes associated with nitrate-dependent Fe(II) oxidation, namely (a) whole-genome transcriptional studies [using FeCO3, Fe(2) (+), and U(IV) oxides as electron donors under denitrifying conditions], (b) Fe(II) oxidation assays performed with knockout mutants targeting primarily highly expressed or upregulated c-type cytochromes, and (c) random transposon-mutagenesis studies with screening for Fe(II) oxidation. Assays of mutants for 26 target genes, most of which were c-type cytochromes, indicated that none of the mutants tested were significantly defective in nitrate-dependent Fe(II) oxidation. The non-defective mutants included the c 1-cytochrome subunit of the cytochrome bc 1 complex (complex III), which has relevance to a previously proposed role for this complex in nitrate-dependent Fe(II) oxidation and to current concepts of reverse electron transfer. A transposon mutant with a disrupted gene associated with NADH:ubiquinone oxidoreductase (complex I) was ~35% defective relative to the wild-type strain; this strain was similarly defective in nitrate reduction with thiosulfate as the electron donor. Overall, our results indicate that nitrate-dependent Fe(II) oxidation in T. denitrificans is not catalyzed by the same c-type cytochromes involved in U(IV) oxidation, nor have other c-type cytochromes yet been implicated in the process.
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Affiliation(s)
- Harry R Beller
- Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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42
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Carlson HK, Iavarone AT, Coates JD. Surfaceomics and surface-enhanced Raman spectroscopy of environmental microbes: Matching cofactors with redox-active surface proteins. Proteomics 2013; 13:2761-5. [DOI: 10.1002/pmic.201300010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Hans K. Carlson
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility; University of California; Berkeley CA USA
| | - John D. Coates
- Department of Plant and Microbial Biology; University of California; Berkeley CA USA
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43
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Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions. J Bacteriol 2013; 195:3260-8. [PMID: 23687275 DOI: 10.1128/jb.00058-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO(3)(-)) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO(2)(-)/NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO(2)(-), NO, and N(2)O in the environment.
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Abstract
Today high Fe(II) environments are relegated to oxic-anoxic habitats with opposing gradients of O2 and Fe(II); however, during the late Archaean and early Proterozoic eons, atmospheric O2 concentrations were much lower and aqueous Fe(II) concentrations were significantly higher. In current Fe(II)-rich environments, such as hydrothermal vents, mudflats, freshwater wetlands or the rhizosphere, rusty mat-like deposits are common. The presence of abundant biogenic microtubular or filamentous iron oxyhydroxides readily reveals the role of FeOB (iron-oxidizing bacteria) in iron mat formation. Cultivation and cultivation-independent techniques, confirm that FeOB are abundant in these mats. Despite remarkable similarities in morphological characteristics between marine and freshwater FeOB communities, the resident populations of FeOB are phylogenetically distinct, with marine populations related to the class Zetaproteobacteria, whereas freshwater populations are dominated by members of the Gallionallaceae, a family within the Betaproteobacteria. Little is known about the mechanism of how FeOB acquire electrons from Fe(II), although it is assumed that it involves electron transfer from the site of iron oxidation at the cell surface to the cytoplasmic membrane. Comparative genomics between freshwater and marine strains reveals few shared genes, except for a suite of genes that include a class of molybdopterin oxidoreductase that could be involved in iron oxidation via extracellular electron transport. Other genes are implicated as well, and the overall genomic analysis reveals a group of organisms exquisitely adapted for growth on iron.
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45
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Van Trump JI, Rivera Vega FJ, Coates JD. Natural organic matter as global antennae for primary production. ASTROBIOLOGY 2013; 13:476-482. [PMID: 23683047 PMCID: PMC3657287 DOI: 10.1089/ast.2012.0913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 03/02/2012] [Indexed: 06/02/2023]
Abstract
Humic substances (HS) are high-molecular-weight complex refractory organics that are ubiquitous in terrestrial and aquatic environments. While resistant to microbial degradation, these compounds nevertheless support microbial metabolism via oxidation or reduction of their (hydro)quinone moieties. As such, they are known to be important electron sinks for respiratory and fermentative bacteria and electron sources for denitrifying and perchlorate-reducing bacteria. HS also strongly promote abiotic reduction of Fe(III) when irradiated with light. Here, we show that HS-enhanced Fe(III) photoreduction can also drive chemolithotrophic microbial respiration by producing Fe(II), which functions as a respiratory electron donor. Due to their molecular complexity, HS absorb most of the electromagnetic spectrum and can act as broad-spectrum antennae converting radiant energy into bioavailable chemical energy. The finding that chemolithotrophic organisms can utilize this energy has important implications for terrestrial, and possibly extraterrestrial, microbial processes and offers an alternative mechanism of radiation-driven primary productivity to that of phototrophy.
