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Gao W, Duan X, Chen X, Wei L, Wang S, Wu J, Zhu Z. Iron‑carbon complex types and bonding forms jointly control organic carbon mineralization in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 953:176117. [PMID: 39245374 DOI: 10.1016/j.scitotenv.2024.176117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 09/02/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
The crucial role of iron (Fe) oxides in stabilizing soil organic carbon (SOC) is well recognized, but their effects on SOC mineralization remain poorly understood. To address this knowledge gap, we evaluated the effects of four typical Fe-bound OC (Fe-OC) complexes including adsorbed ferrihydrite (Fh)- and goethite (Goe)- 13C, coprecipitated Fh/Goe-13C and 13C-glucose as the control, on OC mineralization during an 80-day anaerobic incubation in a paddy soil. 13C-tracing indicated that Fe-13C complexes significantly stimulated CO2 emissions from both the input 13C and SOC compared with glucose alone. In contrast, the addition of Fh- and Goe-C complexes consistently inhibited CH4 emissions by 72-91 % and 21-61 % compared with glucose addition, respectively. Fe-OC complexes reduced the CO2 equivalent by 62-71 % and 17-41 % in soils with Fh-C and Goe-C complexes, respectively. We concluded that Fe crystallinity and its bonding forms with organic carbon jointly control SOC mineralization. The coprecipitated Goe-C complexes had the lowest OC mineralization rate and highest OC residence time among four Fe-OC complexes. These findings highlighted that promoting the formation of coprecipitated well-ordered minerals would increase SOC sequestration by reducing OC mineralization and mitigating the global warming effect in paddy management.
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Affiliation(s)
- Wei Gao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Xun Duan
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Xiangbi Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China.
| | - Liang Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Shuang Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, PR China
| | - Zhenke Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China; Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, PR China.
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Zhou X, Zhang X, Wang D, Luo R, Qin Z, Lin F, Xia X, Liu X, Hu G. Efficient Biosynthesis of Salidroside via Artificial in Vivo enhanced UDP-Glucose System Using Cheap Sucrose as Substrate. ACS OMEGA 2024; 9:22386-22397. [PMID: 38799314 PMCID: PMC11112596 DOI: 10.1021/acsomega.4c02060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Salidroside, a valuable phenylethanoid glycoside, is obtained from plants belonging to the Rhodiola genus, known for its diverse biological properties. At present, salidroside is still far from large-scale industrial production due to its lower titer and higher process cost. In this study, we have for the first time increased salidroside production by enhancing UDP-glucose supply in situ. We constructed an in vivo UDP-glucose regeneration system that works in conjunction with UDP-glucose transferase from Rhodiola innovatively to improve UDP-glucose availability. And a coculture was formed in order to enable de novo salidroside synthesis. Confronted with the influence of tyrosol on strain growth, an adaptive laboratory evolution strategy was implemented to enhance the strain's tolerance. Similarly, salidroside production was optimized through refinement of the fermentation medium, the inoculation ratio of the two microbes, and the inoculation size. The final salidroside titer reached 3.8 g/L. This was the highest titer achieved at the shake flask level in the existing reports. And this marked the first successful synthesis of salidroside in an in situ enhanced UDP-glucose system using sucrose. The cost was reduced by 93% due to the use of inexpensive substrates. This accomplishment laid a robust foundation for further investigations into the synthesis of other notable glycosides and natural compounds.
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Affiliation(s)
- Xiaojie Zhou
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Xiaoxiao Zhang
- AgroParisTech, 22 place de l’Agronomie, 91120 Palaiseau, France
| | - Dan Wang
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Ruoshi Luo
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Zhao Qin
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Fanzhen Lin
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Xue Xia
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Xuemei Liu
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
| | - Ge Hu
- Department
of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, P. R. China
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Li Y, Cao M, Gupta VK, Wang Y. Metabolic engineering strategies to enable microbial electrosynthesis utilization of CO 2: recent progress and challenges. Crit Rev Biotechnol 2024; 44:352-372. [PMID: 36775662 DOI: 10.1080/07388551.2023.2167065] [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: 06/04/2022] [Revised: 10/17/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
Microbial electrosynthesis (MES) is a promising technology that mainly utilizes microbial cells to convert CO2 into value-added chemicals using electrons provided by the cathode. However, the low electron transfer rate is a solid bottleneck hindering the further application of MES. Thus, as an effective strategy, genetic tools play a key role in MES for enhancing the electron transfer rate and diversity of production. We describe a set of genetic strategies based on fundamental characteristics and current successes and discuss their functional mechanisms in driving microbial electrocatalytic reactions to fully comprehend the roles and uses of genetic tools in MES. This paper also analyzes the process of nanomaterial application in extracellular electron transfer (EET). It provides a technique that combines nanomaterials and genetic tools to increase MES efficiency, because nanoparticles have a role in the production of functional genes in EET although genetic tools can subvert MES, it still has issues with difficult transformation and low expression levels. Genetic tools remain one of the most promising future strategies for advancing the MES process despite these challenges.
