1
|
Wang Y, Bai Y, Su J, Xu L, Ren M, Cao M. Manganese(IV) reduction coupled with ammonium oxidation mediated by a single strain Aromatoleum evansii MAY27: Performance, metabolomics, and mechanism. BIORESOURCE TECHNOLOGY 2024; 409:131235. [PMID: 39121511 DOI: 10.1016/j.biortech.2024.131235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/28/2024] [Accepted: 08/06/2024] [Indexed: 08/11/2024]
Abstract
Manganese(IV) (Mn(IV)) reduction coupled to anaerobic ammonium (NH4+-N) oxidation (Mnammox) is a recently identified metal oxide-mediated nitrogen (N) loss pathway, holding potential value for the efficient removal of NH4+-N from wastewater. However, little is known about the application of Mnammox in wastewater treatment. Here, a novel Mnammox bacterium Aromatoleum evansii (strain MAY27) was screened. Strain MAY27 can utilize MnO2 as an electron acceptor to achieve NH4+-N removal under a low C/N condition (C/N = 0.5). The influencing factors in the Mnammox process and the Mn(IV) reduction driving effect on NH4+-N oxidation were investigated. The physiological characteristics of strain MAY27 and differential metabolic pathways were identified through whole-genome sequencing and metabolomic analyses. A significant up-regulation of several key pathways upon the addition of MnO2, including glycolysis/gluconeogenesis, transmembrane transporter activity, and oxidoreductase activity. This study contributes to the advancement of biotechnological approaches for treating N-containing wastewater.
Collapse
Affiliation(s)
- Yue Wang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Yihan Bai
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Liang Xu
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Miqi Ren
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Meng Cao
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| |
Collapse
|
2
|
Hou L, Zheng B, Jiang Z, Hu Y, Shi L, Dong Y, Jiang Y. The dmsEFABGH operon encodes an essential and modular electron transfer pathway for extracellular iodate reduction by Shewanella oneidensis MR-1. Microbiol Spectr 2024; 12:e0051224. [PMID: 38916364 PMCID: PMC11302344 DOI: 10.1128/spectrum.00512-24] [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: 02/27/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Extracellular iodate reduction by Shewanella spp. contributes to iodide generation in the biogeochemical cycling of iodine. However, there is a disagreement on whether Shewanella spp. use different extracellular electron transfer pathways with dependence on electron donors in iodate reduction. In this study, a series of gene deletion mutants of Shewanella oneidensis MR-1 were created to investigate the roles of dmsEFABGH, mtrCAB, and so4357-so4362 operons in iodate reduction. The iodate-reducing activity of the mutants was tested with lactate, formate, and H2 as the sole electron donors, respectively. In the absence of single-dms gene, iodate reduction efficiency of the mutants was only 12.9%-84.0% with lactate at 24 hours, 22.1%-85.9% with formate at 20 hours, and 19.6%-57.7% with H2 at 42 hours in comparison to complete reduction by the wild type. Progressive inhibition of iodate reduction was observed when the dms homolog from the so4357-so4362 operon was deleted in the single-dms gene mutants. This result revealed complementation of dmsEFABGH by so4357-so4362 at the single-gene level, indicating modularity of the extracellular electron transfer pathway encoded by dmsEFABGH operon. Under the conditions of all electron donors, significant inhibition of iodate reduction and accumulation of H2O2 were detected for ΔmtrCAB. Collectively, these results demonstrated that the dmsEFABGH operon encodes an essential and modular iodate-reducing pathway without electron donor dependence in S. oneidensis MR-1. The mtrCAB operon was involved in H2O2 elimination with all electron donors. The findings in this study improved the understanding of molecular mechanisms underlying extracellular iodate reduction.IMPORTANCEIodine is an essential trace element for human and animals. Recent studies revealed the contribution of microbial extracellular reduction of iodate in biogeochemical cycling of iodine. Multiple reduced substances can be utilized by microorganisms as energy source for iodate reduction. However, varied electron transfer pathways were proposed for iodate reduction with different electron donors in the model strain Shewanella oneidensis MR-1. Here, through a series of gene deletion and iodate reduction experiments, we discovered that the dmsEFABGH operon was essential for iodate reduction with at least three electron donors, including lactate, formate, and H2. The so4357-so4362 operon was first demonstrated to be capable of complementing the function of dmsEFABGH at single-gene level.
Collapse
Affiliation(s)
- Lingyu Hou
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Beiling Zheng
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Zhou Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Yidan Hu
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
| | - Liang Shi
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yiran Dong
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Yongguang Jiang
- Department of Biological Sciences and Technology, School of Environmental Studies, China University of Geosciences, Wuhan, Hubei, China
- Hubei Key Laboratory of Wetland Evolution & Eco-Restoration, Wuhan, Hubei, China
| |
Collapse
|
3
|
Wang J, Jiao D, Yuan S, Chen H, Dai J, Wang X, Guo Y, Qiu D. Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains. JOURNAL OF HAZARDOUS MATERIALS 2024; 477:135370. [PMID: 39088956 DOI: 10.1016/j.jhazmat.2024.135370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 07/17/2024] [Accepted: 07/27/2024] [Indexed: 08/03/2024]
Abstract
Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.
Collapse
Affiliation(s)
- Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Han Chen
- Jingchu University of Technology, Jingmen 448000, China
| | - Jingcheng Dai
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Guo
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| |
Collapse
|
4
|
Agee A, Pace G, Yang V, Segalman R, Furst AL. Mixed Conducting Polymers Alter Electron Transfer Thermodynamics to Boost Current Generation from Electroactive Microbes. J Am Chem Soc 2024; 146:19728-19736. [PMID: 39001879 PMCID: PMC11276794 DOI: 10.1021/jacs.4c01288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024]
Abstract
Electroactive microbes that can release or take up electrons are essential components of nearly every ecological niche and are powerful tools for the development of alternative energy technologies. Small-molecule mediators are critical for this electron transfer but remain difficult to study and engineer because they perform concerted two-electron transfer in native systems but only individual, one-electron transfers in electrochemical studies. Here, we report that electrode modification with ion- and electron-conductive polymers yields biosimilar, concerted two-electron transfer from Shewanella oneidensis via flavin mediators. S. oneidensis biofilms on these polymers show significantly improved per-microbe current generation and morphologies that more closely resemble native systems, setting a new paradigm for the study and optimization of these electron transfer processes. The unprecedented concerted electron transfer was found to be due to altered mediator electron transfer thermodynamics, enabling biologically relevant studies of electroactive biofilms in the lab for the first time. These important findings pave the way for a complete understanding of the ecological role of electroactive microbes and their broad application in sustainable technologies.
Collapse
Affiliation(s)
- Alec Agee
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Gordon Pace
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Victoria Yang
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| | - Rachel Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Ariel L. Furst
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
5
|
Gamlin J, Caird R, Sachdeva N, Miao Y, Walecka-Hutchison C, Mahendra S, K De Long S. Developing a microbial community structure index (MCSI) as an approach to evaluate and optimize bioremediation performance. Biodegradation 2024:10.1007/s10532-024-10093-2. [PMID: 39017970 DOI: 10.1007/s10532-024-10093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Much attention is placed on organohalide-respiring bacteria (OHRB), such as Dehalococcoides, during the design and performance monitoring of chlorinated solvent bioremediation systems. However, many OHRB cannot function effectively without the support of a diverse group of other microbial community members (MCMs), who play key roles fermenting organic matter into more readily useable electron donors, producing corrinoids such as vitamin B12, or facilitating other important metabolic processes or biochemical reactions. While it is known that certain MCMs support dechlorination, a metric considering their contribution to bioremediation performance has yet to be proposed. Advances in molecular biology tools offer an opportunity to better understand the presence and activity of specific microbes, and their relation to bioremediation performance. In this paper, we test the hypothesis that a specific microbial consortium identified within 16S ribosomal ribonucleic acid (rRNA) gene next generation sequencing (NGS) data can be predictive of contaminant degradation rates. Field-based data from multiple contaminated sites indicate that increasing relative abundance of specific MCMs correlates with increasing first-order degradation rates. Based on these results, we present a framework for computing a simplified metric using NGS data, the Microbial Community Structure Index, to evaluate the adequacy of the microbial ecosystem during assessment of bioremediation performance.
Collapse
Affiliation(s)
- Jeff Gamlin
- GSI Environmental Inc, 13949 West Colfax Ave, Suite 210, Lakewood, CO, 80401, USA.
| | - Renee Caird
- Jacobs, 120 St. James Ave, Boston, MA, 02116, USA
| | - Neha Sachdeva
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado, CO, 80523, USA
| | - Yu Miao
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115, USA
| | | | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Susan K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, Colorado, CO, 80523, USA
| |
Collapse
|
6
|
Zhao YC, Sha C, Zhao XM, Du JX, Zou L, Yong YC. Unnatural Direct Interspecies Electron Transfer Enabled by Living Cell-Cell Click Chemistry. Angew Chem Int Ed Engl 2024; 63:e202402318. [PMID: 38710653 DOI: 10.1002/anie.202402318] [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: 02/01/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
Direct interspecies electron transfer (DIET) is essential for maintaining the function and stability of anaerobic microbial consortia. However, only limited natural DIET modes have been identified and DIET engineering remains highly challenging. In this study, an unnatural DIET between Shewanella oneidensis MR-1 (SO, electron donating partner) and Rhodopseudomonas palustris (RP, electron accepting partner) was artificially established by a facile living cell-cell click chemistry strategy. By introducing alkyne- or azide-modified monosaccharides onto the cell outer surface of the target species, precise covalent connections between different species in high proximity were realized through a fast click chemistry reaction. Remarkably, upon covalent connection, outer cell surface C-type cytochromes mediated DIET between SO and RP was achieved and identified, although this was never realized naturally. Moreover, this connection directly shifted the natural H2 mediated interspecies electron transfer (MIET) to DIET between SO and RP, which delivered superior interspecies electron exchange efficiency. Therefore, this work demonstrated a naturally unachievable DIET and an unprecedented MIET shift to DIET accomplished by cell-cell distance engineering, offering an efficient and versatile solution for DIET engineering, which extends our understanding of DIET and opens up new avenues for DIET exploration and applications.
