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Shi Z, Zhang Y, Chen W, Yu Z. Crosstalk between 6-methyladenine and 4-methylcytosine in Geobacter sulfurreducens exposed to extremely low-frequency electromagnetic field. iScience 2024; 27:110607. [PMID: 39262814 PMCID: PMC11388800 DOI: 10.1016/j.isci.2024.110607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/05/2024] [Accepted: 07/25/2024] [Indexed: 09/13/2024] Open
Abstract
4-Methylcytosine (4mC) and 6-methyladenine (6mA) are the most prevalent types of DNA modifications in prokaryotes. However, whether there is crosstalk between 4mC and 6mA remain unknown. Here, methylomes and transcriptomes of Geobacter sulfurreducens exposed to different intensities of extremely low frequency electromagnetic fields (ELF-EMF) were investigated. Results showed that the second adenine of all the 5'-GTACAG-3' motif was modified to 6mA (M-6mA). For the other 6mA (O-6mA), the variation in their distance from the neighboring M-6mA increased with the intensity of ELF-EMF. Moreover, cytosine adjacent to O-6mA has a much higher probability of being modified to 4mC than cytosine adjacent to M-6mA, and the closer an unmodified cytosine is to 4mC, the higher the probability that the cytosine will be modified to 4mC. Furthermore, there was no significant correlation between DNA methylation and gene expression regulation. These results suggest a reference signal that goes from M-6mA to O-6mA to 4mC.
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Affiliation(s)
- Zhenhua Shi
- College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Cang Shan District, Fuzhou, Fujian 350002, China
| | - Yingrong Zhang
- College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Cang Shan District, Fuzhou, Fujian 350002, China
| | - Wanqiu Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shang Xia Dian Road, Cang Shan District, Fuzhou, Fujian 350002, China
| | - Zhen Yu
- Fujian Provincial Key Laboratory of Medical Analysis, Fujian Academy of Medical Sciences, 7 Wu Si Road, Gu Lou District, Fuzhou, Fujian 350001, China
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Timilsina A, Lokesh S, Shahriar A, Numan T, Schramm T, Stincone P, Nyarko LK, Dewey C, Boiteau R, Petras D, Yang Y. Identifying Quinones in Complex Aqueous Environmental Media (Biochar Extracts) through Tagging with Cysteine and Cysteine-Contained Peptides and High Resolution Mass Spectrometry Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:16432-16443. [PMID: 39226134 DOI: 10.1021/acs.est.4c04049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Quinones are among the most important components in natural organic matter (NOM) for redox reactions; however, no quinones in complex environmental media have been identified. To aid the identification of quinone-containing molecules in ultracomplex environmental samples, we developed a chemical tagging method that makes use of a Michael addition reaction between quinones and thiols (-SH) in cysteine (Cys) and cysteine-contained peptides (CCP). After the tagging, candidates of quinones in representative aqueous environmental samples (water extractions of biochar) were identified through high-resolution mass spectrometry (HRMS) analysis. The MS and UV spectra analysis showed rapid reactions between Cys/CCP and model quinones with β-carbon from the same benzene ring available for Michael addition. The tagging efficiency was not influenced by other co-occurring nonquinone representative compounds, including caffeic acid, cinnamic acid, and coumaric acid. Cys and CCP were used to tag quinones in water extractions of biochars, and possible candidates of quinones (20 and 53 based on tagging with Cys and CCP, respectively) were identified based on the HRMS features for products of reactions with Cys/CCP. This study has successfully demonstrated that such a Michael addition reaction can be used to tag quinones in complex environmental media and potentially determine their identities. The method will enable an in-depth understanding of the redox chemistry of NOM and its critical chemical compositions and structures.
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Affiliation(s)
- Anil Timilsina
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1644 N. Virgina Street, Reno, Nevada 89523, United States
| | - Srinidhi Lokesh
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1644 N. Virgina Street, Reno, Nevada 89523, United States
| | - Abrar Shahriar
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1644 N. Virgina Street, Reno, Nevada 89523, United States
| | - Travis Numan
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1644 N. Virgina Street, Reno, Nevada 89523, United States
| | - Tilman Schramm
- CMFI Cluster of Excellence, University of Tuebingen, Auf der Morgenstelle 24, 72076 Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, 169 Aberdeen Dr, Riverside, California 92507, United States
| | - Paolo Stincone
- CMFI Cluster of Excellence, University of Tuebingen, Auf der Morgenstelle 24, 72076 Tuebingen, Germany
| | - Laurinda Korang Nyarko
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, 1500 SW Jefferson Way, Corvallis, Oregon 97331, United States
| | - Christian Dewey
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Se, Minneapolis, Minnesota 55455, United States
| | - Rene Boiteau
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Se, Minneapolis, Minnesota 55455, United States
| | - Daniel Petras
- CMFI Cluster of Excellence, University of Tuebingen, Auf der Morgenstelle 24, 72076 Tuebingen, Germany
- Department of Biochemistry, University of California Riverside, 169 Aberdeen Dr, Riverside, California 92507, United States
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada, Reno, 1644 N. Virgina Street, Reno, Nevada 89523, United States
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Gupta D, Chen K, Elliott SJ, Nayak DD. MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport in Methanosarcina acetivorans. Nat Commun 2024; 15:3300. [PMID: 38632227 PMCID: PMC11024163 DOI: 10.1038/s41467-024-47564-2] [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: 08/22/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Methanogens are a diverse group of Archaea that obligately couple energy conservation to the production of methane. Some methanogens encode alternate pathways for energy conservation, like anaerobic respiration, but the biochemical details of this process are unknown. We show that a multiheme c-type cytochrome called MmcA from Methanosarcina acetivorans is important for intracellular electron transport during methanogenesis and can also reduce extracellular electron acceptors like soluble Fe3+ and anthraquinone-2,6-disulfonate. Consistent with these observations, MmcA displays reversible redox features ranging from -100 to -450 mV versus SHE. Additionally, mutants lacking mmcA have significantly slower Fe3+ reduction rates. The mmcA locus is prevalent in members of the Order Methanosarcinales and is a part of a distinct clade of multiheme cytochromes that are closely related to octaheme tetrathionate reductases. Taken together, MmcA might act as an electron conduit that can potentially support a variety of energy conservation strategies that extend beyond methanogenesis.
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Affiliation(s)
- Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keying Chen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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Xie M, Zhang X, Li S, Maulani N, Cai F, Zheng Y, Cai C, Virdis B, Yuan Z, Hu S. Humic substances as electron acceptor for anaerobic oxidation of methane (AOM) and electron shuttle in Mn (IV)-dependent AOM. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169576. [PMID: 38145665 DOI: 10.1016/j.scitotenv.2023.169576] [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: 09/05/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
Anaerobic methanotrophic archaea (ANME) belonging to the family Methanoperedenaceae are crucial for the global carbon cycle and different biogeochemical processes, owing to their metabolic versatility to couple anaerobic oxidation of methane (AOM) with different electron acceptors. A universal feature of Methanoperedenaceae is the abundant genes encoded in their genomes associated with extracellular electron transfer (EET) pathways. Candidatus. 'Methanoperedens manganicus', an archaeon belonging to the family Methanoperedenaceae, was recently enriched in a bioreactor performing AOM coupled with Mn (IV) reduction. Using this EET-capable ANME, we tested the hypothesis in this study that ANME can catalyse the humic-dependent AOM for growth. A two-year incubation showed that AOM activity can be sustained by Ca. 'M. manganicus' consortium in a bioreactor fed only with humic acids and methane. An isotopic mass balance batch test confirmed that the observed AOM was coupled to the reduction of humic acids. The increase of relative abundance of Ca. 'M. manganicus', and the total archaea population in the microbial community suggested that Ca. 'M. manganicus' can grow on methane and humic acids. The observation of humic-dependent AOM led to a subsequent hypothesis that humic acids could be used as the electron shuttle to mediate the EET in dissimilatory Mn (IV) reduction by Ca. 'M. manganicus'. We tested this hypothesis by adding humic acids to a Ca. 'M. manganicus' dominated-culture, which showed that the AOM rate was doubled by the addition of humic acids. X-ray photoelectron spectroscopy (XPS) showed that quinone moieties were consumed when humic acids worked as electron acceptors while remaining stable when functioning as a shuttle for electron transfer. The results of our study suggest that humic acids may serve as electron shuttles to allow ANME to access more electron acceptors through long-range EET.
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Affiliation(s)
- Mengying Xie
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia.
| | - Shiqing Li
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Nova Maulani
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Fangrui Cai
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Zhiguo Yuan
- School of Energy and Environment, City University of Hong Kong, Kowloon, Hong Kong 999077, China
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, Faculty of Engineering, Architecture and Information Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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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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6
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Zhang B, Shi S, Tang R, Qiao C, Yang M, You Z, Shao S, Wu D, Yu H, Zhang J, Cao Y, Li F, Song H. Recent advances in enrichment, isolation, and bio-electrochemical activity evaluation of exoelectrogenic microorganisms. Biotechnol Adv 2023; 66:108175. [PMID: 37187358 DOI: 10.1016/j.biotechadv.2023.108175] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023]
Abstract
Exoelectrogenic microorganisms (EEMs) catalyzed the conversion of chemical energy to electrical energy via extracellular electron transfer (EET) mechanisms, which underlay diverse bio-electrochemical systems (BES) applications in clean energy development, environment and health monitoring, wearable/implantable devices powering, and sustainable chemicals production, thereby attracting increasing attentions from academic and industrial communities in the recent decades. However, knowledge of EEMs is still in its infancy as only ~100 EEMs of bacteria, archaea, and eukaryotes have been identified, motivating the screening and capture of new EEMs. This review presents a systematic summarization on EEM screening technologies in terms of enrichment, isolation, and bio-electrochemical activity evaluation. We first generalize the distribution characteristics of known EEMs, which provide a basis for EEM screening. Then, we summarize EET mechanisms and the principles underlying various technological approaches to the enrichment, isolation, and bio-electrochemical activity of EEMs, in which a comprehensive analysis of the applicability, accuracy, and efficiency of each technology is reviewed. Finally, we provide a future perspective on EEM screening and bio-electrochemical activity evaluation by focusing on (i) novel EET mechanisms for developing the next-generation EEM screening technologies, and (ii) integration of meta-omics approaches and bioinformatics analyses to explore nonculturable EEMs. This review promotes the development of advanced technologies to capture new EEMs.