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Affiliation(s)
- Yixin Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen, China
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Edinburgh, UK
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
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Shi XC, Wang K, Xue M, Mao W, Xu K, Tremblay PL, Zhang T. Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens. CHEMOSPHERE 2024; 350:141177. [PMID: 38211787 DOI: 10.1016/j.chemosphere.2024.141177] [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: 07/20/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5-20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.
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Affiliation(s)
- Xiao-Chen Shi
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, 528437, PR China
| | - Kefan Wang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Miao Xue
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Weijia Mao
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Kai Xu
- Center for Material Research and Analysis, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan, 430070, PR China; Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, 312300, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, 572024, PR China.
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5
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Tremblay PL, Zhang T. Genetic tools for the electrotroph Sporomusa ovata and autotrophic biosynthesis. Appl Environ Microbiol 2024; 90:e0175723. [PMID: 38117058 PMCID: PMC10807461 DOI: 10.1128/aem.01757-23] [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: 10/04/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Sporomusa ovata is a Gram-negative acetogen of the Sporomusaceae family with a unique physiology. This anerobic bacterium is a core microbial catalyst for advanced CO2-based biotechnologies including gas fermentation, microbial electrosynthesis, and hybrid photosystem. Until now, no genetic tools exist for S. ovata, which is a critical obstacle to its optimization as an autotrophic chassis and the acquisition of knowledge about its metabolic capacities. Here, we developed an electroporation protocol for S. ovata. With this procedure, it became possible to introduce replicative plasmids such as pJIR751 and its derivatives into the acetogen. This system was then employed to demonstrate the feasibility of heterologous expression by introducing a functional β-glucuronidase enzyme under the promoters of different strengths in S. ovata. Next, a recombinant S. ovata strain producing the non-native product acetone both from an organic carbon substrate and from CO2 was constructed. Finally, a replicative plasmid capable of integrating itself on the chromosome of the acetogen was developed as a tool for genome editing, and gene deletion was demonstrated. These results indicate that S. ovata can be engineered and provides a first-generation genetic toolbox for the optimization of this biotechnological workhorse.IMPORTANCES. ovata harbors unique features that make it outperform most microbes for autotrophic biotechnologies such as a capacity to acquire electrons from different solid donors, a low H2 threshold, and efficient energy conservation mechanisms. The development of the first-generation genetic instruments described in this study is a key step toward understanding the molecular mechanisms involved in these outstanding metabolic and physiological characteristics. In addition, these tools enable the construction of recombinant S. ovata strains that can synthesize a wider range of products in an efficient manner.
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Affiliation(s)
- Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan, China
- Institut WUT-AMU, Wuhan University of Technology, Wuhan, China
- Shaoxing Institute for Advanced Research, Wuhan University of Technology, Shaoxing, China
- Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya, China
- Advanced Engineering Technology Research Institute of Zhongshan City, Wuhan University of Technology, Zhongshan, China
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6
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Zhu Q, Zheng Y, Zhou X, Wang D, Yuan M, Qian D, Liang S, Yu W, Yang J, Hou H, Hu J. c-di-GMP and AHL signals-triggered chemical communication under electrical signaling disruption restores Geobacter sulfurreducens biofilm formation. ISME COMMUNICATIONS 2024; 4:ycae096. [PMID: 39071848 PMCID: PMC11283642 DOI: 10.1093/ismeco/ycae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]
Abstract
Electrogenic biofilms, which have attracted considerable attention in simultaneous wastewater treatment and energy recovery in bioelectrochemical systems, are regulated by chemical communication and potassium channel-mediated electrical signaling. However, how these two communication pathways interact with each other has not been thoroughly investigated. This study first explored the roles of chemical communication, including intracellular bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) and extracellular N-acyl-homoserine lactone (AHL)-mediated quorum sensing, in electrogenic biofilm formation through an integrated analysis of transcriptomics and metabolomics. Electrical signaling disruption inhibited the formation and electroactivity of Geobacter sulfurreducens biofilm, which was mainly ascribed to the reduction in biofilm viability and extracellular protein/polysaccharide ratio. The upregulation of expression levels of genes encoding c-di-GMP and AHL synthesis by transcriptomic analysis, and the increased secretion of N-butanoyl-L-homoserine lactone by metabolomic analysis confirmed the enhancement of chemical communication under electrical signaling disruption, thus indicating a compensatory mechanism among different signaling pathways. Furthermore, protein-protein interaction network showed the convergence of different signaling pathways, with c-di-GMP-related genes acting as central bridges. This study highlights the interaction of different signaling pathways, especially the resilience of c-di-GMP signaling to adverse external stresses, thereby laying the foundation for facilitating electrogenic biofilm formation under adverse conditions in practical applications.