Collapse
Affiliation(s)
- Yi-Cheng Zhao
- Biofuel Institute and Institute for Energy Research, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Chong Sha
- Biofuel Institute and Institute for Energy Research, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Xing-Ming Zhao
- Biofuel Institute and Institute for Energy Research, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Jia-Xin Du
- Biofuel Institute and Institute for Energy Research, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Long Zou
- Nanchang Key Laboratory of Microbial Resources Exploitation & Utilization from Poyang Lake Wetland, College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yang-Chun Yong
- Biofuel Institute and Institute for Energy Research, School of Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| |
Collapse
|
7
|
Suzuki S, Ishii S, Chadwick GL, Tanaka Y, Kouzuma A, Watanabe K, Inagaki F, Albertsen M, Nielsen PH, Nealson KH. A non-methanogenic archaeon within the order Methanocellales. Nat Commun 2024; 15:4858. [PMID: 38871712 DOI: 10.1038/s41467-024-48185-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
Serpentinization, a geochemical process found on modern and ancient Earth, provides an ultra-reducing environment that can support microbial methanogenesis and acetogenesis. Several groups of archaea, such as the order Methanocellales, are characterized by their ability to produce methane. Here, we generate metagenomic sequences from serpentinized springs in The Cedars, California, and construct a circularized metagenome-assembled genome of a Methanocellales archaeon, termed Met12, that lacks essential methanogenesis genes. The genome includes genes for an acetyl-CoA pathway, but lacks genes encoding methanogenesis enzymes such as methyl-coenzyme M reductase, heterodisulfide reductases and hydrogenases. In situ transcriptomic analyses reveal high expression of a multi-heme c-type cytochrome, and heterologous expression of this protein in a model bacterium demonstrates that it is capable of accepting electrons. Our results suggest that Met12, within the order Methanocellales, is not a methanogen but a CO2-reducing, electron-fueled acetogen without electron bifurcation.
Collapse
Affiliation(s)
- Shino Suzuki
- Geobiology and Astrobiology Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Kanagawa, Japan.
- School of Physical Sciences, SOKENDAI (Graduate University for Advanced Studies), Sagamihara, Kanagawa, Japan.
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine and Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Shun'ichi Ishii
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine and Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Grayson L Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Yugo Tanaka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Fumio Inagaki
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Kanagawa, Japan
- Department of Earth Science, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
8
|
Cerda Á, Rodríguez C, González M, González H, Serrano J, Leiva E. Feammox bacterial biofilm formation in HFMB. CHEMOSPHERE 2024; 358:142072. [PMID: 38657691 DOI: 10.1016/j.chemosphere.2024.142072] [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: 11/16/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Nitrogen pollution has been increasing with the development of industrialization. Consequently, the excessive deposition of reactive nitrogen in the environment has generated the loss of biodiversity and eutrophication of different ecosystems. In 2005, a Feammox process was discovered that anaerobically metabolizes ammonium. Feammox with the use of hollow fiber membrane bioreactors (HFMB), based on the formation of biofilms of bacterial communities, has emerged as a possible efficient and sustainable method for ammonium removal in environments with high iron concentrations. This work sought to study the possibility of implementing, at laboratory scale, an efficient method by evaluating the use of HFMB. Samples from an internal circulation reactor (IC) incubated in culture media for Feammox bacteria. The cultures were enriched in a batch reactor to evaluate growth conditions. Next, HFMB assembly was performed, and Feammox parameters were monitored. Also, conventional PCR and scanning electron microscopy (SEM) analysis were performed to characterize the bacterial communities associated with biofilm formation. The use of sodium acetate presented the best performance for Feammox activity. The HFMB operation showed an ammonium (NH4+) removal of 50%. SEM analysis of the fibers illustrated the formation of biofilm networks formed by bacteria, which were identified as Albidiferax ferrireducens, Geobacter spp, Ferrovum myxofaciens, Shewanella spp., and Anammox. Functional genes Archaea/Bacteria ammonia monooxygenase, nrxA, hzsB, nirS and nosZ were also identified. The implementation of HFMB Feammox could be used as a sustainable tool for the removal of ammonium from wastewater produced because of anthropogenic activities.
Collapse
Affiliation(s)
- Ámbar Cerda
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Carolina Rodríguez
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Macarena González
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Heylin González
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| | - Jennyfer Serrano
- Escuela de Biotecnología, Universidad Mayor, Camino La Pirámide 5750, Huechuraba, Santiago 8580745, Chile.
| | - Eduardo Leiva
- Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile; Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Macul, 7820436, Santiago, Chile.
| |
Collapse
|
9
|
Baker IR, Girguis PR. Sulfur cycling likely obscures dynamic biologically-driven iron redox cycling in contemporary methane seep environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13263. [PMID: 38705733 PMCID: PMC11070330 DOI: 10.1111/1758-2229.13263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 04/06/2024] [Indexed: 05/07/2024]
Abstract
Deep-sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe2+) can be produced by organoclastic iron reduction, methanotrophic-coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate-reducing bacteria at these sites. The prevalence of Fe2+in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron-oxidising microbes. However, it is unclear to what extent Fe2+ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron-oxidising bacteria, operating under the reasoning that if iron-oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe2+ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially-driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate-depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate-containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep-derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria-domainated ecosystem to one dominated by Rhodobacteraceae (Alphaproteobacteria). Our data suggest that, in most cases, sulfur cycling may restrict the biological "ferrous wheel" in contemporary environments through a combination of the sulfur-adapted sediment-dwelling ecosystems and the abiotic reactions they influence.
Collapse
Affiliation(s)
- Isabel R. Baker
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
- Department of Earth and Planetary ScienceJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Peter R. Girguis
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| |
Collapse
|
10
|
Alsharif SM, Ismaeil M, Saeed AM, El-Sayed WS. Metagenomic 16S rRNA analysis and predictive functional profiling revealed intrinsic organohalides respiration and bioremediation potential in mangrove sediment. BMC Microbiol 2024; 24:176. [PMID: 38778276 PMCID: PMC11110206 DOI: 10.1186/s12866-024-03291-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Mangrove sediment microbes are increasingly attracting scientific attention due to their demonstrated capacity for diverse bioremediation activities, encompassing a wide range of environmental contaminants. MATERIALS AND METHODS The microbial communities of five Avicennia marina mangrove sediment samples collected from Al Rayyis White Head, Red Sea (KSA), were characterized using Illumina amplicon sequencing of the 16S rRNA genes. RESULTS Our study investigated the microbial composition and potential for organohalide bioremediation in five mangrove sediments from the Red Sea. While Proteobacteria dominated four microbiomes, Bacteroidetes dominated the fifth. Given the environmental concerns surrounding organohalides, their bioremediation is crucial. Encouragingly, we identified phylogenetically diverse organohalide-respiring bacteria (OHRB) across all samples, including Dehalogenimonas, Dehalococcoides, Anaeromyxobacter, Desulfuromonas, Geobacter, Desulfomonile, Desulfovibrio, Shewanella and Desulfitobacterium. These bacteria are known for their ability to dechlorinate organohalides through reductive dehalogenation. PICRUSt analysis further supported this potential, predicting the presence of functional biomarkers for organohalide respiration (OHR), including reductive dehalogenases targeting tetrachloroethene (PCE) and 3-chloro-4-hydroxyphenylacetate in most sediments. Enrichment cultures studies confirmed this prediction, demonstrating PCE dechlorination by the resident microbial community. PICRUSt also revealed a dominance of anaerobic metabolic processes, suggesting the microbiome's adaptation to the oxygen-limited environment of the sediments. CONCLUSION This study provided insights into the bacterial community composition of five mangrove sediments from the Red Sea. Notably, diverse OHRB were detected across all samples, which possess the metabolic potential for organohalide bioremediation through reductive dehalogenation pathways. Furthermore, PICRUSt analysis predicted the presence of functional biomarkers for OHR in most sediments, suggesting potential intrinsic OHR activity by the enclosed microbial community.