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Affiliation(s)
- Baocai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Sicheng Shi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rui Tang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chunxiao Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Meiyi Yang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shulin Shao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Huan Yu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Junqi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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7
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Zhang L, Kang-Yun CS, Lu X, Chang J, Liang X, Pierce EM, Semrau JD, Gu B. Adsorption and intracellular uptake of mercuric mercury and methylmercury by methanotrophs and methylating bacteria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 331:121790. [PMID: 37187279 DOI: 10.1016/j.envpol.2023.121790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/25/2023] [Accepted: 05/07/2023] [Indexed: 05/17/2023]
Abstract
The cell surface adsorption and intracellular uptake of mercuric Hg(II) and methylmercury (MeHg) are important in determining the fate and transformation of Hg in the environment. However, current information is limited about their interactions with two important groups of microorganisms, i.e., methanotrophs and Hg(II)-methylating bacteria, in aquatic systems. This study investigated the adsorption and uptake dynamics of Hg(II) and MeHg by three strains of methanotrophs, Methylomonas sp. Strain EFPC3, Methylosinus trichosporium OB3b, and Methylococcus capsulatus Bath, and two Hg(II)-methylating bacteria, Pseudodesulfovibrio mercurii ND132 and Geobacter sulfurreducens PCA. Distinctive behaviors of these microorganisms towards Hg(II) and MeHg adsorption and intracellular uptake were observed. The methanotrophs generally took up 60-80% of inorganic Hg(II) inside cells after 24 h incubation, lower than methylating bacteria (>90%). Approximately 80-95% of MeHg was rapidly taken up by all the tested methanotrophs within 24 h. In contrast, after the same time, G. sulfurreducens PCA adsorbed 70% but took up <20% of MeHg, while P. mercurii ND132 only adsorbed 20% but took up negligible amounts of MeHg. These results suggest that microbial surface adsorption and intracellular uptake of Hg(II) and MeHg depend on the specific types of microbes and appear to be related to microbial physiology that requires further detailed investigation. Despite being incapable of methylating Hg(II), methanotrophs play important roles in immobilizing both Hg(II) and MeHg, potentially influencing their bioavailability and trophic transfer. Therefore, methanotrophs are not only important sinks for methane but also for Hg(II) and MeHg and can influence the global cycling of C and Hg.
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Affiliation(s)
- Lijie Zhang
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
| | - Christina S Kang-Yun
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xia Lu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Chang
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xujun Liang
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biosystems Engineering and Soil Science, University of Tennesee, Knoxville, TN 37996, USA
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8
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Naderi A, Kakavandi B, Giannakis S, Angelidaki I, Rezaei Kalantary R. Putting the electro-bugs to work: A systematic review of 22 years of advances in bio-electrochemical systems and the parameters governing their performance. ENVIRONMENTAL RESEARCH 2023; 229:115843. [PMID: 37068722 DOI: 10.1016/j.envres.2023.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Wastewater treatment using bioelectrochemical systems (BESs) can be considered as a technology finding application in versatile areas such as for renewable energy production and simultaneous reducing environmental problems, biosensors, and bioelectrosynthesis. This review paper reports and critically discusses the challenges, and advances in bio-electrochemical studies in the 21st century. To sum and critically analyze the strides of the last 20+ years on the topic, this study first provides a comprehensive analysis on the structure, performance, and application of BESs, which include Microbial Fuel Cells (MFCs), Microbial Electrolysis Cells (MECs) and Microbial Desalination Cells (MDCs). We focus on the effect of various parameters, such as electroactive microbial community structure, electrode material, configuration of bioreactors, anode unit volume, membrane type, initial COD, co-substrates and the nature of the input wastewater in treatment process and the amount of energy and fuel production, with the purpose of showcasing the modes of operation as a guide for future studies. The results of this review show that the BES have great potential in reducing environmental pollution, purifying saltwater, and producing energy and fuel. At a larger scale, it aspires to facilitate the path of achieving sustainable development and practical application of BES in real-world scenarios.
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Affiliation(s)
- Azra Naderi
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Babak Kakavandi
- Research Center for Health, Safety and Environment, Alborz University of Medical Sciences, Karaj, Iran; Department of Environmental Health Engineering, Alborz University of Medical Sciences, Karaj, Iran
| | - Stefanos Giannakis
- Universidad Politécnica de Madrid, E.T.S. de Ingenieros de Caminos, Canales y Puertos, Departamento de Ingeniería Civil: Hidráulica, Energía y Medio Ambiente, Environment, Coast and Ocean Research Laboratory (ECOREL-UPM), C/Profesor Aranguren, s/n, ES-28040, Madrid, Spain
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Roshanak Rezaei Kalantary
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran.
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9
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Fessler M, Madsen JS, Zhang Y. Conjugative plasmids inhibit extracellular electron transfer in Geobacter sulfurreducens. Front Microbiol 2023; 14:1150091. [PMID: 37007462 PMCID: PMC10063792 DOI: 10.3389/fmicb.2023.1150091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/19/2023] Open
Abstract
Geobacter sulfurreducens is part of a specialized group of microbes with the unique ability to exchange electrons with insoluble materials, such as iron oxides and electrodes. Therefore, G. sulfurreducens plays an essential role in the biogeochemical iron cycle and microbial electrochemical systems. In G. sulfurreducens this ability is primarily dependent on electrically conductive nanowires that link internal electron flow from metabolism to solid electron acceptors in the extracellular environment. Here we show that when carrying conjugative plasmids, which are self-transmissible plasmids that are ubiquitous in environmental bacteria, G. sulfurreducens reduces insoluble iron oxides at much slower rates. This was the case for all three conjugative plasmids tested (pKJK5, RP4 and pB10). Growth with electron acceptors that do not require expression of nanowires was, on the other hand, unaffected. Furthermore, iron oxide reduction was also inhibited in Geobacter chapellei, but not in Shewanella oneidensis where electron export is nanowire-independent. As determined by transcriptomics, presence of pKJK5 reduces transcription of several genes that have been shown to be implicated in extracellular electron transfer in G. sulfurreducens, including pilA and omcE. These results suggest that conjugative plasmids can in fact be very disadvantageous for the bacterial host by imposing specific phenotypic changes, and that these plasmids may contribute to shaping the microbial composition in electrode-respiring biofilms in microbial electrochemical reactors.
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Affiliation(s)
- Mathias Fessler
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Yifeng Zhang,
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10
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Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
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Naderi A, Rezaee A, Pasalari H, Esrafili A, Kalantary RR. Bio-electrical stimulation process on degradation of Phenanthrene from aqueous solution using a novel anode modified with carbon cloth: Operational performance, microbial activity and energy. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113654. [PMID: 35643029 DOI: 10.1016/j.ecoenv.2022.113654] [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: 01/10/2022] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Phenanthrene as the hazardous PAHs-component are extensively detected in industrial wastewater. However, the impacts of bioelectrostimulation process on Phenanthrene degradation in aerobic reactors remained unclear. Here, a novel bioelectrostimulation process equipped with carbon cloth as electrodes was developed to investigate the removal efficiency of Phenanthrene and ATPase enzyme activity in the synthetic wastewater. The results obtained from the present study indicated that a complete Phenanthrene degradation (100%) can be achieved using microbial electrostimulation systems steel mesh coated with carbon cloth (MES-CC) as anode under optimal operational conditions (electrical current: 4 mA, HA concentration: 15 mg L-1) within 18 h. The conductive carbon cloth provides a biofilm carrier to easily transfer the electrons between electrodes and microbial communities. In addition, the highest ATPase enzyme activity (5176 U) was observed when the aerobic MES-CC reactors were operated with electrical current 4 mA. Furthermore, the COD removal efficiency in MES-CC increased from 49% to 96% when the C: N ratio decreased from 20 to 5. The highest value of Vmax in MES-CC for suspended and attached growth were determined to be 2.87 and 0.54 g COD g-1 biomass. Overall, the results demonstrated that MES equipped with carbon cloth and continuous electrical current mode has good potential for efficient Phenanthrene wastewater treatment.
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Affiliation(s)
- Azra Naderi
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Abbas Rezaee
- Department of Environmental Health Engineering, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hasan Pasalari
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Esrafili
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Roshanak Rezaei Kalantary
- Research Center for Environmental Health Technology, Iran University of Medical Sciences, Tehran, Iran; Department of Environmental Health Engineering, School of Public Health, Iran University of Medical Sciences, Tehran, Iran.
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12
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Tian L, Yan X, Wang D, Du Q, Wan Y, Zhou L, Li T, Liao C, Li N, Wang X. Two key Geobacter species of wastewater-enriched electroactive biofilm respond differently to electric field. WATER RESEARCH 2022; 213:118185. [PMID: 35183018 DOI: 10.1016/j.watres.2022.118185] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Electroactive biofilms have attracted increasing attention due to their unique ability to exchange electrons with electrodes. Geobacter spp. are widely found to be dominant in biofilms in acetate-rich environments when an appropriate voltage is applied, but it is still largely unknown how these bacteria are selectively enriched. Herein, two key Geobacter spp. that have been demonstrated predominant in wastewater-enriched electroactive biofilm after long-term operation, G. sulfurreducens and G. anodireducens, responded to electric field (EF) differently, leading to a higher abundance of EF-sensitive G. anodireducens in the strong EF region after cocultivation with G. sulfurreducens. Transcriptome analysis indicated that two-component systems containing sensor histidine kinases and response regulators were the key for EF sensing in G. anodireducens rather than in G. sulfurreducens, which are closely connected to chemotaxis, c-di-GMP, fatty acid metabolism, pilus, oxidative phosphorylation and transcription, resulting in an increase in extracellular polymeric substance secretion and rapid cell proliferation. Our data reveal the mechanism by which EF select specific Geobacter spp. over time, providing new insights into Geobacter biofilm formation regulated by electricity.