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Affiliation(s)
- Qian Zhu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- College of Chemistry and Chemical Engineering, Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, Hubei Normal University, 11 Cihu Road, Huangshi 435002, Hubei, China
| | - Yanyan Zheng
- College of Chemistry and Chemical Engineering, Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, Hubei Normal University, 11 Cihu Road, Huangshi 435002, Hubei, China
| | - Xingwang Zhou
- College of Chemistry and Chemical Engineering, Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, Hubei Normal University, 11 Cihu Road, Huangshi 435002, Hubei, China
| | - Dunjia Wang
- College of Chemistry and Chemical Engineering, Hubei Key Laboratory of Pollutant Analysis and Reuse Technology, Hubei Normal University, 11 Cihu Road, Huangshi 435002, Hubei, China
| | - Mengjiao Yuan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Dingkang Qian
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Sha Liang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Wenbo Yu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Jiakuan Yang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Huijie Hou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
| | - Jingping Hu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei,, China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan 430074, Hubei, China
- State Key Laboratory of Coal Combustion, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, Hubei, China
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Chu N, Jiang Y, Wang D, Li D, Zeng RJ. Super-fast Charging Biohybrid Batteries through a Power-to-formate-to-bioelectricity Process by Combining Microbial Electrochemistry and CO 2 Electrolysis. Angew Chem Int Ed Engl 2023; 62:e202312147. [PMID: 37801326 DOI: 10.1002/anie.202312147] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/24/2023] [Accepted: 10/06/2023] [Indexed: 10/07/2023]
Abstract
Extensive study on renewable energy storage has been sparked by the growing worries regarding global warming. In this study, incorporating the latest advancements in microbial electrochemistry and electrochemical CO2 reduction, a super-fast charging biohybrid battery was introduced by using pure formic acid as an energy carrier. CO2 electrolyser with a slim-catholyte layer and a solid electrolyte layer was built, which made it possible to use affordable anion exchange membranes and electrocatalysts that are readily accessible. The biohybrid battery only required a 3-minute charging to accomplish an astounding 25-hour discharging phase. In the power-to-formate-to-bioelectricity process, bioconversion played a vital role in restricting both the overall Faradaic efficiency and Energy efficiency. The CO2 electrolyser was able to operate continuously for an impressive total duration of 164 hours under Gas Stand-By model, by storing N2 gas in the extraction chamber during stand-by periods. Additionally, the electric signal generated during the discharging phase was utilized for monitoring water biotoxicity. Functional genes related to formate metabolism were identified in the bioanode and electrochemically active bacteria were discovered. On the other hand, Paracoccus was predominantly found in the used air cathode. These results advance our current knowledge of exploiting biohybrid technology.
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Affiliation(s)
- Na Chu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Jiang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Donglin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Daping Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Raymond Jianxiong Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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8
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Liu JQ, Min D, He RL, Cheng ZH, Wu J, Liu DF. Efficient and precise control of gene expression in Geobacter sulfurreducens through new genetic elements and tools for pollutant conversion. Biotechnol Bioeng 2023; 120:3001-3012. [PMID: 37209207 DOI: 10.1002/bit.28433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Geobacter species, exhibiting exceptional extracellular electron transfer aptitude, hold great potential for applications in pollution remediation, bioenergy production, and natural elemental cycles. Nonetheless, a scarcity of well-characterized genetic elements and gene expression tools constrains the effective and precise fine-tuning of gene expression in Geobacter species, thereby limiting their applications. Here, we examined a suite of genetic elements and developed a new genetic editing tool in Geobacter sulfurreducens to enhance their pollutant conversion capacity. First, the performances of the widely used inducible promoters, constitutive promoters, and ribosomal binding sites (RBSs) elements in G. sulfurreducens were quantitatively evaluated. Also, six native promoters with superior expression levels than constitutive promoters were identified on the genome of G. sulfurreducens. Employing the characterized genetic elements, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system was constructed in G. sulfurreducens to achieve the repression of an essential gene-aroK and morphogenic genes-ftsZ and mreB. Finally, applying the engineered strain to the reduction of tungsten trioxide (WO3 ), methyl orange (MO), and Cr(VI), We found that morphological elongation through ftsZ repression amplified the extracellular electron transfer proficiency of G. sulfurreducens and facilitated its contaminant transformation efficiency. These new systems provide rapid, versatile, and scalable tools poised to expedite advancements in Geobacter genomic engineering to favor environmental and other biotechnological applications.