Collapse
Affiliation(s)
- Sultan M Alsharif
- Department of Biology, College of Science, Taibah University, Al-Madinah, Kingdom of Saudi Arabia
| | - Mohamed Ismaeil
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt.
| | - Ali M Saeed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Wael S El-Sayed
- Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| |
Collapse
|
11
|
Xie P, Xu Y, Tang J, Wu S, Gao H. Multifaceted regulation of siderophore synthesis by multiple regulatory systems in Shewanella oneidensis. Commun Biol 2024; 7:498. [PMID: 38664541 PMCID: PMC11045786 DOI: 10.1038/s42003-024-06193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Siderophore-dependent iron uptake is a mechanism by which microorganisms scavenge and utilize iron for their survival, growth, and many specialized activities, such as pathogenicity. The siderophore biosynthetic system PubABC in Shewanella can synthesize a series of distinct siderophores, yet how it is regulated in response to iron availability remains largely unexplored. Here, by whole genome screening we identify TCS components histidine kinase (HK) BarA and response regulator (RR) SsoR as positive regulators of siderophore biosynthesis. While BarA partners with UvrY to mediate expression of pubABC post-transcriptionally via the Csr regulatory cascade, SsoR is an atypical orphan RR of the OmpR/PhoB subfamily that activates transcription in a phosphorylation-independent manner. By combining structural analysis and molecular dynamics simulations, we observe conformational changes in OmpR/PhoB-like RRs that illustrate the impact of phosphorylation on dynamic properties, and that SsoR is locked in the 'phosphorylated' state found in phosphorylation-dependent counterparts of the same subfamily. Furthermore, we show that iron homeostasis global regulator Fur, in addition to mediating transcription of its own regulon, acts as the sensor of iron starvation to increase SsoR production when needed. Overall, this study delineates an intricate, multi-tiered transcriptional and post-transcriptional regulatory network that governs siderophore biosynthesis.
Collapse
Affiliation(s)
- Peilu Xie
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yuanyou Xu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiaxin Tang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Shihua Wu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
12
|
Phan J, Macwan S, Gralnick JA, Yee N. Extracellular organic disulfide reduction by Shewanella oneidensis MR-1. Microbiol Spectr 2024; 12:e0408123. [PMID: 38415659 PMCID: PMC10986466 DOI: 10.1128/spectrum.04081-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
Microbial reduction of organic disulfides affects the macromolecular structure and chemical reactivity of natural organic matter. Currently, the enzymatic pathways that mediate disulfide bond reduction in soil and sedimentary organic matter are poorly understood. In this study, we examined the extracellular reduction of 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) by Shewanella oneidensis strain MR-1. A transposon mutagenesis screen performed with S. oneidensis resulted in the isolation of a mutant that lost ~90% of its DTNB reduction activity. Genome sequencing of the mutant strain revealed that the transposon was inserted into the dsbD gene, which encodes for an oxidoreductase involved in cytochrome c maturation. Complementation of the mutant strain with the wild-type dsbD partially restored DTNB reduction activity. Because DsbD catalyzes a critical step in the assembly of multi-heme c-type cytochromes, we further investigated the role of extracellular electron transfer cytochromes in organic disulfide reduction. The results indicated that mutants lacking proteins in the Mtr system were severely impaired in their ability to reduce DTNB. These findings provide new insights into extracellular organic disulfide reduction and the enzymatic pathways of organic sulfur redox cycling.IMPORTANCEOrganic sulfur compounds in soils and sediments are held together by disulfide bonds. This study investigates how Shewanella oneidensis breaks apart extracellular organic sulfur compounds. The results show that an enzyme involved in the assembly of c-type cytochromes as well as proteins in the Mtr respiratory pathway is needed for S. oneidensis to transfer electrons from the cell surface to extracellular organic disulfides. These findings have important implications for understanding how organic sulfur decomposes in terrestrial ecosystems.
Collapse
Affiliation(s)
- Jonathan Phan
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Shine Macwan
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, Twin Cities, Minnesota, USA
| | - Nathan Yee
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey, USA
| |
Collapse
|
13
|
Hao X, Zhao Q, Zhou X, Huang Q, Liu YR. Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133122. [PMID: 38056276 DOI: 10.1016/j.jhazmat.2023.133122] [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: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2-8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.
Collapse
Affiliation(s)
- Xiuli Hao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinquan Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
14
|
Gao Y, Zhou Y, Ji X, Graham AJ, Dundas CM, Miniel Mahfoud IE, Tibbett BM, Tan B, Partipilo G, Dodabalapur A, Rivnay J, Keitz BK. A hybrid transistor with transcriptionally controlled computation and plasticity. Nat Commun 2024; 15:1598. [PMID: 38383505 PMCID: PMC10881478 DOI: 10.1038/s41467-024-45759-1] [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: 09/20/2023] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Organic electrochemical transistors (OECTs) are ideal devices for translating biological signals into electrical readouts and have applications in bioelectronics, biosensing, and neuromorphic computing. Despite their potential, developing programmable and modular methods for living systems to interface with OECTs has proven challenging. Here we describe hybrid OECTs containing the model electroactive bacterium Shewanella oneidensis that enable the transduction of biological computations to electrical responses. Specifically, we fabricated planar p-type OECTs and demonstrated that channel de-doping is driven by extracellular electron transfer (EET) from S. oneidensis. Leveraging this mechanistic understanding and our ability to control EET flux via transcriptional regulation, we used plasmid-based Boolean logic gates to translate biological computation into current changes within the OECT. Finally, we demonstrated EET-driven changes to OECT synaptic plasticity. This work enables fundamental EET studies and OECT-based biosensing and biocomputing systems with genetically controllable and modular design elements.
Collapse
Affiliation(s)
- Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuchen Zhou
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
| | - Xudong Ji
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Austin J Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christopher M Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Ismar E Miniel Mahfoud
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Bailey M Tibbett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Benjamin Tan
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ananth Dodabalapur
- Department of Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, University of Texas at Austin, Austin, TX, 78758, USA
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
15
|
Tan X, Zhang M, Liu S, Xiao X, Zhang Y, Jian H. Prophage enhances the ability of deep-sea bacterium Shewanella psychrophila WP2 to utilize D-amino acid. Microbiol Spectr 2024; 12:e0326323. [PMID: 38170979 PMCID: PMC10845958 DOI: 10.1128/spectrum.03263-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Prophages are prevalent in the marine bacterial genomes and reshape the physiology and metabolism of their hosts. However, whether and how prophages influence the microbial degradation of D-amino acids (D-AAs), which is one of the widely distributed recalcitrant dissolved organic matters (RDOMs) in the ocean, remain to be explored. In this study, we addressed this issue in a representative marine bacterium, Shewanella psychrophila WP2 (WP2), and its integrated prophage SP1. Notably, compared to the WP2 wild-type strain, the SP1 deletion mutant of WP2 (WP2ΔSP1) exhibited a significantly lower D-glutamate (D-Glu) consumption rate and longer lag phase when D-Glu was used as the sole nitrogen source. The subsequent transcriptome analysis identified 1,523 differentially expressed genes involved in diverse cellular processes, especially that multiple genes related to inorganic nitrogen metabolism were highly upregulated. In addition, the dynamic profiles of ammonium, nitrate, and nitrite were distinct between the culture media of WP2 and WP2ΔSP1. Finally, we provide evidence that SP1 conferred a competitive advantage to WP2 when D-Glu was used as the sole nitrogen source and SP1-like phages may be widely distributed in the global ocean. Taken together, these findings offer novel insight into the influences of prophages on host metabolism and RDOM cycling in marine environments.IMPORTANCEThis work represents the first exploration of the impact of prophages on the D-amino acid (D-AA) metabolism of deep-sea bacteria. By using S. psychrophila WP2 and its integrated prophage SP1 as a representative system, we found that SP1 can significantly increase the catabolism rate of WP2 to D-glutamate and produce higher concentrations of ammonium, resulting in faster growth and competitive advantages. Our findings not only deepen our understanding of the interaction between deep-sea prophages and hosts but also provide new insights into the ecological role of prophages in refractory dissolved organic matter and the nitrogen cycle in deep oceans.
Collapse
Affiliation(s)
- Xiaoli Tan
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| |
Collapse
|
16
|
Cai Y, Chen X, Qi H, Bu F, Shaaban M, Peng QA. Genome analysis of Shewanella putrefaciens 4H revealing the potential mechanisms for the chromium remediation. BMC Genomics 2024; 25:136. [PMID: 38308218 PMCID: PMC10837877 DOI: 10.1186/s12864-024-10031-9] [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: 08/04/2023] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Microbial remediation of heavy metal polluted environment is ecofriendly and cost effective. Therefore, in the present study, Shewanella putrefaciens stain 4H was previously isolated by our group from the activated sludge of secondary sedimentation tank in a dyeing wastewater treatment plant. The bacterium was able to reduce chromate effectively. The strains showed significant ability to reduce Cr(VI) in the pH range of 8.0 to 10.0 (optimum pH 9.0) and 25-42 ℃ (optimum 30 ℃) and were able to reduce 300 mg/L of Cr(VI) in 72 h under parthenogenetic anaerobic conditions. In this paper, the complete genome sequence was obtained by Nanopore sequencing technology and analyzed chromium metabolism-related genes by comparative genomics The genomic sequence of S. putrefaciens 4H has a length of 4,631,110 bp with a G + C content of 44.66% and contains 4015 protein-coding genes and 3223, 2414, 2343 genes were correspondingly annotated into the COG, KEGG, and GO databases. The qRT-PCR analysis showed that the expression of chrA, mtrC, and undA genes was up-regulated under Cr(VI) stress. This study explores the Chromium Metabolism-Related Genes of S. putrefaciens 4H and will help to deepen our understanding of the mechanisms of Cr(VI) tolerance and reduction in this strain, thus contributing to the better application of S. putrefaciens 4H in the field of remediation of chromium-contaminated environments.