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Affiliation(s)
- 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
| | - 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
| | - Dongbin Wang
- School of Public Health, Guangdong Medical University, Xincheng Road, Dongguan 523000, China
| | - Qing Du
- School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China
| | - Yuxuan Wan
- 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
| | - Lean Zhou
- School of Hydraulic Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Tian Li
- 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
| | - 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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13
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From iron to bacterial electroconductive filaments: Exploring cytochrome diversity using Geobacter bacteria. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Finkelstein J, Swartz J, Koffas M. Bioelectrosynthesis systems. Curr Opin Biotechnol 2021; 74:211-219. [PMID: 34979469 DOI: 10.1016/j.copbio.2021.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022]
Abstract
Bioelectrosynthesis (BES) systems exploit extracellular electron transport pathways to augment cellular metabolism. This strategy can be used to improve the economic viability of bio-based syntheses versus conventional methods, most notably petrochemical-based syntheses. It also has the potential to reduce the carbon footprint of biomanufacturing processes. Efficient channeling of cathode-derived electrons towards biosynthesis requires a better understanding of the biological mechanisms of electron transport as well as detailed evaluation of all aspects of process performance. More advanced solutions may deploy cell free systems that use ex situ generated reducing equivalents to improve economic performance.
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Affiliation(s)
- Joshua Finkelstein
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - James Swartz
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Mattheos Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Stainless steel corrosion via direct iron-to-microbe electron transfer by Geobacter species. THE ISME JOURNAL 2021; 15:3084-3093. [PMID: 33972726 PMCID: PMC8443633 DOI: 10.1038/s41396-021-00990-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 03/28/2021] [Accepted: 04/14/2021] [Indexed: 02/01/2023]
Abstract
Microbial corrosion of iron-based materials is a substantial economic problem. A mechanistic understanding is required to develop mitigation strategies, but previous mechanistic studies have been limited to investigations with relatively pure Fe(0), which is not a common structural material. We report here that the mechanism for microbial corrosion of stainless steel, the metal of choice for many actual applications, can be significantly different from that for Fe(0). Although H2 is often an intermediary electron carrier between the metal and microbes during Fe(0) corrosion, we found that H2 is not abiotically produced from stainless steel, making this corrosion mechanism unlikely. Geobacter sulfurreducens and Geobacter metallireducens, electrotrophs that are known to directly accept electrons from other microbes or electrodes, extracted electrons from stainless steel via direct iron-to-microbe electron transfer. Genetic modification to prevent H2 consumption did not negatively impact on stainless steel corrosion. Corrosion was inhibited when genes for outer-surface cytochromes that are key electrical contacts were deleted. These results indicate that a common model of microbial Fe(0) corrosion by hydrogenase-positive microbes, in which H2 serves as an intermediary electron carrier between the metal surface and the microbe, may not apply to the microbial corrosion of stainless steel. However, direct iron-to-microbe electron transfer is a feasible route for stainless steel corrosion.
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Liu X, Walker DJF, Nonnenmann SS, Sun D, Lovley DR. Direct Observation of Electrically Conductive Pili Emanating from Geobacter sulfurreducens. mBio 2021; 12:e0220921. [PMID: 34465020 PMCID: PMC8406130 DOI: 10.1128/mbio.02209-21] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 11/20/2022] Open
Abstract
Geobacter sulfurreducens is a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport in G. sulfurreducens. However, it has recently been reported that G. sulfurreducens does not express e-pili and that filaments comprised of multi-heme c-type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90% of the filaments emanating from wild-type cells had a diameter (3 nm) and conductance consistent with previous reports of e-pili harvested from G. sulfurreducens or heterologously expressed in Escherichia coli from the G. sulfurreducens pilin gene. The remaining 10% of filaments had a morphology consistent with filaments comprised of the c-type cytochrome OmcS. A strain expressing a modified pilin gene designed to yield poorly conductive pili expressed 90% filaments with a 3-nm diameter, but greatly reduced conductance, further indicating that the 3-nm diameter conductive filaments in the wild-type strain were e-pili. A strain in which genes for five of the most abundant outer-surface c-type cytochromes, including OmcS, were deleted yielded only 3-nm-diameter filaments with the same conductance as in the wild type. These results demonstrate that e-pili are the most abundant conductive filaments expressed by G. sulfurreducens, consistent with previous functional studies demonstrating the need for e-pili for long-range extracellular electron transfer. IMPORTANCE Electroactive microbes have significant environmental impacts, as well as applications in bioenergy and bioremediation. The composition, function, and even existence of electrically conductive pili (e-pili) has been one of the most contentious areas of investigation in electromicrobiology, in part because e-pili offer a mechanism for long-range electron transport that does not involve the metal cofactors common in much of biological electron transport. This study demonstrates that e-pili are abundant filaments emanating from Geobacter sulfurreducens, which serves as a model for long-range extracellular electron transfer in direct interspecies electron transfer, dissimilatory metal reduction, microbe-electrode exchange, and corrosion caused by direct electron uptake from Fe(0). The methods described in this study provide a simple strategy for evaluating the distribution of conductive filaments throughout the microbial world with an approach that avoids artifactual production and/or enrichment of filaments that may not be physiologically relevant.
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Affiliation(s)
- Xinying Liu
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - David J. F. Walker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Stephen S. Nonnenmann
- Institute for Applied Life Sciences, university of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Department of Mechanical and Industrial Engineering, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Dezhi Sun
- College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Institute for Applied Life Sciences, university of Massachusetts—Amherst, Amherst, Massachusetts, USA
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Fernandes TM, Morgado L, Turner DL, Salgueiro CA. Protein Engineering of Electron Transfer Components from Electroactive Geobacter Bacteria. Antioxidants (Basel) 2021; 10:844. [PMID: 34070486 PMCID: PMC8227773 DOI: 10.3390/antiox10060844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/20/2021] [Indexed: 01/02/2023] Open
Abstract
Electrogenic microorganisms possess unique redox biological features, being capable of transferring electrons to the cell exterior and converting highly toxic compounds into nonhazardous forms. These microorganisms have led to the development of Microbial Electrochemical Technologies (METs), which include applications in the fields of bioremediation and bioenergy production. The optimization of these technologies involves efforts from several different disciplines, ranging from microbiology to materials science. Geobacter bacteria have served as a model for understanding the mechanisms underlying the phenomenon of extracellular electron transfer, which is highly dependent on a multitude of multiheme cytochromes (MCs). MCs are, therefore, logical targets for rational protein engineering to improve the extracellular electron transfer rates of these bacteria. However, the presence of several heme groups complicates the detailed redox characterization of MCs. In this Review, the main characteristics of electroactive Geobacter bacteria, their potential to develop microbial electrochemical technologies and the main features of MCs are initially highlighted. This is followed by a detailed description of the current methodologies that assist the characterization of the functional redox networks in MCs. Finally, it is discussed how this information can be explored to design optimal Geobacter-mutated strains with improved capabilities in METs.
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Affiliation(s)
- Tomás M. Fernandes
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - Leonor Morgado
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República (EAN), 2780-157 Oeiras, Portugal;
| | - Carlos A. Salgueiro
- UCIBIO, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal; (T.M.F.); (L.M.)
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18
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Kulikova NA, Perminova IV. Interactions between Humic Substances and Microorganisms and Their Implications for Nature-like Bioremediation Technologies. Molecules 2021; 26:2706. [PMID: 34063010 PMCID: PMC8124324 DOI: 10.3390/molecules26092706] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/02/2021] [Accepted: 05/02/2021] [Indexed: 12/22/2022] Open
Abstract
The state of the art of the reported data on interactions between microorganisms and HSs is presented herein. The properties of HSs are discussed in terms of microbial utilization, degradation, and transformation. The data on biologically active individual compounds found in HSs are summarized. Bacteria of the phylum Proteobacteria and fungi of the phyla Basidiomycota and Ascomycota were found to be the main HS degraders, while Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes were found to be the predominant phyla in humic-reducing microorganisms (HRMs). Some promising aspects of interactions between microorganisms and HSs are discussed as a feasible basis for nature-like biotechnologies, including the production of enzymes capable of catalyzing the oxidative binding of organic pollutants to HSs, while electron shuttling through the utilization of HSs by HRMs as electron shuttles may be used for the enhancement of organic pollutant biodegradation or lowering bioavailability of some metals. Utilization of HSs by HRMs as terminal electron acceptors may suppress electron transfer to CO2, reducing the formation of CH4 in temporarily anoxic systems. The data reported so far are mostly related to the use of HSs as redox compounds. HSs are capable of altering the composition of the microbial community, and there are environmental conditions that determine the efficiency of HSs. To facilitate the development of HS-based technologies, complex studies addressing these factors are in demand.
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Affiliation(s)
- Natalia A. Kulikova
- Department of Soil Science, Lomonosov Moscow State University, Leninskiye Gory 1-12, 119991 Moscow, Russia;
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Center, Russian Academy of Sciences, pr. Leninskiy 33, 119071 Moscow, Russia
| | - Irina V. Perminova
- Department of Chemistry, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russia
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Abstract
Extracellular electron transfer (EET) is an important biological process in microbial physiology as found in dissimilatory metal oxidation/reduction and interspecies electron transfer in syntrophy in natural environments. EET also plays a critical role in microorganisms relevant to environmental biotechnology in metal-contaminated areas, metal corrosion, bioelectrochemical systems, and anaerobic digesters. Geobacter species exist in a diversity of natural and artificial environments. One of the outstanding features of Geobacter species is the capability of direct EET with solid electron donors and acceptors, including metals, electrodes, and other cells. Therefore, Geobacter species are pivotal in environmental biogeochemical cycles and biotechnology applications. Geobacter sulfurreducens, a representative Geobacter species, has been studied for direct EET as a model microorganism. G. sulfurreducens employs electrically conductive pili (e-pili) and c-type cytochromes for the direct EET. The biological function and electronics applications of the e-pili have been reviewed recently, and this review focuses on the cytochromes. Geobacter species have an unusually large number of cytochromes encoded in their genomes. Unlike most other microorganisms, Geobacter species localize multiple cytochromes in each subcellular fraction, outer membrane, periplasm, and inner membrane, as well as in the extracellular space, and differentially utilize these cytochromes for EET with various electron donors and acceptors. Some of the cytochromes are functionally redundant. Thus, the EET in Geobacter is complicated. Geobacter coordinates the cytochromes with other cellular components in the elaborate EET system to flourish in the environment.