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Affiliation(s)
- J Ian Van Trump
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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Nitrate-dependent ferrous iron oxidation by anaerobic ammonium oxidation (anammox) bacteria. Appl Environ Microbiol 2013; 79:4087-93. [PMID: 23624480 DOI: 10.1128/aem.00743-13] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined nitrate-dependent Fe(2+) oxidation mediated by anaerobic ammonium oxidation (anammox) bacteria. Enrichment cultures of "Candidatus Brocadia sinica" anaerobically oxidized Fe(2+) and reduced NO3(-) to nitrogen gas at rates of 3.7 ± 0.2 and 1.3 ± 0.1 (mean ± standard deviation [SD]) nmol mg protein(-1) min(-1), respectively (37°C and pH 7.3). This nitrate reduction rate is an order of magnitude lower than the anammox activity of "Ca. Brocadia sinica" (10 to 75 nmol NH4(+) mg protein(-1) min(-1)). A (15)N tracer experiment demonstrated that coupling of nitrate-dependent Fe(2+) oxidation and the anammox reaction was responsible for producing nitrogen gas from NO3(-) by "Ca. Brocadia sinica." The activities of nitrate-dependent Fe(2+) oxidation were dependent on temperature and pH, and the highest activities were seen at temperatures of 30 to 45°C and pHs ranging from 5.9 to 9.8. The mean half-saturation constant for NO3(-) ± SD of "Ca. Brocadia sinica" was determined to be 51 ± 21 μM. Nitrate-dependent Fe(2+) oxidation was further demonstrated by another anammox bacterium, "Candidatus Scalindua sp.," whose rates of Fe(2+) oxidation and NO3(-) reduction were 4.7 ± 0.59 and 1.45 ± 0.05 nmol mg protein(-1) min(-1), respectively (20°C and pH 7.3). Co-occurrence of nitrate-dependent Fe(2+) oxidation and the anammox reaction decreased the molar ratios of consumed NO2(-) to consumed NH4(+) (ΔNO2(-)/ΔNH4(+)) and produced NO3(-) to consumed NH4(+) (ΔNO3(-)/ΔNH4(+)). These reactions are preferable to the application of anammox processes for wastewater treatment.
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Kopf S, Henny C, Newman DK. Ligand-enhanced abiotic iron oxidation and the effects of chemical versus biological iron cycling in anoxic environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:2602-11. [PMID: 23402562 PMCID: PMC3604861 DOI: 10.1021/es3049459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This study introduces a newly isolated, genetically tractable bacterium ( Pseudogulbenkiania sp. strain MAI-1) and explores the extent to which its nitrate-dependent iron-oxidation activity is directly biologically catalyzed. Specifically, we focused on the role of iron chelating ligands in promoting chemical oxidation of Fe(II) by nitrite under anoxic conditions. Strong organic ligands such as nitrilotriacetate and citrate can substantially enhance chemical oxidation of Fe(II) by nitrite at circumneutral pH. We show that strain MAI-1 exhibits unambiguous biological Fe(II) oxidation despite a significant contribution (∼30-35%) from ligand-enhanced chemical oxidation. Our work with the model denitrifying strain Paracoccus denitrificans further shows that ligand-enhanced chemical oxidation of Fe(II) by microbially produced nitrite can be an important general side effect of biological denitrification. Our assessment of reaction rates derived from literature reports of anaerobic Fe(II) oxidation, both chemical and biological, highlights the potential competition and likely co-occurrence of chemical Fe(II) oxidation (mediated by microbial production of nitrite) and truly biological Fe(II) oxidation.
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Affiliation(s)
- Sebastian
H. Kopf
- Division
of Geologial and Planetary Sciences and Division of Biology, California Institute of Technology,
Pasadena, California, United States
| | - Cynthia Henny
- Research Center for
Limnology, LIPI, Cibinong, Indonesia
| | - Dianne K. Newman
- Division
of Geologial and Planetary Sciences and Division of Biology, California Institute of Technology,
Pasadena, California, United States
- Howard Hughes Medical
Institute, Pasadena, California, United States
- Phone: 626-395-3543. Fax: 626-395-4135. E-mail:
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The prokaryotic Mo/W-bisPGD enzymes family: a catalytic workhorse in bioenergetic. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:1048-85. [PMID: 23376630 DOI: 10.1016/j.bbabio.2013.01.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/21/2013] [Accepted: 01/23/2013] [Indexed: 01/05/2023]
Abstract
Over the past two decades, prominent importance of molybdenum-containing enzymes in prokaryotes has been put forward by studies originating from different fields. Proteomic or bioinformatic studies underpinned that the list of molybdenum-containing enzymes is far from being complete with to date, more than fifty different enzymes involved in the biogeochemical nitrogen, carbon and sulfur cycles. In particular, the vast majority of prokaryotic molybdenum-containing enzymes belong to the so-called dimethylsulfoxide reductase family. Despite its extraordinary diversity, this family is characterized by the presence of a Mo/W-bis(pyranopterin guanosine dinucleotide) cofactor at the active site. This review highlights what has been learned about the properties of the catalytic site, the modular variation of the structural organization of these enzymes, and their interplay with the isoprenoid quinones. In the last part, this review provides an integrated view of how these enzymes contribute to the bioenergetics of prokaryotes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
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Induction of nitrate-dependent Fe(II) oxidation by Fe(II) in Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Appl Environ Microbiol 2012; 79:748-52. [PMID: 23144134 DOI: 10.1128/aem.02709-12] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We evaluated the inducibility of nitrate-dependent Fe(II)-EDTA oxidation (NDFO) in non-growth, chloramphenicol-amended, resting-cell suspensions of Dechloromonas sp. strain UWNR4 and Acidovorax sp. strain 2AN. Cells previously incubated with Fe(II)-EDTA oxidized ca. 6-fold more Fe(II)-EDTA than cells previously incubated with Fe(III)-EDTA. This is the first report of induction of NDFO by Fe(II).
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Emerson D, Roden E, Twining BS. The microbial ferrous wheel: iron cycling in terrestrial, freshwater, and marine environments. Front Microbiol 2012; 3:383. [PMID: 23118735 PMCID: PMC3484406 DOI: 10.3389/fmicb.2012.00383] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 10/14/2012] [Indexed: 11/24/2022] Open
Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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