Collapse
Affiliation(s)
- Yajun Cai
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China
- Clean Production of Textile Printing and Dyeing Engineering Research Center of Ministry of Education, Wuhan, 430200, China
| | - Xu Chen
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Hanghang Qi
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Fantong Bu
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China
| | - Muhammad Shaaban
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Qi-An Peng
- College of Environmental Engineering, Wuhan Textile University, Wuhan, 430200, China.
- Clean Production of Textile Printing and Dyeing Engineering Research Center of Ministry of Education, Wuhan, 430200, China.
| |
Collapse
|
17
|
Ford KC, TerAvest MA. The electron transport chain of Shewanella oneidensis MR-1 can operate bidirectionally to enable microbial electrosynthesis. Appl Environ Microbiol 2024; 90:e0138723. [PMID: 38117056 PMCID: PMC10807441 DOI: 10.1128/aem.01387-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Extracellular electron transfer is a process by which bacterial cells can exchange electrons with a redox-active material located outside of the cell. In Shewanella oneidensis, this process is natively used to facilitate respiration using extracellular electron acceptors such as Fe(III) or an anode. Previously, it was demonstrated that this process can be used to drive the microbial electrosynthesis (MES) of 2,3-butanediol (2,3-BDO) in S. oneidensis exogenously expressing butanediol dehydrogenase (BDH). Electrons taken into the cell from a cathode are used to generate NADH, which in turn is used to reduce acetoin to 2,3-BDO via BDH. However, generating NADH via electron uptake from a cathode is energetically unfavorable, so NADH dehydrogenases couple the reaction to proton motive force. We therefore need to maintain the proton gradient across the membrane to sustain NADH production. This work explores accomplishing this task by bidirectional electron transfer, where electrons provided by the cathode go to both NADH formation and oxygen (O2) reduction by oxidases. We show that oxidases use trace dissolved oxygen in a microaerobic bioelectrical chemical system (BES), and the translocation of protons across the membrane during O2 reduction supports 2,3-BDO generation. Interestingly, this process is inhibited by high levels of dissolved oxygen in this system. In an aerated BES, O2 molecules react with the strong reductant (cathode) to form reactive oxygen species, resulting in cell death.IMPORTANCEMicrobial electrosynthesis (MES) is increasingly employed for the generation of specialty chemicals, such as biofuels, bioplastics, and cancer therapeutics. For these systems to be viable for industrial scale-up, it is important to understand the energetic requirements of the bacteria to mitigate unnecessary costs. This work demonstrates sustained production of an industrially relevant chemical driven by a cathode. Additionally, it optimizes a previously published system by removing any requirement for phototrophic energy, thereby removing the additional cost of providing a light source. We also demonstrate the severe impact of oxygen intrusion into bioelectrochemical systems, offering insight to future researchers aiming to work in an anaerobic environment. These studies provide insight into both the thermodynamics of electrosynthesis and the importance of the bioelectrochemical systems' design.
Collapse
Affiliation(s)
- Kathryne C. Ford
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Michaela A. TerAvest
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
18
|
Jiang Y, Dong Y, Sui M, Yu J, Wu J, Fu D. Towards a new understanding of bioelectrochemical systems from the perspective of microecosystems: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168410. [PMID: 37939951 DOI: 10.1016/j.scitotenv.2023.168410] [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: 09/06/2023] [Revised: 11/04/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
Bioelectrochemical system (BES) holds promise for sustainable energy generation and wastewater treatment. The microbial communities, as the core of BES, play a crucial role in its performance, thus needing to be systematically studied. However, researches considering microbial communities in BES from an ecological perspective are limited. This review provided a comprehensive summary of the BES with special emphasis on microecological principles, commencing with the dynamic formation and succession of the microbial communities. It also clarified the intricate interspecies relationships and quorum-sensing mechanisms regulated by dominant species. Furthermore, this review addressed the crucial themes in BES-related researches on ecological processes, including growth patterns, ecological structures, and defense strategies against external disturbances. By offering this novel perspective, it would contribute to enhancing the understanding of BES-centered technologies and facilitating future research in this field.
Collapse
Affiliation(s)
- Yiying Jiang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Yue Dong
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Mingrui Sui
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China.
| | - Jimeng Yu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Jiaxin Wu
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China
| | - Daxuan Fu
- College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing 210098, China
| |
Collapse
|
19
|
Fei Y, Tang N, Chen Y, Xu M, Tao Q, Liu Y, Xiong X. Rapid screening of electrochemically active bacteria based on a biocathode-functional bipolar electrode-electrochemiluminescence platform. Food Chem 2023; 429:136919. [PMID: 37494754 DOI: 10.1016/j.foodchem.2023.136919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/10/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023]
Abstract
A functional bipolar electrode-electrochemiluminescence (BPE-ECL) platform based on biocathode reducing oxygen was constructed for detecting electrochemically active bacteria (EAB) in this paper. Firstly, thiolated trimethylated chitosan quaternary ammonium salt (TMC-SH) layer was assembled on the gold-plated cathode of BPE. TMC-SH contains quaternary ammonium salt branch chain, which can inhibit the growth of microorganisms on the surface or in the surrounding environment while absorbing bacteria. Then, the peristaltic pump was used to flow all of the samples through the cathode, and the EAB was electrostatically adsorbed on the electrode surface. Finally, applying a constant potential to the BPE, bacteria can catalyze electrochemical reduction of O2, and decrease the overpotential of O2 reduction at the cathode, which in turn generates an ECL reporting intensity change at the anode. In this way, live and dead bacteria can be distinguished, and the influence of complex food substrates on detection can be greatly reduced.
Collapse
Affiliation(s)
- Yunjie Fei
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China
| | - Ning Tang
- School of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Yin Chen
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China
| | - Mingyao Xu
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China
| | - Qin Tao
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China
| | - Yuanjian Liu
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China.
| | - Xiaohui Xiong
- Coll Food Sci & Light Ind, Nanjing Tech University, Nanjing 211800, China
| |
Collapse
|
20
|
Zhang Y, Pan M, Wang Q, Wang L, Liao L. Complete Genome Sequence and Pan-Genome Analysis of Shewanella oncorhynchi Z-P2, a Siderophore Putrebactin-Producing Bacterium. Microorganisms 2023; 11:2961. [PMID: 38138105 PMCID: PMC10745600 DOI: 10.3390/microorganisms11122961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, we reported the complete genome sequence of Shewanella oncorhynchi for the first time. S. oncorhynchi Z-P2 is a bacterium that produces the siderophore putrebactin. Its genome consists of a circular chromosome of 5,034,612 bp with a G + C content of 45.4%. A total of 4544 protein-coding genes, 109 tRNAs and 31 rRNAs were annotated by the RAST. Five non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene clusters were identified by the antiSMASH analysis. The pan-genome analysis of Z-P2 and 10 Shewanella putrefaciens revealed 9228 pan-gene clusters and 2681 core gene clusters, with Z-P2 having 618 unique gene clusters. Additionally, the gene cluster involved in putrebactin biosynthesis in Z-P2 was annotated, and the mechanism of putrebactin biosynthesis was analyzed. The putrebactin produced by Z-P2 was detected using UPLC-MS analysis, with an [M + H]+ molecular ion at m/z 373.21. These findings provide valuable support for further research on the genetic engineering of putrebactin biosynthetic genes of Z-P2 and their potential applications.
Collapse
Affiliation(s)
- Ying Zhang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Mengjie Pan
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Qiaoyun Wang
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China; (M.P.); (Q.W.)
| | - Lan Wang
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
| | - Li Liao
- Key Laboratory of Cold Chain Logistics Technology for Agro-Product, Ministry of Agriculture and Rural Affairs/Institute of Agro-Product Processing and Nuclear Agricultural Technology, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (Y.Z.); (L.W.)
| |
Collapse
|
21
|
Hu D, Zeng Q, Zhu J, He C, Shi Q, Dong H. Promotion of Humic Acid Transformation by Abiotic and Biotic Fe Redox Cycling in Nontronite. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:19760-19771. [PMID: 37972299 DOI: 10.1021/acs.est.3c05646] [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: 11/19/2023]
Abstract
The redox activity of Fe-bearing minerals is coupled with the transformation of organic matter (OM) in redox dynamic environments, but the underlying mechanism remains unclear. In this work, a Fe redox cycling experiment of nontronite (NAu-2), an Fe-rich smectite, was performed via combined abiotic and biotic methods, and the accompanying transformation of humic acid (HA) as a representative OM was investigated. Chemical reduction and subsequent abiotic reoxidation of NAu-2 produced abundant hydroxyl radicals (thereafter termed as ·OH) that effectively transformed the chemical and molecular composition of HA. More importantly, transformed HA served as a more premium electron donor/carbon source to couple with subsequent biological reduction of Fe(III) in reoxidized NAu-2 by Geobacter sulfurreducens, a model Fe-reducing bacterium. Destruction of aromatic structures and formation of carboxylates were mechanisms responsible for transforming HA into an energetically more bioavailable substrate. Relative to unaltered HA, transformed HA increased the extent of the bioreduction by 105%, and Fe(III) reduction was coupled with oxidation and even mineralization of transformed HA, resulting in bleached HA and formation of microbial products and cell debris. ·OH transformation slightly decreased the electron shuttling capacity of HA in bioreduction. Our results provide a mechanistic explanation for rapid OM mineralization driven by Fe redox cycling in redox-fluctuating environments.