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Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
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20
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Chang J, Wu Q, Liang P, Huang X. Enhancement of nitrite-dependent anaerobic methane oxidation via Geobacter sulfurreducens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 766:144230. [PMID: 33418257 DOI: 10.1016/j.scitotenv.2020.144230] [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: 09/03/2020] [Revised: 11/11/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Nitrite-dependent anaerobic methane-oxidation (n-damo) is a potential novel technology for nitrogen removal in anaerobic wastewater treatment. In this study, Geobacter sulfurreducens (G) was applied to stimulate n-damo activity. Conductive materials such as nano-magnetite (M) or aggregating agents such as hydroxylapatite (H) were co-added with G. sulfurreducens to further investigate the enhancement effect. Results showed that the nitrite reduction activity of the n-damo culture was promoted by G. sulfurreducens, with 1.71-2.38 times higher in treatment G, G + M, and G + H than that in the control, but was inhibited by the single addition of hydroxylapatite. N-damo bacterial abundances based on the qPCR of the n-damo-specific pmoA gene increased in treatments with G. sulfurreducens, compared with that of the control. High-throughput sequencing analysis revealed the enrichment of uncultured phylum WPS-2 in treatments with G. sulfurreducens. Fluorescence in situ hybridization verified the co-occurrence pattern of n-damo bacteria (NC10), G. sulfurreducens, and type-I aerobic methanotrophs (Methylomonas spp.). The above results corroborated the microbial interspecies electron transfer (MIET) potentiality of the n-damo enrichment. Our study provides a novel pathway for enhancing MIET to stimulate n-damo process.
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Affiliation(s)
- Jiali Chang
- Division of Environmental Engineering, School of Chemistry, Resources and Environment, Leshan Normal University, Sichuan 614000, China; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qing Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Peng Liang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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Pham DM, Kasai T, Yamaura M, Katayama A. Humin: No longer inactive natural organic matter. CHEMOSPHERE 2021; 269:128697. [PMID: 33139048 DOI: 10.1016/j.chemosphere.2020.128697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 06/11/2023]
Abstract
The discovery of the function of humin (HM), an insoluble fraction of humic substances (HSs), as an extracellular electron mediator (EEM) in 2012 has provided insight into the role of HM in nature and its potential for in situ bioremediation of pollutants. The EEM function is thought to enable the energy network of various microorganisms using HM. Recently, a number of studies on the application of HM as EEM in anaerobic microbial cultures have been conducted. Even so, there is a need for developing a holistic view of HM EEM function. In this paper, we summarize all the available information on the properties of HM EEM function, its applications, possible redox-active structures, and the interaction between HM and microbial cells. We also suggest scopes for future HM research.
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Affiliation(s)
- Duyen Minh Pham
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan
| | - Takuya Kasai
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan; Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Mirai Yamaura
- Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Arata Katayama
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, 464-8603, Japan; Department of Civil Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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22
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Yang X, Chen S. Microorganisms in sediment microbial fuel cells: Ecological niche, microbial response, and environmental function. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 756:144145. [PMID: 33303196 DOI: 10.1016/j.scitotenv.2020.144145] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
A sediment microbial fuel cell (SMFC) is a device that harvests electrical energy from sediments rich in organic matter. SMFCs have been attracting increasing amounts of interest in environmental remediation, since they are capable of providing a clean and inexhaustible source of electron donors or acceptors and can be easily controlled by adjusting the electrochemical parameters. The microorganisms inhabiting sediments and the overlying water play a pivotal role in SMFCs. Since the SMFC is applied in an open environment rather than in an enclosed chamber, the effects of the environment on the microbes should be intense and the microbial community succession should be extremely complex. Thus, this review aims to provide an overview of the microorganisms in SMFCs, which few previous review papers have reported. In this study, the anodic and cathodic niches for the microorganisms in SMFCs are summarized, how the microbial population and community interact with the SMFC environment is discussed, a new microbial succession strategy called the electrode stimulation succession is proposed, and recent developments in the environmental functions of SMFCs are discussed from the perspective of microorganisms. Future studies are needed to investigate the electrode stimulation succession, the environmental function and the electron transfer mechanism in order to boost the application of SMFCs for power generation and environmental remediation.
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Affiliation(s)
- Xunan Yang
- 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, 510070, China.
| | - Shanshan Chen
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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Shi Z, Yu Z, Chen W. 4-Methylcytosine distribution follows the power function in Geobacter sulfurreducens genome. Biochem Biophys Res Commun 2021; 547:65-68. [PMID: 33596482 DOI: 10.1016/j.bbrc.2021.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/07/2021] [Indexed: 10/22/2022]
Abstract
Single-molecule real-time DNA sequencing revealed that 4-methylcytosine (m4C) commonly exists in bacterial genomes. In this work, samples with different m4C methylation patterns were studied. Results reveal that m4C modification is a biochemical reaction with distance effect, and its distribution follows the power function in the positive, negative, and double strands of genomic DNA sequences of Geobacter sulfurreducens. Furthermore, the value of regression coefficient in the fitting formula for double strands was the sum of those in the fitting formulae for positive and negative strands. Meanwhile, the value of exponent coefficient was the average, implicating an interesting mathematical phenomenon about power function. Considering the potent role of m4C in gene expression and the present results being obtained from the same genomic DNA sequence, this work suggests that the patterns of m4C distribution may be served as a signal for G. sulfurreducens to rapidly identify the genes to respond to environmental stresses or signals. This study opens a new avenue to extend our knowledge about the modification mechanisms and the epigenetic information of m4C modification in prokaryotes.
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Affiliation(s)
- Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian, 350002, China.
| | - Zhen Yu
- Fujian Provincial Key Laboratory of Medical Texting, Fujian Academy of Medical Sciences, Fuzhou, 350001, China
| | - Wanqiu Chen
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, No.15 Shangxiadian Road, Cangshan District, Fuzhou, Fujian, 350002, China
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Rahman Z, Thomas L. Chemical-Assisted Microbially Mediated Chromium (Cr) (VI) Reduction Under the Influence of Various Electron Donors, Redox Mediators, and Other Additives: An Outlook on Enhanced Cr(VI) Removal. Front Microbiol 2021; 11:619766. [PMID: 33584585 PMCID: PMC7875889 DOI: 10.3389/fmicb.2020.619766] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Chromium (Cr) (VI) is a well-known toxin to all types of biological organisms. Over the past few decades, many investigators have employed numerous bioprocesses to neutralize the toxic effects of Cr(VI). One of the main process for its treatment is bioreduction into Cr(III). Key to this process is the ability of microbial enzymes, which facilitate the transfer of electrons into the high valence state of the metal that acts as an electron acceptor. Many underlying previous efforts have stressed on the use of different external organic and inorganic substances as electron donors to promote Cr(VI) reduction process by different microorganisms. The use of various redox mediators enabled electron transport facility for extracellular Cr(VI) reduction and accelerated the reaction. Also, many chemicals have employed diverse roles to improve the Cr(VI) reduction process in different microorganisms. The application of aforementioned materials at the contaminated systems has offered a variety of influence on Cr(VI) bioremediation by altering microbial community structures and functions and redox environment. The collective insights suggest that the knowledge of appropriate implementation of suitable nutrients can strongly inspire the Cr(VI) reduction rate and efficiency. However, a comprehensive information on such substances and their roles and biochemical pathways in different microorganisms remains elusive. In this regard, our review sheds light on the contributions of various chemicals as electron donors, redox mediators, cofactors, etc., on microbial Cr(VI) reduction for enhanced treatment practices.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
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Wei W, Plymale A, Zhu Z, Ma X, Liu F, Yu XY. In Vivo Molecular Insights into Syntrophic Geobacter Aggregates. Anal Chem 2020; 92:10402-10411. [PMID: 32614167 DOI: 10.1021/acs.analchem.0c00653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.