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Affiliation(s)
- Jia-Qi Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Di Min
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Ru-Li He
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Zhou-Hua Cheng
- School of Life Sciences, University of Science & Technology of China, Hefei, China
| | - Jie Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei, China
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9
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Han Y, Liao C, Meng X, Zhao Q, Yan X, Tian L, Liu Y, Li N, Wang X. Switchover of electrotrophic and heterotrophic respirations enables the biomonitoring of low concentration of BOD in oxygen-rich environment. WATER RESEARCH 2023; 235:119897. [PMID: 36963309 DOI: 10.1016/j.watres.2023.119897] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 06/18/2023]
Abstract
Biochemical oxygen demand (BOD) is a key indicator of water quality. However, there is still no technique to directly measure BOD at low concentrations in oxygen-rich environments. Here, we propose a new scheme using facultative electrotrophs as the sensing element, and confirmed aerobic Acinetobacter venetianus RAG-1 immobilized on electrode was able to measure BOD via the switchover between electrotrophic and heterotrophic respirations. The hybrid binder of Nafion and polytetrafluoroethylene (PTFE) maximized the baseline current (127 ± 2 A/m2) and sensitivity (2.5 ± 0.1 (mA/m2)/(mg/L)). The current decrease and the BOD5 concentration fitted well with a linear model in the case of known contaminants, verified with both lab samples of acetate and glucose (R2>0.96) and in standard curves of real environmental samples collected from the lake and the effluent of wastewater treatment plant (R2>0.98). Importantly, the biosensor tested actual contaminated water samples with an error of 0.4∼10% compared to BOD5 in the case of unknown contaminants. Transcriptomics revealed that reverse oxidative TCA may involve in the electrotrophic respiration of RAG-1 since citrate synthase (gltA) was highly expressed, which was partly downregulated when heterotrophic metabolism was triggered by BOD. This can be returned to electrotroph when BOD was depleted. Our results showed a new way to rapidly measure BOD in oxygen-rich environment, demonstrating the possibility to employ bacteria with two competitive respiration pathways for pollution detection.
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Affiliation(s)
- Yilian Han
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Xinyi Meng
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Qian Zhao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Xuejun Yan
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Lili Tian
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Ying Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 35 Yaguan Road, Jinnan District, Tianjin 300350, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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10
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Singh A, Kumar M, Chakdar H, Pandiyan K, Kumar SC, Zeyad MT, Singh BN, Ravikiran KT, Mahto A, Srivastava AK, Saxena AK. Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion. Front Microbiol 2022; 13:1033158. [PMID: 36452918 PMCID: PMC9702084 DOI: 10.3389/fmicb.2022.1033158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/20/2022] [Indexed: 08/29/2023] Open
Abstract
Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.
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Affiliation(s)
- Arjun Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Kuppusamy Pandiyan
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
- Ginning Training Center, ICAR-Central Institute for Research on Cotton Technology, Nagpur, India
| | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | | | - K. T. Ravikiran
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
| | - Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | | | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
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11
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Frühauf‐Wyllie HM, Holtmann D. Geobacter sulfurreducens metabolism at different donor/acceptor ratios. Microbiologyopen 2022; 11:e1322. [PMID: 36314758 PMCID: PMC9494351 DOI: 10.1002/mbo3.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/11/2022] Open
Abstract
Geobacter species have great application potential in remediation processes and electrobiotechnology. In all applications, understanding the metabolism will enable target-oriented optimization of the processes. The typical electron donor and carbon source of the Geobacter species is acetate, while fumarate is the usual electron acceptor. Here, we could show that depending on the donor/acceptor ratio in batch cultivation of Geobacter sulfurreducens different product patterns occur. With a donor/acceptor ratio of 1:2.5 malate accumulated as an intermediate product but was metabolized to succinate subsequently. At the end of the cultivation, the ratio of fumarate consumed and succinate produced was approximately 1:1. When fumarate was added in excess, malate accumulated in the fermentation broth without further metabolization. After the addition of acetate to stationary cells, malate concentration decreased immediately and additional succinate was synthesized. Finally, it was shown that also resting cells of G. sulfurreducens could efficiently convert fumarate to malate without an additional electron donor. Overall, it was demonstrated that by altering the donor/acceptor ratio, targeted optimization of the metabolite conversion by G. sulfurreducens can be realized.