Collapse
Affiliation(s)
- Dafu Hu
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
| | - Qiang Zeng
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
- Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China
| | - Jin Zhu
- Zhejiang Institute of Metrology, Hangzhou, Zhejiang 310018, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Hailiang Dong
- Center for Geomicrobiology and Biogeochemistry Research, State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China
- Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China
| |
Collapse
|
22
|
Liang ZH, Sun H, Li Y, Hu A, Tang Q, Yu HQ. Enforcing energy consumption promotes microbial extracellular respiration for xenobiotic bioconversion. Environ Microbiol 2023; 25:2943-2957. [PMID: 37602917 DOI: 10.1111/1462-2920.16484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
Extracellular electron transfer (EET) empowers electrogens to catalyse the bioconversion of a wide range of xenobiotics in the environment. Synthetic bioengineering has proven effective in promoting EET output. However, conventional strategies mainly focus on modifications of EET-related genes or pathways, which leads to a bottleneck due to the intricate nature of electrogenic metabolic properties and intricate pathway regulation that remain unelucidated. Herein, we propose a novel EET pathway-independent approach, from an energy manipulation perspective, to enhance microbial EET output. The Controlled Hydrolyzation of ATP to Enhance Extracellular Respiration (CHEER) strategy promotes energy utilization and persistently reduces the intracellular ATP level in Shewanella oneidensis, a representative electrogenic microbe. This approach leads to the accelerated consumption of carbon substrate, increased biomass accumulation and an expanded intracellular NADH pool. Both microbial electrolysis cell and microbial fuel cell tests exhibit that the CHEER strain substantially enhances EET capability. Analysis of transcriptome profiles reveals that the CHEER strain considerably bolsters biomass synthesis and metabolic activity. When applied to the bioconversion of model xenobiotics including methyl orange, Cr(VI) and U(VI), the CHEER strain consistently exhibits enhanced removal efficiencies. This work provides a new perspective and a feasible strategy to enhance microbial EET for efficient xenobiotic conversion.
Collapse
Affiliation(s)
- Zi-Han Liang
- Department of Environmental Science and Technology, University of Science and Technology of China, Hefei, China
| | - Hong Sun
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yang Li
- CAS Key Laboratory of Urban Pollutant Conversion, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Qiang Tang
- Department of Environmental Science and Technology, University of Science and Technology of China, Hefei, China
| | - Han-Qing Yu
- Department of Environmental Science and Technology, University of Science and Technology of China, Hefei, China
| |
Collapse
|
23
|
Boucher DG, Carroll E, Nguyen ZA, Jadhav RG, Simoska O, Beaver K, Minteer SD. Bioelectrocatalytic Synthesis: Concepts and Applications. Angew Chem Int Ed Engl 2023; 62:e202307780. [PMID: 37428529 DOI: 10.1002/anie.202307780] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/11/2023]
Abstract
Bioelectrocatalytic synthesis is the conversion of electrical energy into value-added products using biocatalysts. These methods merge the specificity and selectivity of biocatalysis and energy-related electrocatalysis to address challenges in the sustainable synthesis of pharmaceuticals, commodity chemicals, fuels, feedstocks and fertilizers. However, the specialized experimental setups and domain knowledge for bioelectrocatalysis pose a significant barrier to adoption. This review introduces key concepts of bioelectrosynthetic systems. We provide a tutorial on the methods of biocatalyst utilization, the setup of bioelectrosynthetic cells, and the analytical methods for assessing bioelectrocatalysts. Key applications of bioelectrosynthesis in ammonia production and small-molecule synthesis are outlined for both enzymatic and microbial systems. This review serves as a necessary introduction and resource for the non-specialist interested in bioelectrosynthetic research.
Collapse
Affiliation(s)
- Dylan G Boucher
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Emily Carroll
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Zachary A Nguyen
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Rohit G Jadhav
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Olja Simoska
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Kevin Beaver
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Shelley D Minteer
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
24
|
Li Y, Luo Q, Su J, Dong G, Cao M, Wang Y. Metabolic regulation of Shewanella oneidensis for microbial electrosynthesis: From extracellular to intracellular. Metab Eng 2023; 80:1-11. [PMID: 37673324 DOI: 10.1016/j.ymben.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023]
Abstract
Shewanella oneidensis MR-1 (S. oneidensis MR-1) has been shown to benefit from microbial electrosynthesis (MES) due to its exceptional electron transfer efficiency. In this study, genes involved in both extracellular electron uptake (EEU) and intracellular CO2 conversion processes were examined and regulated to enhance MES performance. The key genes identified for MES in the EEU process were mtrB, mtrC, mtrD, mtrE, omcA and cctA. Overexpression of these genes resulted in 1.5-2.1 times higher formate productivity than that of the wild-type strains (0.63 mmol/(L·μg protein)), as 0.94-1.61 mmol/(L·μg protein). In the intracellular CO2 conversion process, overexpression of the nadE, nadD, nadR, nadV, pncC and petC genes increased formate productivity 1.3-fold-3.4-fold. Moreover, overexpression of the formate dehydrogenase genes fdhA1, fdhB1 and fdhX1 in modified strains led to a 2.3-fold-3.1-fold increase in formate productivity compared to wild-type strains. The co-overexpression of cctA, fdhA1 and nadV in the mutant strain resulted in 5.59 times (3.50 mmol/(L·μg protein)) higher formate productivity than that of the wild-type strains. These findings revealed that electrons of MES derived from the electrode were utilized in the energy module for synthesizing ATP and NADH, followed by the synthesis of formate in formate dehydrogenase by the combinatorial effects of ATP, NADH, electrons and CO2. The results provide new insights into the mechanism of MES in S. oneidensis MR-1 and pave the way for genetic improvements that could facilitate the further application of MES.
Collapse
Affiliation(s)
- Yixin Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China
| | - Qingliu Luo
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Jiaying Su
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China; School of Resource and Chemical Engineering, Sanming University, Sanming, 365004, China
| | - Guowen Dong
- School of Resource and Chemical Engineering, Sanming University, Sanming, 365004, China
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China.
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, 361005, China.
| |
Collapse
|
25
|
Sun W, Xu Y, Liang Y, Yu Q, Gao H. A novel bacterial sulfite dehydrogenase that requires three c-type cytochromes for electron transfer. Appl Environ Microbiol 2023; 89:e0110823. [PMID: 37732808 PMCID: PMC10617556 DOI: 10.1128/aem.01108-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
c-type Cytochromes (c-Cyts), primarily as electron carriers and oxidoreductases, play a key role in energy transduction processes in virtually all living organisms. Many bacteria, such as Shewanella oneidensis, are particularly rich in c-Cyts, supporting respiratory versatility not seen in eukaryotes. Unfortunately, a large number of c-Cyts are underexplored, and their biological functions remain unknown. In this study, we identify SorCABD of S. oneidensis as a novel sulfite dehydrogenase (SDH), which catalyzes the oxidation of sulfite to sulfate. In addition to catalytic subunit SorA, this enzymatic complex includes three c-Cyt subunits, which all together carry out electron transfer. The electrons extracted from sulfite oxidation are ultimately delivered to oxygen, leading to oxygen reduction, a process relying on terminal oxidase cyt cbb3. Genomic analysis suggests that the homologs of this SDH are present in a small number of bacterial genera, Shewanella and Vibrio in particular. Because these bacteria are generally capable of reducing sulfite under anaerobic conditions, the co-existence of a sulfite oxidation system implies that they may play especially important roles in the transformation of sulfur species in natural environments.Importancec-type Cytochromes (c-Cyts) endow bacteria with high flexibility in their oxidative/respiratory systems, allowing them to extracellularly transform diverse inorganic and organic compounds for survival and growth. However, a large portion of the bacterial c-Cyts remain functionally unknown. Here, we identify three c-Cyts that work together as essential electron transfer partners for the catalytic subunit of a novel SDH in sulfite oxidation in Shewanella oneidensis. This characteristic makes S. oneidensis the first organism known to be capable of oxidizing and reducing sulfite. The findings suggest that Shewanella, along with a small number of other aquatic bacteria, would serve as a particular driving force in the biogeochemical sulfur cycle in nature.
Collapse
Affiliation(s)
- Weining Sun
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanyou Xu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yawen Liang
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingzi Yu
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| |
Collapse
|
26
|
Chen S, Ding Y. A bibliography study of Shewanella oneidensis biofilm. FEMS Microbiol Ecol 2023; 99:fiad124. [PMID: 37796898 PMCID: PMC10630087 DOI: 10.1093/femsec/fiad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/28/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
This study employs a bibliography study method to evaluate 472 papers focused on Shewanella oneidensis biofilms. Biofilms, which are formed when microorganisms adhere to surfaces or interfaces, play a crucial role in various natural, engineered, and medical settings. Within biofilms, microorganisms are enclosed in extracellular polymeric substances (EPS), creating a stable working environment. This characteristic enhances the practicality of biofilm-based systems in natural bioreactors, as they are less susceptible to temperature and pH fluctuations compared to enzyme-based bioprocesses. Shewanella oneidensis, a nonpathogenic bacterium with the ability to transfer electrons, serves as an example of a species isolated from its environment that exhibits extensive biofilm applications. These applications, such as heavy metal removal, offer potential benefits for environmental engineering and human health. This paper presents a comprehensive examination and review of the biology and engineering aspects of Shewanella biofilms, providing valuable insights into their functionality.