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Affiliation(s)
- Wenchao Wei
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China.,Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Andrew Plymale
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Zihua Zhu
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiang Ma
- Department of Chemistry, Grand View University, Des Moines, Iowa 50316, United States
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China
| | - Xiao-Ying Yu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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van Vliet DM, Lin Y, Bale NJ, Koenen M, Villanueva L, Stams AJM, Sánchez-Andrea I. Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers. Microorganisms 2020; 8:microorganisms8060920. [PMID: 32570748 PMCID: PMC7356697 DOI: 10.3390/microorganisms8060920] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, we isolated two marine strains, F1T and F21T, which together with Kiritimatiella glycovorans L21-Fru-ABT are the only pure cultures of the class Kiritimatiellae within the phylum Verrucomicrobiota. Here, we present an in-depth genome-guided characterization of both isolates with emphasis on their exopolysaccharide synthesis. The strains only grew fermentatively on simple carbohydrates and sulfated polysaccharides. Strains F1T, F21T and K. glycovorans reduced elemental sulfur, ferric citrate and anthraquinone-2,6-disulfonate during anaerobic growth on sugars. Both strains produced exopolysaccharides during stationary phase, probably with intracellularly stored glycogen as energy and carbon source. Exopolysaccharides included N-sulfated polysaccharides probably containing hexosamines and thus resembling glycosaminoglycans. This implies that the isolates can both degrade and produce sulfated polysaccharides. Both strains encoded an unprecedently high number of glycoside hydrolase genes (422 and 388, respectively), including prevalent alpha-L-fucosidase genes, which may be necessary for degrading complex sulfated polysaccharides such as fucoidan. Strain F21T encoded three putative glycosaminoglycan sulfotransferases and a putative sulfate glycosaminoglycan biosynthesis gene cluster. Based on phylogenetic and chemotaxonomic analyses, we propose the taxa Pontiella desulfatans F1T gen. nov., sp. nov. and Pontiella sulfatireligans F21T sp. nov. as representatives of the Pontiellaceae fam. nov. within the class Kiritimatiellae.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands;
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483486
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Bai YN, Wang XN, Zhang F, Wu J, Zhang W, Lu YZ, Fu L, Lau TC, Zeng RJ. High-rate anaerobic decolorization of methyl orange from synthetic azo dye wastewater in a methane-based hollow fiber membrane bioreactor. JOURNAL OF HAZARDOUS MATERIALS 2020; 388:121753. [PMID: 31806438 DOI: 10.1016/j.jhazmat.2019.121753] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/23/2019] [Accepted: 11/23/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic biological techniques are widely used in the reductive decolorization of textile wastewater. However, the decolorization efficiency of textile wastewater by conventional anaerobic biological techniques is generally limited due to the low biomass retention capacity and short hydraulic retention time (HRT). In this study, a methane-based hollow fiber membrane bioreactor (HfMBR) was initially inoculated with an enriched anaerobic methane oxidation (AOM) culture to rapidly form an anaerobic biofilm. Then, synthetic azo dye wastewater containing methyl orange (MO) was fed into the HfMBR. MO decolorization efficiency of ∼ 100 % (HRT = 2 to 1.5 days) and maximum decolorization rate of 883 mg/L/day (HRT = 0.5 day) were obtained by the stepwise increase of the MO loading rate into the methane-based HfMBR. Scanning electron microscopy (SEM) and fluorescence in situ hybridization (FISH) analysis visually revealed that archaea clusters formed synergistic consortia with adjacent bacteria. Quantitative PCR (qPCR), phylogenetic and high-throughput sequencing analysis results further confirmed the biological consortia formation of methane-related archaea and partner bacteria, which played a synergistic role in MO decolorization. The high removal efficiency and stable microbial structure in HfMBR suggest it is a potentially effective technique for high-toxic azo dyes removal from textile wastewater.
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Affiliation(s)
- Ya-Nan Bai
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China
| | - Xiu-Ning Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Fang Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
| | - Jun Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Wei Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Yong-Ze Lu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Liang Fu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China
| | - Tai-Chu Lau
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; State Key Laboratory in Marine Pollution, Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Raymond J Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China; Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; CAS Key Laboratory of Urban Pollutant Conversion, Department of Applied Chemistry, University of Science and Technology of China, Hefei 230026, PR China.
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Wang H, Lu L, Chen X, Bian Y, Ren ZJ. Geochemical and microbial characterizations of flowback and produced water in three shale oil and gas plays in the central and western United States. WATER RESEARCH 2019; 164:114942. [PMID: 31401327 DOI: 10.1016/j.watres.2019.114942] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Limited understanding of wastewater streams produced from shale oil and gas wells impedes best practices of wastewater treatment and reuse. This study provides a comprehensive and comparative analysis of flowback and produced water from three major and newly developed shale plays (the Bakken shale, North Dakota; the Barnett shale, Texas; and the Denver-Julesburg (DJ) basin, Colorado) in central and western United States. Geochemical features that included more than 10 water quality parameters, dissolved organic matter, as well as microbial community structures were characterized and compared. Results showed that wastewater from Bakken and Barnett shales has extremely high salinity (∼295 g/L total dissolved solids (TDS)) and low organic concentration (80-252 mg/L dissolved organic carbon (DOC)). In contrast, DJ basin showed an opposite trend with low TDS (∼30 g/L) and high organic content (644 mg/L DOC). Excitation-emission matrix (EEM) fluorescence spectra demonstrated that more humic acid and fluvic acid-like organics with higher aromaticity existed in Bakken wastewater than that in Barnett and DJ basin. Microbial communities of Bakken samples were dominated by Fe (III)-reducing bacteria Geobacter, lactic acid bacteria Lactococcus and Enterococcus, and Bradyrhizobium, while DJ basin water showed higher abundance of Rhodococcus, Thermovirga, and sulfate reducing bacteria Thermotoga and Petrotoga. All these bacteria are capable of hydrocarbon degradation. Hydrogenotrophic methanogens dominated the archaeal communities in all samples.
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Affiliation(s)
- Huan Wang
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Lu Lu
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Xi Chen
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Yanhong Bian
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States.
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
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Bai YN, Wang XN, Wu J, Lu YZ, Fu L, Zhang F, Lau TC, Zeng RJ. Humic substances as electron acceptors for anaerobic oxidation of methane driven by ANME-2d. WATER RESEARCH 2019; 164:114935. [PMID: 31387057 DOI: 10.1016/j.watres.2019.114935] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Humic substances (humics) are ubiquitous in terrestrial and aquatic environments where they can serve as electron acceptors for anaerobic oxidation of organic compounds. Methane is a powerful greenhouse gas, as well as the least reactive organic molecule. Anaerobic oxidation of methane (AOM) coupled to microbial reduction of various electron acceptors plays a crucial role in mitigating methane emissions. Here, we reported that humics could serve as terminal electron acceptors for AOM using enriched nitrate-reducing AOM microorganisms. AOM coupled to the reduction of humics was demonstrated based on the production of 13C-labelled carbon dioxide, and AOM activity was evaluated with different methane partial pressures and electron acceptor concentrations. After three-cycle reduction, both AOM activity and copy numbers of the archaea 16S rRNA and mcrA genes were the highest when anthraquinone-2,6-disulfonic acid and anthraquinone-2-sulfonic acid were electron acceptors. The high-throughput sequencing results suggested that ANME-2d were the dominant methane oxidation archaea after humics reduction, although the partner bacteria NC10 trended downward, other reported humics reduction bacteria (Geobactor and Anammox) appeared. The potential electron transfer models from ANME-2d to humics were proposed. These results enable a better understanding of available electron acceptors for AOM in natural environments and broaden our insight into the significant role of ANME-2d.
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Affiliation(s)
- Ya-Nan Bai
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, PR China
| | - Xiu-Ning Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Jun Wu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Yong-Ze Lu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Liang Fu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, PR China
| | - Fang Zhang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
| | - Tai-Chu Lau
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; State Key Laboratory in Marine Pollution, Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong
| | - Raymond J Zeng
- Advanced Laboratory for Environmental Research and Technology, USTC-CityU, Suzhou, PR China; School of Life Sciences, University of Science and Technology of China, Hefei, 230026, PR China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
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Wang H, Lu L, Mao D, Huang Z, Cui Y, Jin S, Zuo Y, Ren ZJ. Dominance of electroactive microbiomes in bioelectrochemical remediation of hydrocarbon-contaminated soils with different textures. CHEMOSPHERE 2019; 235:776-784. [PMID: 31280046 DOI: 10.1016/j.chemosphere.2019.06.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 06/12/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
Bioelectrochemical systems (BESs) are known to enhance the remediation of hydrocarbon-contaminated soil and sediments compared with natural attenuation, and the primary mechanism has been assumed as anaerobic degradation facilitated by electroactive bacteria (EAB) using the electrode as electron acceptor. However, known EAB were rarely found on the anodes of reported BESs, which challenged the fundamental mechanism of BESs although significant current generation was always observed during degradation of these recalcitrant substrates. This study however found the abundant EAB Geobacter (∼27.3%) in the anodic biofilms, which confirmed the role of electroactive bio-anode on the conversion of hydrocarbons into the current for the enhancement of remediation. Widespread occurrence of aerobic hydrocarbon-degrading bacteria (HDB) (e.g. ∼24.0% Parvibaculum and ∼30.6% Pseudomonas) was observed in soils with limited dissolved oxygen (∼0.4 mg/L). The higher abundance of dehydrogenase genes was found in the anode biofilms than that in soils, indicating anodic microorganisms may be mainly responsible for the removal of intermediates of aerobic hydrocarbons degradation in soils. High water saturation level and sandy soil texture showed positive impacts on bioelectrochemical remediation, while clay soil and unsaturation condition pose challenges in mass transfers in the matrix. The reactor performance was consistent with the phylogenetic molecular ecological network (pMENs) analysis, which showed that sandy soil BESs had tighter microbial network interactions than clay soil reactors.
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Affiliation(s)
- Huan Wang
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Lu Lu
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Deqiang Mao
- Department of Earth & Environmental Science, New Mexico Tech, Socorro, NM, 87801, United States.
| | - Zhe Huang
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Yixiao Cui
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
| | - Song Jin
- Advanced Environmental Technologies, LLC, Fort Collins, CO, 80525, United States.
| | - Yi Zuo
- Chevron Energy Technology Company, San Ramon, CA, 94583, United States.
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering and Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, United States; Department of Civil, Environmental, and Architectural Engineering, University of Colorado Boulder, Boulder, CO, 80309, United States.
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A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer. mBio 2019; 10:mBio.00789-19. [PMID: 31431545 PMCID: PMC6703419 DOI: 10.1128/mbio.00789-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The discovery of a methanogen that can conserve energy to support growth solely from the oxidation of organic carbon coupled to the reduction of an extracellular electron acceptor expands the possible environments in which methanogens might thrive. The potential importance of c-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea was previously proposed, but these studies with Methanosarcina acetivorans provide the first genetic evidence for cytochrome-based extracellular electron transfer in Archaea. The results suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which multiheme outer-surface c-type cytochromes are an essential component for electrical communication with the extracellular environment. M. acetivorans offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens but possibly also for Archaea that anaerobically oxidize methane. Extracellular electron exchange in Methanosarcina species and closely related Archaea plays an important role in the global carbon cycle and enhances the speed and stability of anaerobic digestion by facilitating efficient syntrophic interactions. Here, we grew Methanosarcina acetivorans with methanol provided as the electron donor and the humic analogue, anthraquione-2,6-disulfonate (AQDS), provided as the electron acceptor when methane production was inhibited with bromoethanesulfonate. AQDS was reduced with simultaneous methane production in the absence of bromoethanesulfonate. Transcriptomics revealed that expression of the gene for the transmembrane, multiheme, c-type cytochrome MmcA was higher in AQDS-respiring cells than in cells performing methylotrophic methanogenesis. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction but grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenzyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable the survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of M. acetivorans makes it an excellent model microbe for evaluating c-type cytochrome-dependent extracellular electron transfer in Archaea.