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Affiliation(s)
- Hanna Marianne Frühauf‐Wyllie
- Department of Chemical TechnologyDECHEMA ForschungsinstitutFrankfurt am MainGermany
- Technische Hochschule Mittelhessen, Institut für Bioverfahrenstechnik und Pharmazeutische TechnologieGießenGermany
| | - Dirk Holtmann
- Technische Hochschule Mittelhessen, Institut für Bioverfahrenstechnik und Pharmazeutische TechnologieGießenGermany
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12
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Santos Correa S, Schultz J, Lauersen KJ, Soares Rosado A. Natural carbon fixation and advances in synthetic engineering for redesigning and creating new fixation pathways. J Adv Res 2022; 47:75-92. [PMID: 35918056 PMCID: PMC10173188 DOI: 10.1016/j.jare.2022.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 06/30/2022] [Accepted: 07/25/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Autotrophic carbon fixation is the primary route through which organic carbon enters the biosphere, and it is a key step in the biogeochemical carbon cycle. The Calvin-Benson-Bassham pathway, which is predominantly found in plants, algae, and some bacteria (mainly cyanobacteria), was previously considered to be the sole carbon-fixation pathway. However, the discovery of a new carbon-fixation pathway in sulfurous green bacteria almost two decades ago encouraged further research on previously overlooked ancient carbon-fixation pathways in taxonomically and phylogenetically distinct microorganisms. AIM OF REVIEW In this review, we summarize the six known natural carbon-fixation pathways and outline the newly proposed additions to this list. We also discuss the recent achievements in synthetic carbon fixation and the importance of the metabolism of thermophilic microorganisms in this field. KEY SCIENTIFIC CONCEPTS OF REVIEW Currently, at least six carbon-fixation routes have been confirmed in Bacteria and Archaea. Other possible candidate routes have also been suggested on the basis of emerging "omics" data analyses, expanding our knowledge and stimulating discussions on the importance of these pathways in the way organisms acquire carbon. Notably, the currently known natural fixation routes cannot balance the excessive anthropogenic carbon emissions in a highly unbalanced global carbon cycle. Therefore, significant efforts have also been made to improve the existing carbon-fixation pathways and/or design new efficient in vitro and in vivo synthetic pathways.
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Affiliation(s)
- Sulamita Santos Correa
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Junia Schultz
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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13
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Shi XC, Tremblay PL, Xue M, Song X, Zhang T. Fumarate disproportionation by Geobacter sulfurreducens and its involvement in biocorrosion and interspecies electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154251. [PMID: 35245554 DOI: 10.1016/j.scitotenv.2022.154251] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/26/2022] [Indexed: 06/14/2023]
Abstract
The model electroactive bacterium Geobacter sulfurreducens can acquire electrons directly from solid donors including metals and other species. Reports on this physiology concluding that solid donors are the only electron sources were conducted with fumarate believed to serve exclusively as the terminal electron acceptor (TEA). Here, G. sulfurreducens was repeatedly transferred for adaptation within a growth medium containing only fumarate and no other solid or soluble substrate. The resulting evolved strain grew efficiently with either the C4-dicarboxylate fumarate or malate acting simultaneously as electron donor, carbon source, and electron acceptor via disproportionation. Whole-genome sequencing identified 38 mutations including one in the regulator PilR known to repress the expression of the C4-dicarboxylate antiporter DcuB essential to G. sulfurreducens when growing with fumarate. Futhermore, the PilR mutation was identical to the sole mutation previously reported in an evolved G. sulfurreducens grown in a co-culture assumed to derive energy solely from direct interspecies electron transfer, but cultivated with fumarate as the TEA. When cultivating the fumarate-adapted strain in the presence of stainless steel and fumarate, biocorrosion was observed and bacterial growth was accelerated 2.3 times. These results suggest that G. sulfurreducens can conserve energy concomitantly from C4-dicarboxylate disproportionation and the oxidation of a solid electron donor. This co-metabolic capacity confers an advantage to Geobacter for survival and colonization and explains in part why these microbes are omnipresent in different anaerobic ecosystems.
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Affiliation(s)
- Xiao-Chen Shi
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, PR China; Wuhan University of Technology Advanced Engineering Technology Research Institute of Zhongshan City, Zhongshan 528437, PR China
| | - Pier-Luc Tremblay
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya 572024, PR China
| | - Miao Xue
- Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China
| | - Xinyi Song
- Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan 430070, PR China; Institut WUT-AMU, Wuhan University of Technology, Wuhan 430070, PR China; State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; Sanya Science and Education Innovation Park, Wuhan University of Technology, Sanya 572024, PR China.
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14
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Lou H, Yang Y, Zheng S, Ma Z, Chen W, Yu C, Song L, Wu J. Identification of key genes contributing to amino acid biosynthesis in Torreya grandis using transcriptome and metabolome analysis. Food Chem 2022; 379:132078. [PMID: 35063846 DOI: 10.1016/j.foodchem.2022.132078] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/29/2022]
Abstract
Torreya grandis has high economic and nutritional value due to the high nutrients in its kernels. The kernels of different development stages vary enormously in their amino acids content. However, the molecular basis and the regulatory mechanism of amino acid biosynthesis remain unclear. Here, transcriptome and metabolome analysis were performed. Correlation analysis result showed that 4 unigenes were significantly and positively correlated with at least 10 amino acids. The full length CDS of 2 unigenes (TgDAHP2 and TgASA1) were successfully cloned from the 4 unigenes for DAHP, ASA and CITS. Subcelluar localization analysis showed that both TgDAHP2 and TgASA1 were localized to the chloroplast. Overexpression of TgDAHP2 and TgASA1 in Arabidopsis can greatly increase the content of most amino acids. Moreover, 3 transcription factors were found to positively regulate the expression of TgASA1. This research contributes to understand the molecular regulatory mechanisms of amino acid biosynthesis in T. grandis.