Collapse
Affiliation(s)
- Shan Chen
- Department of Applied Social Sciences, The Hong Kong Polytechnic University, 11 Yuk Choi Rd, Hung Hom, Hong Kong, China
| | - Yuanzhao Ding
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford OX1 3QY, United Kingdom
| |
Collapse
|
27
|
Yao S, Zhang X, Lin A, Xia X, Lin L, Yang G, Zhuang L. Characterization of two novel Fe(III)-reducing and electrogenic bacteria, Shewanella ferrihydritica sp. nov. and Shewanella electrica sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37823787 DOI: 10.1099/ijsem.0.006044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
Three novel strains in the genus Shewanella, designated A3AT, C31T and C32, were isolated from mangrove sediment samples. They were facultative anaerobic, Gram-stain-negative, rod-shaped, flagellum-harbouring, oxidase- and catalase-positive, electrogenic and capable of using Fe(III) as an electron acceptor during anaerobic growth. Results of phylogenetic analysis based on 16S rRNA gene and genomic sequences revealed that the strains should be assigned to the genus Shewanella. The 16S rRNA gene similarity, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their closely related species were below the respective cut-off values for species differentiation. The 16S rRNA gene similarity, ANI and dDDH values between strains C31T and C32 were 99.7, 99.9 and 99.9 %, respectively, indicating that they should belong to the same genospecies. Based on polyphasic taxonomic approach, two novel species are proposed, Shewanella ferrihydritica sp. nov. with type strain A3AT (GDMCC 1.2732T=JCM 34899T) and Shewanella electrica sp. nov. with type strain C31T (GDMCC 1.2736T=JCM 34902T).
Collapse
Affiliation(s)
- Sijie Yao
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xueying Zhang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Annian Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Xue Xia
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Lijun Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou, 510632, PR China
| |
Collapse
|
28
|
Zhang X, Joyce GH, Leu AO, Zhao J, Rabiee H, Virdis B, Tyson GW, Yuan Z, McIlroy SJ, Hu S. Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens'. Nat Commun 2023; 14:6118. [PMID: 37777538 PMCID: PMC10542353 DOI: 10.1038/s41467-023-41847-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023] Open
Abstract
Anaerobic methanotrophic archaea (ANME) carry out anaerobic oxidation of methane, thus playing a crucial role in the methane cycle. Previous genomic evidence indicates that multi-heme c-type cytochromes (MHCs) may facilitate the extracellular electron transfer (EET) from ANME to different electron sinks. Here, we provide experimental evidence supporting cytochrome-mediated EET for the reduction of metals and electrodes by 'Candidatus Methanoperedens nitroreducens', an ANME acclimated to nitrate reduction. Ferrous iron-targeted fluorescent assays, metatranscriptomics, and single-cell imaging suggest that 'Ca. M. nitroreducens' uses surface-localized redox-active cytochromes for metal reduction. Electrochemical and Raman spectroscopic analyses also support the involvement of c-type cytochrome-mediated EET for electrode reduction. Furthermore, several genes encoding menaquinone cytochrome type-c oxidoreductases and extracellular MHCs are differentially expressed when different electron acceptors are used.
Collapse
Affiliation(s)
- Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Georgina H Joyce
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Jing Zhao
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- Ecological Engineering of Mine Wastes, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Hesamoddin Rabiee
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Chemical Engineering, The University of Queensland, Brisbane, QLD, Australia
- Centre for Future Materials, University of Southern Queensland, Springfield, QLD, Australia
| | - Bernardino Virdis
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia.
| |
Collapse
|
29
|
Yi Y, Liu S, Hao Y, Sun Q, Lei X, Wang Y, Wang J, Zhang M, Tang S, Tang Q, Zhang Y, Liu X, Wang Y, Xiao X, Jian H. A systematic analysis of marine lysogens and proviruses. Nat Commun 2023; 14:6013. [PMID: 37758717 PMCID: PMC10533544 DOI: 10.1038/s41467-023-41699-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are ubiquitous in the oceans, exhibiting high abundance and diversity. Here, we systematically analyze existing genomic sequences of marine prokaryotes to compile a Marine Prokaryotic Genome Dataset (MPGD, consisting of over 12,000 bacterial and archaeal genomes) and a Marine Temperate Viral Genome Dataset (MTVGD). At least 40% of the MPGD genomes contain one or more proviral sequences, indicating that they are lysogens. The MTVGD includes over 12,900 viral contigs or putative proviruses, clustered into 10,897 viral genera. We show that lysogens and proviruses are abundant in marine ecosystems, particularly in the deep sea, and marine lysogens differ from non-lysogens in multiple genomic features and growth properties. We reveal several virus-host interaction networks of potential ecological relevance, and identify proviruses that appear to be able to infect (or to be transferred between) different bacterial classes and phyla. Auxiliary metabolic genes in the MTVGD are enriched in functions related to carbohydrate metabolism. Finally, we experimentally demonstrate the impact of a prophage on the transcriptome of a representative marine Shewanella bacterium. Our work contributes to a better understanding of the ecology of marine prokaryotes and their viruses.
Collapse
Affiliation(s)
- Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinjuan Lei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yecheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiahua Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Qingxue Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xipeng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
| |
Collapse
|
30
|
Cruz-Balladares V, Avalos V, Vera-Villalobos H, Cameron H, Gonzalez L, Leyton Y, Riquelme C. Identification of a Shewanella halifaxensis Strain with Algicidal Effects on Red Tide Dinoflagellate Prorocentrum triestinum in Culture. Mar Drugs 2023; 21:501. [PMID: 37755114 PMCID: PMC10532897 DOI: 10.3390/md21090501] [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: 06/22/2023] [Revised: 09/16/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023] Open
Abstract
The dinoflagellate Prorocentrum triestinum forms high biomass blooms that discolor the water (red tides), which may pose a serious threat to marine fauna and aquaculture exploitations. In this study, the algicidal effect of a bacterial strain (0YLH) belonging to the genus Shewanella was identified and evaluated against P. triestinum. The algicidal effects on the dinoflagellate were observed when P. triestinum was exposed to cell-free supernatant (CFS) from stationary-phase cultures of the 0YLH strain. After 24 h exposure, a remarkable reduction in the photosynthetic efficiency of P. triestinum was achieved (55.9%), suggesting the presence of extracellular bioactive compounds produced by the bacteria with algicidal activity. Furthermore, the CFS exhibited stability and maintained its activity across a wide range of temperatures (20-120 °C) and pH values (3-11). These findings highlight the algicidal potential of the bacterium Shewanella halifaxensis 0YLH as a promising tool for the environmentally friendly biological control of P. triestinum blooms.
Collapse
Affiliation(s)
- Victoria Cruz-Balladares
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Vladimir Avalos
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Hernán Vera-Villalobos
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Henry Cameron
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Leonel Gonzalez
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Yanett Leyton
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
| | - Carlos Riquelme
- Centro de Bioinnovación de Antofagasta, Universidad de Antofagasta, Antofagasta 1240000, Chile (H.V.-V.); (H.C.); (C.R.)
- Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta 1240000, Chile
| |
Collapse
|
31
|
Gao Y, Zhou Y, Ji X, Graham AJ, Dundas CM, Mahfoud IEM, Tibbett BM, Tan B, Partipilo G, Dodabalapur A, Rivnay J, Keitz BK. A Hybrid Transistor with Transcriptionally Controlled Computation and Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553547. [PMID: 37645977 PMCID: PMC10462107 DOI: 10.1101/2023.08.16.553547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Organic electrochemical transistors (OECTs) are ideal devices for translating biological signals into electrical readouts and have applications in bioelectronics, biosensing, and neuromorphic computing. Despite their potential, developing programmable and modular methods for living systems to interface with OECTs has proven challenging. Here we describe hybrid OECTs containing the model electroactive bacterium Shewanella oneidensis that enable the transduction of biological computations to electrical responses. Specifically, we fabricated planar p-type OECTs and demonstrated that channel de-doping is driven by extracellular electron transfer (EET) from S. oneidensis. Leveraging this mechanistic understanding and our ability to control EET flux via transcriptional regulation, we used plasmid-based Boolean logic gates to translate biological computation into current changes within the OECT. Finally, we demonstrated EET-driven changes to OECT synaptic plasticity. This work enables fundamental EET studies and OECT-based biosensing and biocomputing systems with genetically controllable and modular design elements.
Collapse
Affiliation(s)
- Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Yuchen Zhou
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Xudong Ji
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Austin J. Graham
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christopher M. Dundas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismar E. Miniel Mahfoud
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Bailey M. Tibbett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Benjamin Tan
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ananth Dodabalapur
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Jonathan Rivnay
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| |
Collapse
|
32
|
Zhang M, Hao Y, Yi Y, Liu S, Sun Q, Tan X, Tang S, Xiao X, Jian H. Unexplored diversity and ecological functions of transposable phages. THE ISME JOURNAL 2023; 17:1015-1028. [PMID: 37069234 PMCID: PMC10284936 DOI: 10.1038/s41396-023-01414-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/19/2023]
Abstract
Phages are prevalent in diverse environments and play major ecological roles attributed to their tremendous diversity and abundance. Among these viruses, transposable phages (TBPs) are exceptional in terms of their unique lifestyle, especially their replicative transposition. Although several TBPs have been isolated and the life cycle of the representative phage Mu has been extensively studied, the diversity distribution and ecological functions of TBPs on the global scale remain unknown. Here, by mining TBPs from enormous microbial genomes and viromes, we established a TBP genome dataset (TBPGD), that expands the number of accessible TBP genomes 384-fold. TBPs are prevalent in diverse biomes and show great genetic diversity. Based on taxonomic evaluations, we propose the categorization of TBPs into four viral groups, including 11 candidate subfamilies. TBPs infect multiple bacterial phyla, and seem to infect a wider range of hosts than non-TBPs. Diverse auxiliary metabolic genes (AMGs) are identified in the TBP genomes, and genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis are highly enriched. Finally, the influences of TBPs on their hosts are experimentally examined by using the marine bacterium Shewanella psychrophila WP2 and its infecting transposable phage SP2. Collectively, our findings greatly expand the genetic diversity of TBPs, and comprehensively reveal their potential influences in various ecosystems.