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Adediran GA, Liem-Nguyen V, Song Y, Schaefer JK, Skyllberg U, Björn E. Microbial Biosynthesis of Thiol Compounds: Implications for Speciation, Cellular Uptake, and Methylation of Hg(II). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:8187-8196. [PMID: 31257868 DOI: 10.1021/acs.est.9b01502] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cellular uptake of inorganic divalent mercury (Hg(II)) is a key step in microbial formation of neurotoxic methylmercury (MeHg), but the mechanisms remain largely unidentified. We show that the iron reducing bacterium Geobacter sulfurreducens produces and exports appreciable amounts of low molecular mass thiol (LMM-RSH) compounds reaching concentrations of about 100 nM in the assay medium. These compounds largely control the chemical speciation and bioavailability of Hg(II) by the formation of Hg(LMM-RS)2 complexes (primarily with cysteine) in assays without added thiols. By characterizing these effects, we show that the thermodynamic stability of Hg(II)-complexes is a principal controlling factor for Hg(II) methylation by this bacterium such that less stable complexes with mixed ligation involving LMM-RSH, OH-, and Cl- are methylated at higher rates than the more stable Hg(LMM-RS)2 complexes. The Hg(II) methylation rate across different Hg(LMM-RS)2 compounds is also influenced by the chemical structure of the complexes. In contrast to the current perception of microbial uptake of Hg, our results adhere to generalized theories for metal biouptake based on metal complexation with cell surface ligands and refine the mechanistic understanding of Hg(II) availability for microbial methylation.
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Affiliation(s)
| | - Van Liem-Nguyen
- Department of Chemistry , Umeå University , SE- 90187 Umeå , Sweden
- School of Science and Technology , Örebro University , SE-70182 Örebro , Sweden
| | - Yu Song
- Department of Forest Ecology and Management , Swedish University of Agricultural Sciences , SE-901 83 Umeå , Sweden
| | - Jeffra K Schaefer
- Department of Environmental Sciences , Rutgers University , 14 College Farm Road , New Brunswick , New Jersey 08901 , United States
| | - Ulf Skyllberg
- Department of Forest Ecology and Management , Swedish University of Agricultural Sciences , SE-901 83 Umeå , Sweden
| | - Erik Björn
- Department of Chemistry , Umeå University , SE- 90187 Umeå , Sweden
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Tang HY, Holmes DE, Ueki T, Palacios PA, Lovley DR. Iron Corrosion via Direct Metal-Microbe Electron Transfer. mBio 2019; 10:e00303-19. [PMID: 31088920 PMCID: PMC6520446 DOI: 10.1128/mbio.00303-19] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/08/2019] [Indexed: 11/20/2022] Open
Abstract
The concept that anaerobic microorganisms can directly accept electrons from Fe(0) has been controversial because direct metal-microbe electron transfer has previously only been indirectly inferred. Fe(0) oxidation was studied with Geobacter sulfurreducens strain ACL, an autotrophic strain that was previously shown to grow with electrons derived from a graphite cathode as the sole electron donor. Strain ACL grew with Fe(0) as the sole electron donor and fumarate as the electron acceptor. However, it appeared that at least a portion of the electron transfer was via H2 produced nonenzymatically from the oxidation of Fe(0) to Fe(II). H2, which accumulated in abiotic controls, was consumed during the growth of strain ACL, the cells were predominately planktonic, and genes for the uptake hydrogenase were highly expressed. Strain ACLHF was constructed to prevent growth on H2 or formate by deleting the genes for the uptake of hydrogenase and formate dehydrogenases from strain ACL. Strain ACLHF also grew with Fe(0) as the sole electron donor, but H2 accumulated in the culture, and cells heavily colonized Fe(0) surfaces with no visible planktonic growth. Transcriptomics suggested that the outer surface c-type cytochromes OmcS and OmcZ were important during growth of strain ACLHF on Fe(0). Strain ACLHF did not grow on Fe(0) if the gene for either of these cytochromes was deleted. The specific attachment of strain ACLHF to Fe(0), coupled with requirements for known extracellular electrical contacts, suggest that direct metal-microbe electron transfer is the most likely option for Fe(0) serving as an electron donor.IMPORTANCE The anaerobic corrosion of iron structures is expensive to repair and can be a safety and environmental concern. It has been known for over 100 years that the presence of anaerobic respiratory microorganisms can accelerate iron corrosion. Multiple studies have suggested that there are sulfate reducers, methanogens, and acetogens that can directly accept electrons from Fe(0) to support sulfate or carbon dioxide reduction. However, all of the strains studied can also use H2 as an electron donor for growth, which is known to be abiotically produced from Fe(0). Furthermore, no proteins definitely shown to function as extracellular electrical contacts with Fe(0) were identified. The studies described here demonstrate that direct electron transfer from Fe(0) can support anaerobic respiration. They also map out a simple genetic approach to the study of iron corrosion mechanisms in other microorganisms. A better understanding of how microorganisms promote iron corrosion is expected to lead to the development of strategies that can help reduce adverse impacts from this process.
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Affiliation(s)
- Hai-Yan Tang
- Department of Microbiology, Morrill IV Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waster Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Dawn E Holmes
- Department of Microbiology, Morrill IV Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Toshiyuki Ueki
- Department of Microbiology, Morrill IV Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Paola A Palacios
- Department of Microbiology, Morrill IV Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Derek R Lovley
- Department of Microbiology, Morrill IV Science Center, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Rodriguez SY, Cantú ME, Garcia-Reyes B, Garza-Gonzalez MT, Meza-Escalante ER, Serrano D, Alvarez LH. Biotransformation of 4-nitrophenol by co-immobilized Geobacter sulfurreducens and anthraquinone-2-sulfonate in barium alginate beads. CHEMOSPHERE 2019; 221:219-225. [PMID: 30640004 DOI: 10.1016/j.chemosphere.2019.01.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 12/13/2018] [Accepted: 01/06/2019] [Indexed: 05/17/2023]
Abstract
Geobacter sulfurreducens and anthraquinone-2-sulfonate (AQS) were used suspended and immobilized in barium alginate during the biotransformation of 4-nitrophenol (4-NP). The assays were conducted at different concentrations of 4-NP (50-400 mg/L) and AQS, either in suspended (0-400 μM) or immobilized form (0 or 760 μM), and under different pH values (5-9). G. sulfurreducens showed low capacity to reduce 4-NP in absence of AQS, especially at the highest concentrations of the contaminant. AQS improved the reduction rates from 0.0086 h-1, without AQS, to 0.149 h-1 at 400 μM AQS, which represent an increment of 17.3-fold. The co-immobilization of AQS and G. sulfurreducens in barium alginate beads (AQSi-Gi) increased the reduction rates up to 4.8- and 7.2-fold, compared to incubations with G. sulfurreducens in suspended and immobilized form, but in absence of AQS. AQSi-Gi provides to G. sulfurreducens a barrier against the possibly inhibiting effects of 4-NP.
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Affiliation(s)
- Sujei Y Rodriguez
- Universidad Autonoma de Nuevo Leon (UANL), Facultad de Ciencias Quimicas, Av. Universidad S/N, Cd. Universitaria, San Nicolas de los Garza, 66455, Nuevo Leon, Mexico
| | - Maria E Cantú
- Universidad Autonoma de Nuevo Leon (UANL), Facultad de Ciencias Quimicas, Av. Universidad S/N, Cd. Universitaria, San Nicolas de los Garza, 66455, Nuevo Leon, Mexico
| | - Bernardo Garcia-Reyes
- Universidad Autonoma de Nuevo Leon (UANL), Facultad de Ciencias Quimicas, Av. Universidad S/N, Cd. Universitaria, San Nicolas de los Garza, 66455, Nuevo Leon, Mexico
| | - Maria T Garza-Gonzalez
- Universidad Autonoma de Nuevo Leon (UANL), Facultad de Ciencias Quimicas, Av. Universidad S/N, Cd. Universitaria, San Nicolas de los Garza, 66455, Nuevo Leon, Mexico
| | - Edna R Meza-Escalante
- Instituto Tecnologico de Sonora (ITSON), Departamento de Ciencias del Agua y Medio Ambiente, 5 de Febrero 818 Sur, C.P. 85000, Cuidad Obregon, Sonora, Mexico
| | - Denisse Serrano
- Instituto Tecnologico de Sonora (ITSON), Departamento de Ciencias del Agua y Medio Ambiente, 5 de Febrero 818 Sur, C.P. 85000, Cuidad Obregon, Sonora, Mexico
| | - Luis H Alvarez
- Universidad Autonoma de Nuevo Leon (UANL), Facultad de Ciencias Quimicas, Av. Universidad S/N, Cd. Universitaria, San Nicolas de los Garza, 66455, Nuevo Leon, Mexico; Instituto Tecnologico de Sonora (ITSON), Departamento de Ciencias Agronomicas y Veterinarias, 5 de Febrero 818 Sur, C.P. 85000, Cuidad Obregon, Sonora, Mexico.