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Affiliation(s)
- Heqiang Lou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Yi Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Shan Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Zhenmin Ma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wenchao Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Chenliang Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China.
| | - Lili Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
| | - Jiasheng Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China; NFGA Engineering Research Center for Torreya Grandis 'Merrillii', Zhejiang A&F University, Hangzhou 311300, China.
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15
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Spring S, Rohde M, Bunk B, Spröer C, Will SE, Neumann-Schaal M. New insights into the energy metabolism and taxonomy of Deferribacteres revealed by the characterization of a new isolate from a hypersaline microbial mat. Environ Microbiol 2022; 24:2543-2575. [PMID: 35415868 DOI: 10.1111/1462-2920.15999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022]
Abstract
Strain L21-Ace-BEST , isolated from a lithifying cyanobacterial mat, could be assigned to a novel species and genus within the Deferribacteres. It is an important model organism for the study of anaerobic acetate degradation under hypersaline conditions. The metabolism of strain L21-Ace-BEST was characterized by biochemical studies, comparative genome analyses, and the evaluation of gene expression patterns. The central metabolic pathway is the citric acid cycle, which is mainly controlled by the enzyme succinyl-CoA:acetate-CoA transferase. The potential use of a reversed oxidative citric acid cycle to fix CO2 has been revealed through genome analysis. However, no autotrophic growth was detected in this strain, whereas sulfide and H2 can be used mixotrophically. Preferred electron acceptors for the anaerobic oxidation of acetate are nitrate, fumarate and DMSO, while oxygen can be utilized only under microoxic conditions. Aerotolerant growth by fermentation was observed at higher oxygen concentrations. The redox cycling of sulfur/sulfide enables the generation of reducing power for the assimilation of acetate during growth and could prevent the over-reduction of cells in stationary phase. Extracellular electron transfer appears to be an essential component of the respiratory metabolism in this clade of Deferribacteres and may be involved in the reduction of nitrite to ammonium. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Boyke Bunk
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Department Bioinformatics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Eva Will
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Research Group Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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16
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Abel AJ, Hilzinger JM, Arkin AP, Clark DS. Systems-informed genome mining for electroautotrophic microbial production. Bioelectrochemistry 2022; 145:108054. [DOI: 10.1016/j.bioelechem.2022.108054] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 01/09/2023]
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17
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Mollaei M, Suarez-Diez M, Sedano-Nunez VT, Boeren S, Stams AJM, Plugge CM. Proteomic Analysis of a Syntrophic Coculture of Syntrophobacter fumaroxidans MPOB T and Geobacter sulfurreducens PCA T. Front Microbiol 2021; 12:708911. [PMID: 34950111 PMCID: PMC8691401 DOI: 10.3389/fmicb.2021.708911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
We established a syntrophic coculture of Syntrophobacter fumaroxidans MPOBT (SF) and Geobacter sulfurreducens PCAT (GS) growing on propionate and Fe(III). Neither of the bacteria was capable of growth on propionate and Fe(III) in pure culture. Propionate degradation by SF provides acetate, hydrogen, and/or formate that can be used as electron donors by GS with Fe(III) citrate as electron acceptor. Proteomic analyses of the SF-GS coculture revealed propionate conversion via the methylmalonyl-CoA (MMC) pathway by SF. The possibility of interspecies electron transfer (IET) via direct (DIET) and/or hydrogen/formate transfer (HFIT) was investigated by comparing the differential abundance of associated proteins in SF-GS coculture against (i) SF coculture with Methanospirillum hungatei (SF-MH), which relies on HFIT, (ii) GS pure culture growing on acetate, formate, hydrogen as propionate products, and Fe(III). We noted some evidence for DIET in the SF-GS coculture, i.e., GS in the coculture showed significantly lower abundance of uptake hydrogenase (43-fold) and formate dehydrogenase (45-fold) and significantly higher abundance of proteins related to acetate metabolism (i.e., GltA; 62-fold) compared to GS pure culture. Moreover, SF in the SF-GS coculture showed significantly lower abundance of IET-related formate dehydrogenases, Fdh3 (51-fold) and Fdh5 (29-fold), and the rate of propionate conversion in SF-GS was 8-fold lower than in the SF-MH coculture. In contrast, compared to GS pure culture, we found lower abundance of pilus-associated cytochrome OmcS (2-fold) and piliA (5-fold) in the SF-GS coculture that is suggested to be necessary for DIET. Furthermore, neither visible aggregates formed in the SF-GS coculture, nor the pili-E of SF (suggested as e-pili) were detected. These findings suggest that the IET mechanism is complex in the SF-GS coculture and can be mediated by several mechanisms rather than one discrete pathway. Our study can be further useful in understanding syntrophic propionate degradation in bioelectrochemical and anaerobic digestion systems.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | | | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M. Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, Netherlands