Collapse
Affiliation(s)
- Mujie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yali Hao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Yi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingyang Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoli Tan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shan Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Development Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya, China.
| |
Collapse
|
33
|
Maltman C, Kuzyk SB, Kyndt JA, Lengyel G, Yurkov V. Shewanella metallivivens sp. nov., a deep-sea hydrothermal vent tube worm endobiont capable of dissimilatory anaerobic metalloid oxyanion reduction. Int J Syst Evol Microbiol 2023; 73. [PMID: 37477965 DOI: 10.1099/ijsem.0.005980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
A polyphasic taxonomic study was carried out on a Gram-stain-negative and rod-shaped strain, ER-Te-42B-LightT, isolated from the tissue of a tube worm, Riftia pachyptila, collected near a deep-sea hydrothermal vent of the Juan de Fuca Ridge in the Pacific Ocean. This bacterium was capable of performing anaerobic respiration using tellurite, tellurate, selenite and orthovanadate as terminal electron acceptors. While facultatively anaerobic, it could aerobically resist tellurite, selenite and orthovanadate up to 2000, 7000 and 10000 µg ml-1, respectively, reducing each oxide to elemental forms. Nearly complete 16S rRNA gene sequence similarity related the strain to Shewanella, with 98.8 and 98.7 % similarity to Shewanella basaltis and Shewanella algicola, respectively. The dominant fatty acids were C16 : 0 and C16 : 1. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and MK-7 was the predominant quinone. DNA G+C content was 42.5 mol%. Computation of average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ER-Te-42B-LightT revealed genetic divergence at the species level, which was further substantiated by differences in several physiological characteristics. Based on the obtained results, this bacterium was assigned to the genus Shewanella as a new species with the name Shewanella metallivivens sp. nov., type strain ER-Te-42B-LightT (=VKM B-3580T=DSM 113370T).
Collapse
Affiliation(s)
- Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Steven B Kuzyk
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE, USA
| | - George Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Vladimir Yurkov
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
34
|
Grenfell AW, Intile PJ, McFarlane JA, Leung DC, Abdalla K, Wold MC, Kees ED, Gralnick JA. The Outer Membrane Cytochrome OmcA Is Essential for Infection of Shewanella oneidensis by a Zebrafish-Associated Bacteriophage. J Bacteriol 2023; 205:e0046922. [PMID: 37227287 PMCID: PMC10294696 DOI: 10.1128/jb.00469-22] [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: 12/07/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
The microbiota-the mixture of microorganisms in the intestinal tract of animals-plays an important role in host biology. Bacteriophages are a prominent, though often overlooked, component of the microbiota. The mechanisms that phage use to infect susceptible cells associated with animal hosts, and the broader role they could play in determining the substituents of the microbiota, are poorly understood. In this study, we isolated a zebrafish-associated bacteriophage, which we named Shewanella phage FishSpeaker. This phage infects Shewanella oneidensis strain MR-1, which cannot colonize zebrafish, but it is unable to infect Shewanella xiamenensis strain FH-1, a strain isolated from the zebrafish gut. Our data suggest that FishSpeaker uses the outer membrane decaheme cytochrome OmcA, which is an accessory component of the extracellular electron transfer (EET) pathway in S. oneidensis, as well as the flagellum to recognize and infect susceptible cells. In a zebrafish colony that lacks detectable FishSpeaker, we found that most Shewanella spp. are sensitive to infection and that some strains are resistant to infection. Our results suggest that phage could act as a selectivity filter for zebrafish-associated Shewanella and show that the EET machinery can be targeted by phage in the environment. IMPORTANCE Phage exert selective pressure on bacteria that influences and shapes the composition of microbial populations. However, there is a lack of native, experimentally tractable systems for studying how phage influence microbial population dynamics in complex communities. Here, we show that a zebrafish-associated phage requires both the outer membrane-associated extracellular electron transfer protein OmcA and the flagellum to infect Shewanella oneidensis strain MR-1. Our results suggest that the newly discovered phage-FishSpeaker-could exert selective pressure that restricts which Shewanella spp. colonize zebrafish. Moreover, the requirement of OmcA for infection by FishSpeaker suggests that the phage preferentially infects cells that are oxygen limited, a condition required for OmcA expression and an ecological feature of the zebrafish gut.
Collapse
Affiliation(s)
- Andrew W. Grenfell
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Peter J. Intile
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - John A. McFarlane
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Dani C. Leung
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Khalid Abdalla
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Michael C. Wold
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Eric D. Kees
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A. Gralnick
- BioTechnology Institute, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota, USA
| |
Collapse
|
35
|
Liu J, Guo X, He L, Jiang LP, Zhou Y, Zhu JJ. Enhanced photocatalytic CO 2 reduction on biomineralized CdS via an electron conduit in bacteria. NANOSCALE 2023. [PMID: 37325817 DOI: 10.1039/d3nr00908d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
There is an increasing trend in semi-artificial photosynthesis systems that combine living cells with inorganic semiconductors to activate a bacterial catalytic network. However, these systems face various challenges, including electron-hole recombination, photocorrosion, and the generation of photoexcited radicals by semiconductors, all of which impair the efficiency, stability, and sustainability of biohybrids. We first focus on a reverse strategy to improve highly efficient CO2 photoreduction on biosynthesized inorganic semiconductors using an electron conduit in the electroactive bacterium S. oneidensis MR-1. Due to the suppressed charge recombination and photocorrosion on CdS, the maximum photocatalytic production rate of formate in water was 2650 μmol g-1 h-1 (with a selectivity of ca.100%), which ranks high among all photocatalysts and is the highest for inorganic-biological hybrid systems in an all-inorganic aqueous environment. The reverse enhancement effect of electrogenic bacteria on photocatalysis on semiconductors inspires new insight to develop a new generation of bio-semiconductor catalysts for solar chemical production.
Collapse
Affiliation(s)
- Juan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| | - Xiaoxiao Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| | - Liuyang He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| | - Li-Ping Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| | - Yang Zhou
- State Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials IAM, Nanjing University of Posts & Telecommunications, Nanjing, 210023, PR China.
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China.
| |
Collapse
|
36
|
Wu B, Guan X, Deng T, Yang X, Li J, Zhou M, Wang C, Wang S, Yan Q, Shu L, He Q, He Z. Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution. Microbiol Spectr 2023; 11:e0452822. [PMID: 37154752 PMCID: PMC10269844 DOI: 10.1128/spectrum.04528-22] [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: 11/07/2022] [Accepted: 04/04/2023] [Indexed: 05/10/2023] Open
Abstract
Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.
Collapse
Affiliation(s)
- Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee, USA
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
| |
Collapse
|
37
|
Gan CD, Tang QX, Wang H, Yang JY, Nikitin A. Shewanella oneidensis MR-1 and oxalic acid mediated vanadium reduction and redistribution in vanadium-containing tailings. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131077. [PMID: 36871469 DOI: 10.1016/j.jhazmat.2023.131077] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The microbially- and chemically-mediated redox process is critical in controlling the fate of vanadium (V) in tailing environment. Although the microbial reduction of V has been widely studied, the coupled biotic reduction mediated by beneficiation reagents and the underlying mechanism remain unclear. Herein, the reduction and redistribution of V in V-containing tailings and Fe/Mn oxide aggregates mediated by Shewanella oneidensis MR-1 and oxalic acid were explored. The dissolution of Fe-(hydr)oxides by oxalic acid promoted the microbe-mediated V release from solid-phase. After 48-day of reaction, the dissolved V concentrations in the bio-oxalic acid treatment reached maximum values of 1.72 ± 0.36 mg L-1 and 0.42 ± 0.15 mg L-1 in the tailing system and the aggregate system, respectively, significantly higher than those in control (0.63 ± 0.14 mg L-1 and 0.08 ± 0.02 mg L-1). As the electron donor, oxalic acid enhanced the electron transfer process of S. oneidensis MR-1 for V(V) reduction. The mineralogical characterization of final products indicates that S. oneidensis MR-1 and oxalic acid promoted solid-state conversion from V2O5 to NaV6O15. Collectively, this study demonstrates that microbe-mediated V release and redistribution in solid-phase were promoted by oxalic acid, suggesting that the role of organic agents for the V biogeochemical cycle in natural systems deserves greater attention.