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Chen Z, Zhang Y, Luo Q, Wang L, Liu S, Peng Y, Wang H, Shen L, Li Q, Wang Y. Maghemite (γ-Fe 2O 3) nanoparticles enhance dissimilatory ferrihydrite reduction by Geobacter sulfurreducens: Impacts on iron mineralogical change and bacterial interactions. J Environ Sci (China) 2019; 78:193-203. [PMID: 30665638 DOI: 10.1016/j.jes.2018.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 06/09/2023]
Abstract
Microbially mediated bioreduction of iron oxyhydroxide plays an important role in the biogeochemical cycle of iron. Geobacter sulfurreducens is a representative dissimilatory iron-reducing bacterium that assembles electrically conductive pili and cytochromes. The impact of supplementation with γ-Fe2O3 nanoparticles (NPs) (0.2 and 0.6 g) on the G. sulfurreducens-mediated reduction of ferrihydrite was investigated. In the overall performance of microbial ferrihydrite reduction mediated by γ-Fe2O3 NPs, stronger reduction was observed in the presence of direct contact with γ-Fe2O3 NPs than with indirect contact. Compared to the production of Fe(II) derived from biotic modification with ferrihydrite alone, increases greater than 1.6- and 1.4-fold in the production of Fe(II) were detected in the biotic modifications in which direct contact with 0.2 g and 0.6 g γ-Fe2O3 NPs, respectively, occurred. X-ray diffraction analysis indicated that magnetite was a unique representative iron mineral in ferrihydrite when active G. sulfurreducens cells were in direct contact with γ-Fe2O3 NPs. Because of the sorption of biogenic Fe(II) onto γ-Fe2O3 NPs instead of ferrihydrite, the addition of γ-Fe2O3 NPs could also contribute to increased duration of ferrihydrite reduction by preventing ferrihydrite surface passivation. Additionally, electron microscopy analysis confirmed that the direct addition of γ-Fe2O3 NPs stimulated the electrically conductive pili and cytochromes to stretch, facilitating long-range electron transfer between the cells and ferrihydrite. The obtained findings provide a more comprehensive understanding of the effects of iron oxide NPs on soil biogeochemistry.
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Affiliation(s)
- Zheng Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail: ; Department of Environmental Science, School of Environmental Science and Engineering, Tan Kah Kee College, Xiamen University, Zhangzhou 363105, China; Key Laboratory of Measurement and Control System for Coastal Environment, Fuqing Branch of Fujian Normal University, Fuqing 350300, China; Zhejiang Provincial Key Laboratory of Watershed Science and Health, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Yaxian Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Qingliu Luo
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Liuying Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Shurui Liu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Yajuan Peng
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Haitao Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail:
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361001, China. E-mail: .
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Shi Z. Methylome and Metabolome Analyses Reveal Adaptive Mechanisms in Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors. J Proteome Res 2019; 18:1494-1502. [DOI: 10.1021/acs.jproteome.8b00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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Li D, Li J, Liu D, Ma X, Cheng L, Li W, Qian C, Mu Y, Yu H. Potential regulates metabolism and extracellular respiration of electroactiveGeobacterbiofilm. Biotechnol Bioeng 2019; 116:961-971. [DOI: 10.1002/bit.26928] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/26/2018] [Accepted: 01/17/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Dao‐Bo Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Jie Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Dong‐Feng Liu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Xin Ma
- School of Life Sciences, University of Science and Technology of ChinaHefei China
| | - Lei Cheng
- School of Life Sciences, University of Science and Technology of ChinaHefei China
| | - Wen‐Wei Li
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Chen Qian
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Yang Mu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
| | - Han‐Qing Yu
- Department of Applied ChemistryUniversity of Science and Technology of ChinaHefei China
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Dubé CD, Guiot SR. Characterization of the protein fraction of the extracellular polymeric substances of three anaerobic granular sludges. AMB Express 2019; 9:23. [PMID: 30729349 PMCID: PMC6367495 DOI: 10.1186/s13568-019-0746-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Extracellular polymeric substances (EPS) play major roles in the efficacy of biofilms such as anaerobic granules, ranging from structural stability to more specific functions. The EPS of three granular anaerobic sludges of different origins were studied and compared. Particularly, the peptides from the protein fraction were identified by mass spectrometry. Desulfoglaeba and Treponema bacterial genera and Methanosaeta and Methanobacterium archaeal genera were prominent in all three sludges. Methanosaeta concilii proteins were the most represented in EPS of all three sludges studied. Principally, four proteins found in the three sludges, the S-layer protein, the CO-methylating acetyl-CoA synthase, an ABC transporter substrate-binding protein and the methyl-coenzyme M reductase, were expressed by Methanosaeta concilii. Mainly catabolic enzymes were found from the 45 proteins identified in the protein fraction of EPS. This suggests that EPS may have a role in allowing extracellular catabolic reactions.
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Extracellular Electron Transfer May Be an Overlooked Contribution to Pelagic Respiration in Humic-Rich Freshwater Lakes. mSphere 2019; 4:4/1/e00436-18. [PMID: 30674644 PMCID: PMC6344600 DOI: 10.1128/msphere.00436-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. Humic lakes and ponds receive large amounts of terrestrial carbon and are important components of the global carbon cycle, yet how their redox cycling influences the carbon budget is not fully understood. Here we compared metagenomes obtained from a humic bog and a clear-water eutrophic lake and found a much larger number of genes that might be involved in extracellular electron transfer (EET) for iron redox reactions and humic substance (HS) reduction in the bog than in the clear-water lake, consistent with the much higher iron and HS levels in the bog. These genes were particularly rich in the bog’s anoxic hypolimnion and were found in diverse bacterial lineages, some of which are relatives of known iron oxidizers or iron-HS reducers. We hypothesize that HS may be a previously overlooked electron acceptor and that EET-enabled redox cycling may be important in pelagic respiration and greenhouse gas budget in humic-rich freshwater lakes.
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Wang Q, Jones AAD, Gralnick JA, Lin L, Buie CR. Microfluidic dielectrophoresis illuminates the relationship between microbial cell envelope polarizability and electrochemical activity. SCIENCE ADVANCES 2019; 5:eaat5664. [PMID: 30746438 PMCID: PMC6357865 DOI: 10.1126/sciadv.aat5664] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 11/30/2018] [Indexed: 05/28/2023]
Abstract
Electrons can be transported from microbes to external insoluble electron acceptors (e.g., metal oxides or electrodes in an electrochemical cell). This process is known as extracellular electron transfer (EET) and has received considerable attention due to its applications in environmental remediation and energy conversion. However, the paucity of rapid and noninvasive phenotyping techniques hinders a detailed understanding of microbial EET mechanisms. Most EET phenotyping techniques assess microorganisms based on their metabolism and growth in various conditions and/or performance in electrochemical systems, which requires large sample volumes and cumbersome experimentation. Here, we use microfluidic dielectrophoresis to show a strong correlation between bacterial EET and surface polarizability. We analyzed surface polarizabilities for wild-type strains and cytochrome-deletion mutants of two model EET microbes, Geobacter sulfurreducens and Shewanella oneidensis, and for Escherichia coli strains heterologously expressing S. oneidensis EET pathways in various growth conditions. Dielectrophoretic phenotyping is achieved with small cell culture volumes (~100 μl) in a short amount of time (1 to 2 min per strain). Our work demonstrates that cell polarizability is diminished in response to deletions of crucial outer-membrane cytochromes and enhanced due to additions of EET pathways. Results of this work hold exciting promise for rapid screening of direct EET or other cell envelope phenotypes using cell polarizability as a proxy, especially for microbes difficult to cultivate in laboratory conditions.
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Affiliation(s)
- Qianru Wang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A.-Andrew D. Jones
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota Twin Cities, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Liwei Lin
- Department of Mechanical Engineering, University of California, Berkeley, 1113 Etcheverry Hall #1740, Berkeley, CA 94720-1740, USA
| | - Cullen R. Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Ferreira MR, Salgueiro CA. Biomolecular Interaction Studies Between Cytochrome PpcA From Geobacter sulfurreducens and the Electron Acceptor Ferric Nitrilotriacetate (Fe-NTA). Front Microbiol 2018; 9:2741. [PMID: 30524391 PMCID: PMC6262392 DOI: 10.3389/fmicb.2018.02741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/26/2018] [Indexed: 11/17/2022] Open
Abstract
Geobacter sulfurreducens bacterium exhibits an enormous respiratory versatility, including the utilization of several toxic and radioactive metals as electron acceptors. This versatility is also replicated in the capability of the most abundant cytochrome in G. sulfurreducens, the periplasmic triheme cytochrome PpcA, to reduce uranium, chromium and other metal ions. From all possible electron transfer pathways in G. sulfurreducens, those involved in the iron reduction are the best characterized to date. Previously, we provided structural evidence for the complex interface established between PpcA and the electron acceptor Fe(III)-citrate. However, genetic studies suggested that this acceptor is mainly reduced by outer membrane cytochomes. In the present work, we used UV-visible measurements to demonstrate that PpcA is able to directly reduce the electron acceptor ferric nitrilotriacetate (Fe-NTA), a more outer membrane permeable iron chelated form. In addition, the molecular interactions between PpcA and Fe-NTA were probed by Nuclear Magnetic Resonance (NMR) spectroscopy. The NMR spectra obtained for PpcA samples in the absence and presence of Fe-NTA showed that the interaction is reversible and encompasses a positively charged surface region located in the vicinity of the heme IV. Overall, the study elucidates the formation of an electron transfer complex between PpcA and a readily outer-membrane permeable iron chelated form. The structural and functional relationships obtained explain how a single cytochrome is designed to effectively interact with a wide range of G. sulfurreducens electron acceptors, a feature that can be explored for optimal bioelectrochemical applications.