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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18
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Wang Y, Li J, Huang S, Huang X, Hu W, Pu J, Xu M. Evaluation of NOx removal from flue gas and Fe(II)EDTA regeneration using a novel BTF-ABR integrated system. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125741. [PMID: 34088200 DOI: 10.1016/j.jhazmat.2021.125741] [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: 12/29/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
A promising process is under development for the removal of NOx and regeneration of Fe(II)EDTA in a novel biotrickling filter-anaerobic baffled reactor (BTF-ABR) integrated system at 50 ± 0.5 ℃. In this work, we investigated the NOx removal capacity of a BTF under different O2 concentrations (7.0 vol%, 5.25 vol% and 3.5 vol%), and tested the effect of an ABR on NOx removal and regeneration of Fe(II)EDTA. The results showed that the NOx removal capacity was significantly increased with the O2 concentration reduced from 7.0% to 3.5%. The microoxygen environment produced by the BTF-ABR integrated system was more conducive to the removal of NOx and regeneration of Fe(II)EDTA compared with that in the BTF. Real-time polymerase chain reaction (PCR) analysis showed that the coordinated expression of denitrification genes was the major reason for no N2O emission, along with no nitrate and nitrite accumulation. The 16S rRNA gene amplicon sequencing analysis showed that the cooperation of denitrifying bacteria (Klebsiella, Petrimonas, Rhodococcus and Ochrobactium) and iron-reducing bacteria (Klebsiella, Geobacter and Petrimonas) in the system was the key to the stable and efficient removal of NOx and the regeneration of Fe(II)EDTA simultaneously.
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Affiliation(s)
- Yanling Wang
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
| | - Jianjun Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
| | - Shaobin Huang
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China.
| | - Xingzhu Huang
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
| | - Wenzhe Hu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
| | - Jia Pu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510006, PR China.
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19
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Steffens L, Pettinato E, Steiner TM, Mall A, König S, Eisenreich W, Berg IA. High CO 2 levels drive the TCA cycle backwards towards autotrophy. Nature 2021; 592:784-788. [PMID: 33883741 DOI: 10.1038/s41586-021-03456-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 03/15/2021] [Indexed: 02/02/2023]
Abstract
It has recently been shown that in anaerobic microorganisms the tricarboxylic acid (TCA) cycle, including the seemingly irreversible citrate synthase reaction, can be reversed and used for autotrophic fixation of carbon1,2. This reversed oxidative TCA cycle requires ferredoxin-dependent 2-oxoglutarate synthase instead of the NAD-dependent dehydrogenase as well as extremely high levels of citrate synthase (more than 7% of the proteins in the cell). In this pathway, citrate synthase replaces ATP-citrate lyase of the reductive TCA cycle, which leads to the spending of one ATP-equivalent less per one turn of the cycle. Here we show, using the thermophilic sulfur-reducing deltaproteobacterium Hippea maritima, that this route is driven by high partial pressures of CO2. These high partial pressures are especially important for the removal of the product acetyl coenzyme A (acetyl-CoA) through reductive carboxylation to pyruvate, which is catalysed by pyruvate synthase. The reversed oxidative TCA cycle may have been functioning in autotrophic CO2 fixation in a primordial atmosphere that is assumed to have been rich in CO2.
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Affiliation(s)
- Lydia Steffens
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Eugenio Pettinato
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
| | - Thomas M Steiner
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Achim Mall
- K. G. Jebsen Centre for Deep Sea Research, University of Bergen, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Simone König
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, Medical Faculty, University of Münster, Münster, Germany
| | - Wolfgang Eisenreich
- Bavarian NMR Center-Structural Membrane Biochemistry, Department of Chemistry, Technische Universität München, Garching, Germany.
| | - Ivan A Berg
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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20
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Shi XC, Tremblay PL, Wan L, Zhang T. Improved robustness of microbial electrosynthesis by adaptation of a strict anaerobic microbial catalyst to molecular oxygen. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142440. [PMID: 33254866 DOI: 10.1016/j.scitotenv.2020.142440] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 06/12/2023]
Abstract
Microbial electrosynthesis (MES) and other bioprocesses such as syngas fermentation developed for energy storage and the conversion of carbon dioxide into valuable chemicals often employs acetogens as microbial catalysts. Acetogens are sensitive to molecular oxygen, which means that bioproduction reactors must be maintained under strict anaerobic conditions. This requirement increases cost and does not eliminate the possibility of O2 leakage. For MES, the risk is even greater since the system generates O2 when water splitting is the anodic reaction. Here, we show that O2 from the anode of a MES reactor diffuses into the cathode chamber where strict anaerobes reduce CO2. To overcome this drawback, a stepwise adaptive laboratory evolution (ALE) strategy is used to develop the O2 tolerance of the acetogen Sporomusa ovata. Two heavily-mutated S. ovata strains growing well autotrophically in the presence of 0.5 to 5% O2 were obtained. The adapted strains were more performant in the MES system than the wild type converting electrical energy and CO2 into acetate 1.5 fold faster. This study shows that the O2 tolerance of acetogens can be increased, which leads to improvement of the performance and robustness of energy-storage bioprocesses such as MES where O2 is an inhibitor.
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Affiliation(s)
- Xiao-Chen Shi
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Pier-Luc Tremblay
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Lulu Wan
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Tian Zhang
- State Key Laboratory of Silicate Materials for Architectures, Wuhan University of Technology, Wuhan 430070, PR China; School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, PR China; School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, PR China.
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21
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Complete Genome Sequence of Geobacter sp. Strain FeAm09, a Moderately Acidophilic Soil Bacterium. Microbiol Resour Announc 2021; 10:10/2/e00979-20. [PMID: 33446582 PMCID: PMC7849695 DOI: 10.1128/mra.00979-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A moderately acidophilic Geobacter sp. strain, strain FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp, with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling. A moderately acidophilic Geobacter sp. strain, FeAm09, was isolated from forest soil. The complete genome sequence is 4,099,068 bp with an average GC content of 61.1%. No plasmids were detected. The genome contains a total of 3,843 genes and 3,608 protein-coding genes, including genes supporting iron and nitrogen biogeochemical cycling.
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22
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Mollaei M, Timmers PHA, Suarez-Diez M, Boeren S, van Gelder AH, Stams AJM, Plugge CM. Comparative proteomics of Geobacter sulfurreducens PCA T in response to acetate, formate and/or hydrogen as electron donor. Environ Microbiol 2020; 23:299-315. [PMID: 33185968 PMCID: PMC7894505 DOI: 10.1111/1462-2920.15311] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Geobacter sulfurreducens is a model bacterium to study the degradation of organic compounds coupled to the reduction of Fe(III). The response of G. sulfurreducens to the electron donors acetate, formate, hydrogen and a mixture of all three with Fe(III) citrate as electron acceptor was studied using comparative physiological and proteomic approaches. Variations in the supplied electron donors resulted in differential abundance of proteins involved in the citric acid cycle (CAC), gluconeogenesis, electron transport, and hydrogenases and formate dehydrogenase. Our results provided new insights into the electron donor metabolism of G. sulfurreducens. Remarkably, formate was the preferred electron donor compared to acetate, hydrogen, or acetate plus hydrogen. When hydrogen was the electron donor, formate was formed, which was associated with a high abundance of formate dehydrogenase. Notably, abundant proteins of two CO2 fixation pathways (acetyl-CoA pathway and the reversed oxidative CAC) corroborated chemolithoautotrophic growth of G. sulfurreducens with formate or hydrogen and CO2 , and provided novel insight into chemolithoautotrophic growth of G. sulfurreducens.
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Affiliation(s)
- Monir Mollaei
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peer H A Timmers
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, The Netherlands
| | - Antonie H van Gelder
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Caroline M Plugge
- Wetsus, European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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23
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Xiao KQ, Ge TD, Wu XH, Peacock CL, Zhu ZK, Peng J, Bao P, Wu JS, Zhu YG. Metagenomic and 14 C tracing evidence for autotrophic microbial CO 2 fixation in paddy soils. Environ Microbiol 2020; 23:924-933. [PMID: 32827180 DOI: 10.1111/1462-2920.15204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Autotrophic carbon dioxide (CO2 ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with 14 C-labelling to investigate all known autotrophic pathways and CO2 assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of 14 C-CO2 are assimilated into SOC (74.3-175.8 mg 14 C kg-1 ) and microbial biomass (5.2-24.1 mg 14 C kg-1 ) after 45 days incubation, where more than 70% of 14 C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.
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Affiliation(s)
- Ke-Qing Xiao
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
| | - Ti-Da Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Xiao-Hong Wu
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern China, Central South University of Forestry and Technology, Changsha, Hunan, 410004, China
| | - Caroline L Peacock
- School of Earth and Environment, University of Leeds, Leeds, LS2 9JT, UK
| | - Zhen-Ke Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Jingjing Peng
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Peng Bao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Jin-Shui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region and Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing, 100085, China
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