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Affiliation(s)
- Marisa R Ferreira
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Carlos A Salgueiro
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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42
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Microbial Electrochemical Technologies for Wastewater Treatment: Principles and Evolution from Microbial Fuel Cells to Bioelectrochemical-Based Constructed Wetlands. WATER 2018. [DOI: 10.3390/w10091128] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microbial electrochemical technologies (MET) rely on the presence of the metabolic activity of electroactive bacteria for the use of solid-state electrodes for oxidizing different kinds of compound that can lead to the synthesis of chemicals, bioremediation of polluted matrices, the treatment of contaminants of interest, as well as the recovery of energy. Keeping these possibilities in mind, there has been growing interest in the use of electrochemical technologies for wastewater treatment, if possible with simultaneous power generation, since the beginning of the present century. In the last few years, there has been growing interest in exploring the possibility of merging MET with constructed wetlands offering a new option of an intensified wetland system that could maintain a high performance with a lower footprint. Based on that interest, this paper explains the general principles of MET, and the different known extracellular electron transfer mechanisms ruling the interaction between electroactive bacteria and potential solid-state electron acceptors. It also looks at the adoption of those principles for the development of MET set-ups for simultaneous wastewater treatment and power generation, and the challenges that the technology faces. Ultimately, the most recent developments in setups that merge MET with constructed wetlands are presented and discussed.
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Dantas JM, Ferreira MR, Catarino T, Kokhan O, Pokkuluri PR, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the redox active analogue for humic substances. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:619-630. [PMID: 29777686 DOI: 10.1016/j.bbabio.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/09/2018] [Accepted: 05/15/2018] [Indexed: 01/17/2023]
Abstract
The bacterium Geobacter sulfurreducens can transfer electrons to quinone moieties of humic substances or to anthraquinone-2,6-disulfonate (AQDS), a model for the humic acids. The reduced form of AQDS (AH2QDS) can also be used as energy source by G. sulfurreducens. Such bidirectional utilization of humic substances confers competitive advantages to these bacteria in Fe(III) enriched environments. Previous studies have shown that the triheme cytochrome PpcA from G. sulfurreducens has a bifunctional behavior toward the humic substance analogue. It can reduce AQDS but the protein can also be reduced by AH2QDS. Using stopped-flow kinetic measurements we were able to demonstrate that other periplasmic members of the PpcA-family in G. sulfurreducens (PpcB, PpcD and PpcE) also showed the same behavior. The extent of the electron transfer is thermodynamically controlled favoring the reduction of the cytochromes. NMR spectra recorded for 13C,15N-enriched samples in the presence increasing amounts of AQDS showed perturbations in the chemical shift signals of the cytochromes. The chemical shift perturbations on cytochromes backbone NH and 1H heme methyl signals were used to map their interaction regions with AQDS, showing that each protein forms a low-affinity binding complex through well-defined positive surface regions in the vicinity of heme IV (PpcB, PpcD and PpcE) and I (PpcE). Docking calculations performed using NMR chemical shift perturbations allowed modeling the interactions between AQDS and each cytochrome at a molecular level. Overall, the results obtained provided important structural-functional relationships to rationalize the microbial respiration of humic substances in G. sulfurreducens.
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Affiliation(s)
- Joana M Dantas
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Marisa R Ferreira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157 Oeiras, Portugal; Departamento de Química, Faculdade de Ciências e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA
| | - P Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus Caparica, 2829-516 Caparica, Portugal.
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Costa NL, Clarke TA, Philipp LA, Gescher J, Louro RO, Paquete CM. Electron transfer process in microbial electrochemical technologies: The role of cell-surface exposed conductive proteins. BIORESOURCE TECHNOLOGY 2018; 255:308-317. [PMID: 29444758 DOI: 10.1016/j.biortech.2018.01.133] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/26/2018] [Accepted: 01/27/2018] [Indexed: 06/08/2023]
Abstract
Electroactive microorganisms have attracted significant interest for the development of novel biotechnological systems of low ecological footprint. These can be used for the sustainable production of energy, bioremediation of metal-contaminated environments and production of added-value products. Currently, almost 100 microorganisms from the Bacterial and Archaeal domains are considered electroactive, given their ability to efficiently interact with electrodes in microbial electrochemical technologies. Cell-surface exposed conductive proteins are key players in the electron transfer between cells and electrodes. Interestingly, it seems that among the electroactive organisms identified so far, these cell-surface proteins fall into one of four groups. In this review, the different types of cell-surface conductive proteins found in electroactive organisms will be overviewed, focusing on their structural and functional properties.
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Affiliation(s)
- Nazua L Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Laura-Alina Philipp
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany; Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal
| | - Catarina M Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, 2780-157, Oeiras, Portugal.
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Semenec L, Laloo AE, Schulz BL, Vergara IA, Bond PL, Franks AE. Deciphering the electric code of Geobacter sulfurreducens in cocultures with Pseudomonas aeruginosa via SWATH-MS proteomics. Bioelectrochemistry 2018; 119:150-160. [DOI: 10.1016/j.bioelechem.2017.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/28/2022]
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Ueki T, DiDonato LN, Lovley DR. Toward establishing minimum requirements for extracellular electron transfer in Geobacter sulfurreducens. FEMS Microbiol Lett 2017; 364:3796320. [PMID: 28472266 DOI: 10.1093/femsle/fnx093] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/03/2017] [Indexed: 11/12/2022] Open
Abstract
The highly redundant pathways for extracellular electron transfer in Geobacter sulfurreducens must be simplified for this microorganism to serve as an effective chassis for applications such as the development of sensors and biocomputing. Five homologs of the periplasmic c-type cytochromes, PpcA-E, offer the possibility of multiple routes of electron transfer across the periplasm. The presence of a large number of outer membrane c-type cytochromes allows G. sulfurreducens to adapt to disruption of an electron transfer pathway in the outer membrane. A strain in which genes for all five periplasmic cytochromes, PpcA-E, were deleted did not reduce Fe(III). Introducing ppcA under the control of an IPTG-inducible system in the quintuple deletion strain yielded a strain that reduced Fe(III) only in the presence of IPTG. A strain lacking known major outer membrane cytochromes, OmcB, OmcE, OmcS and OmcT, and putative functional homologs of OmcB, did not reduce Fe(III). Introduction of omcB in this septuple deletion strain restored the ability to reduce Fe(III). These results demonstrate that it is possible to trim redundancy from the extracellular electron transfer pathways in G. sulfurreducens in order to construct strains with defined extracellular electron transfer routes.
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Michelson K, Sanford RA, Valocchi AJ, Werth CJ. Nanowires of Geobacter sulfurreducens Require Redox Cofactors to Reduce Metals in Pore Spaces Too Small for Cell Passage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:11660-11668. [PMID: 28929755 DOI: 10.1021/acs.est.7b02531] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Members of the Geobacteraceae family are ubiquitous metal reducers that utilize conductive "nanowires" to reduce Mn(IV) and Fe(III) oxides in anaerobic sediments. However, it is not currently known if and to what extent the Mn(IV) and Fe(III) oxides in soil grains and low permeability sediments that are sequestered in pore spaces too small for cell passage can be reduced by long-range extracellular electron transport via Geobacter nanowires, and what mechanisms control this reduction. We developed a microfluidic reactor that physically separates Geobacter sulfurreducens from the Mn(IV) mineral birnessite by a 1.4 μm thick wall containing <200 nm pores. Using optical microscopy and Raman spectroscopy, we show that birnessite can be reduced up to 15 μm away from cell bodies, similar to the reported length of Geobacter nanowires. Reduction across the nanoporous wall required reducing conditions, provided by Escherichia coli, and an exogenous supply of riboflavin. Our results discount electron shuttling by dissolved flavins, and instead support their role as bound redox cofactors in electron transport from nanowires to metal oxides. We also show that upon addition of a soluble electron shuttle (i.e., AQDS), reduction extends beyond the reported nanowire length up to 40 μm into a layer of birnessite.
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Affiliation(s)
- Kyle Michelson
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign , 1301 West Green Street, Urbana, Illinois 61801, United States
| | - Albert J Valocchi
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign , 205 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Charles J Werth
- Department of Civil, Architectural, and Environmental Engineering, University of Texas at Austin , 301 E. Dean Keeton Street, Austin, Texas 78712, United States
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He S, Stevens SLR, Chan LK, Bertilsson S, Glavina del Rio T, Tringe SG, Malmstrom RR, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2017; 2:e00277-17. [PMID: 28959738 PMCID: PMC5615132 DOI: 10.1128/msphere.00277-17] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/05/2017] [Indexed: 11/20/2022] Open
Abstract
Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
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Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Geoscience, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Sarah L. R. Stevens
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Liu YN, Zhang F, Li J, Li DB, Liu DF, Li WW, Yu HQ. Exclusive Extracellular Bioreduction of Methyl Orange by Azo Reductase-Free Geobacter sulfurreducens. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8616-8623. [PMID: 28671824 DOI: 10.1021/acs.est.7b02122] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Azo dyes are a class of recalcitrant organic pollutants causing severe environmental pollution. For their biodecolorization, the azo reductase system was considered as the major molecular basis in bacteria. However, the intracellular localization of azo reductase limits their function for efficient azo dye decolorization. This limitation may be circumvented by electrochemically active bacteria (EAB) which is capable of extracellular respiration. To verify the essential role of extracellular respiration in azo dye decolorization, Geobacter sulfurreducens PCA, a model EAB, was used for the bioreduction of methyl orange (MO), a typical azo dye. G. sulfurreducens PCA efficiently reduced MO into amines. Kinetic results showed that G. sulfurreducens PCA had the highest decolorization efficiency among the currently known MO reducing bacteria. Electrons from acetate oxidization by this strain were transferred by the respiratory chain to MO. The mass and electron balances, fluorescent probing and proteinase K treatment experimental results indicate that the biodecolorization of MO by G. sulfurreducens PCA is an exclusive extracellular process. OmcB, OmcC and OmcE were identified as the key outer-membrane proteins for the extracellular MO reduction. This work deepens our understanding of EAB physiology and is useful for the decontamination of environments polluted with azo dyes. The contribution of extracellular respiration to pollutants reduction will broaden the environmental applications of EAB.
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Affiliation(s)
- Yi-Nan Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Feng Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Jie Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Dao-Bo Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Dong-Feng Liu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Wen-Wei Li
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
| | - Han-Qing Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Chemistry, University of Science and Technology of China , Hefei, 230026, China
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