Collapse
Affiliation(s)
- Chun-Dan Gan
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Yibin Institute of Industrial Technology, Sichuan University Yibin Park, Yibin 644000, China
| | - Qi-Xuan Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Hao Wang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jin-Yan Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China; Yibin Institute of Industrial Technology, Sichuan University Yibin Park, Yibin 644000, China; Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, School of Forestry, Northeast Forestry University, Harbin 150040, China.
| | - Aleksander Nikitin
- Institute of Radiobiology of the National Academy of Sciences of Belarus, Fedjuninskogo str., 4, 246007 Gomel, Belarus
| |
Collapse
|
38
|
Zhang Y, Plymale A, Son J, Huang Q, Chen W, Yu XY. Reducing the matrix effect in mass spectral imaging of biofilms using flow-cell culture. Front Chem 2023; 11:1203314. [PMID: 37304684 PMCID: PMC10248399 DOI: 10.3389/fchem.2023.1203314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
The interactions between soil microorganisms and soil minerals play a crucial role in the formation and evolution of minerals and the stability of soil aggregates. Due to the heterogeneity and diversity of the soil environment, the under-standing of the functions of bacterial biofilms in soil minerals at the microscale is limited. A soil mineral-bacterial biofilm system was used as a model in this study, and it was analyzed by time-of-flight secondary ion mass spectrometry (ToF-SIMS) to acquire molecular level information. Static culture in multi-wells and dynamic flow-cell culture in microfluidics of biofilms were investigated. Our results show that more characteristic molecules of biofilms can be observed in SIMS spectra of the flow-cell culture. In contrast, biofilm signature peaks are buried under the mineral components in SIMS spectra in the static culture case. Spectral overlay was used in peak selection prior to performing Principal component analysis (PCA). Comparisons of the PCA results between the static and flow-cell culture show more pronounced molecular features and higher loadings of organic peaks of the dynamic cultured specimens. For example, fatty acids secreted from bacterial biofilm extracellular polymeric substance are likely to be responsible for biofilm dispersal due to mineral treatment up to 48 h. Such findings suggest that the use of microfluidic cells to dynamically culture biofilms be a more suitable method for reducing the matrix effect arisen from the growth medium and minerals as a perturbation fac-tor for improved spectral and multivariate analysis of complex mass spectral data in ToF-SIMS. These results show that the interaction mechanism between biofilms and soil minerals at the molecular level can be better studied using the flow-cell culture and advanced mass spectral imaging techniques like ToF-SIMS.
Collapse
Affiliation(s)
- Yuchen Zhang
- National Research Center for Edible Fungi Biotechnology and Engineering, Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Andrew Plymale
- Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, United States
| | - Jiyoung Son
- Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA, United States
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Ying Yu
- Oak Ridge National Laboratory, Materials Science and Technology Division, Oak Ridge, TN, United States
| |
Collapse
|
39
|
Xia Q, Liu R, Chen X, Chen Z, Zhu JJ. In Vivo Voltammetric Imaging of Metal Nanoparticle-Catalyzed Single-Cell Electron Transfer by Fermi Level-Responsive Graphene. RESEARCH (WASHINGTON, D.C.) 2023; 6:0145. [PMID: 37223464 PMCID: PMC10200910 DOI: 10.34133/research.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/20/2023] [Indexed: 05/25/2023]
Abstract
Metal nanomaterials can facilitate microbial extracellular electron transfer (EET) in the electrochemically active biofilm. However, the role of nanomaterials/bacteria interaction in this process is still unclear. Here, we reported the single-cell voltammetric imaging of Shewanella oneidensis MR-1 at the single-cell level to elucidate the metal-enhanced EET mechanism in vivo by the Fermi level-responsive graphene electrode. Quantified oxidation currents of ~20 fA were observed from single native cells and gold nanoparticle (AuNP)-coated cells in linear sweep voltammetry analysis. On the contrary, the oxidation potential was reduced by up to 100 mV after AuNP modification. It revealed the mechanism of AuNP-catalyzed direct EET decreasing the oxidation barrier between the outer membrane cytochromes and the electrode. Our method offered a promising strategy to understand the nanomaterials/bacteria interaction and guide the rational construction of EET-related microbial fuel cells.
Collapse
Affiliation(s)
- Qing Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Rui Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering,
Nanjing University, Nanjing 210023, P. R. China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, P. R. China
| |
Collapse
|
40
|
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.
Collapse
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.
| |
Collapse
|
41
|
Wei H, He P, Yu D, Liu S, Li C, Qiu D. Characterization of the Positive Transcription Regulator PfaR for Improving Eicosapentaenoic Acid Production in Shewanella putrefaciens W3-18-1. Appl Environ Microbiol 2023; 89:e0002123. [PMID: 36916911 PMCID: PMC10132093 DOI: 10.1128/aem.00021-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/17/2023] [Indexed: 03/15/2023] Open
Abstract
The biosynthetic pathway of eicosapentaenoic acid (EPA) has previously been reported in marine bacteria, while the regulatory mechanism remains poorly understood. In this study, a putative transcriptional regulator PfaR encoded adjacent to the PFA biosynthesis gene cluster (pfaEABCD) was computationally and experimentally characterized. Comparative analyses on the wild type (WT) strain, in-frame deletion, and overexpression mutants revealed that PfaR positively regulated EPA synthesis at low temperature. RNA-Seq and real-time quantitative PCR analyses demonstrated that PfaR stimulated the transcription of pfaABCD. The transcription start site of pfaR was mapped by using primer extension and highly conserved promoter motifs bound by the housekeeping Sigma 70 factor that were identified in the upstream of pfaR. Moreover, overexpression of PfaR in WT strain W3-18-1 at low temperature could improve EPA productivity from 0.07% to 0.13% (percentage of EPA to dry weight, mg/mg) of dry weight. Taken together, these findings could provide important implications into the transcriptional control and metabolic engineering in terms of EPA productivity for industrial strains. IMPORTANCE We have experimentally confirmed that PfaR is a positive transcription regulator that promotes EPA synthesis at low temperature in Shewanella putrefaciens W3-18-1. Overexpression of PfaR in WT strain W3-18-1 could lead to a 1.8-fold increase in EPA productivity at low temperature. It is further shown that PfaR may be regulated by housekeeping Sigma 70 factor at low temperature.
Collapse
Affiliation(s)
- Hehong Wei
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, China
| | - Penghui He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, China
| | - Dianzhen Yu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China
| | - Shuangyuan Liu
- Eco-Environmental Monitoring and Research Center, Pearl River Valley and South China Sea Ecology and Environment Administration, Ministry of Ecology and Environment, Guangzhou, China
| | - Chengtao Li
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Dongru Qiu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| |
Collapse
|
42
|
Li S, Wang J, Liu J, Zhang H, Bao T, Sun C, Fang J, Cao J. Genomic Analysis of the Deep-Sea Bacterium Shewanella sp. MTB7 Reveals Backgrounds Related to Its Deep-Sea Environment Adaptation. Microorganisms 2023; 11:microorganisms11030798. [PMID: 36985371 PMCID: PMC10059138 DOI: 10.3390/microorganisms11030798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/27/2023] [Accepted: 03/18/2023] [Indexed: 03/30/2023] Open
Abstract
Shewanella species are widely distributed in various environments, especially deep-sea sediments, due to their remarkable ability to utilize multiple electron receptors and versatile metabolic capabilities. In this study, a novel facultatively anaerobic, psychrophilic, and piezotolerant bacterium, Shewanella sp. MTB7, was isolated from the Mariana Trench at a depth of 5900 m. Here, we report its complete genome sequence and adaptation strategies for survival in deep-sea environments. MTB7 contains what is currently the third-largest genome among all isolated Shewanella strains and shows higher coding density than neighboring strains. Metabolically, MTB7 is predicted to utilize various carbon and nitrogen sources. D-amino acid utilization and HGT-derived purine-degrading genes could contribute to its oligotrophic adaptation. For respiration, the cytochrome o ubiquinol oxidase genes cyoABCDE, typically expressed at high oxygen concentrations, are missing. Conversely, a series of anaerobic respiratory genes are employed, including fumarate reductase, polysulfide reductase, trimethylamine-N-oxide reductase, crotonobetaine reductase, and Mtr subunits. The glycine reductase genes and the triplication of dimethyl sulfoxide reductase genes absent in neighboring strains could also help MTB7 survive in low-oxygen environments. Many genes encoding cold-shock proteins, glycine betaine transporters and biosynthetic enzymes, and reactive oxygen species-scavenging proteins could contribute to its low-temperature adaptation. The genomic analysis of MTB7 will deepen our understanding of microbial adaptation strategies in deep-sea environments.
Collapse
Affiliation(s)
- Sicong Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jie Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Hongcai Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Tianqiang Bao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Chengwen Sun
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
| |
Collapse
|
43
|
Yang J, Zhai X, Dong X, Zhao L, Zhang Y, Xiao H, Ju P, Duan J, Tang X, Hou B. Peroxidase-like phosphate hydrate nanosheets bio-synthesized by a marine Shewanella algae strain for highly sensitive dopamine detection. Colloids Surf B Biointerfaces 2023; 225:113248. [PMID: 36905834 DOI: 10.1016/j.colsurfb.2023.113248] [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: 12/21/2022] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
The sensitive and rapid detection of dopamine (DA) is of great significance for early diagnosis of related diseases. Current detection strategies of DA are time-consuming, expensive and inaccurate, while biosynthetic nanomaterials were considered highly stable and environment friendly, which were promising on colorimetric sensing. Thus, in this study, novel zinc phosphate hydrate nanosheets (SA@ZnPNS) biosynthesized by Shewanella algae were designed for the detection of DA. SA@ZnPNS showed high peroxidase-like activity which catalyzed the oxidation reaction of 3,3',5,5'-tetramethylbenzidine in the presence of H2O2. Results showed that the catalytic reaction of SA@ZnPNS followed Michaelis-Menton kinetics, and catalytic process conformed to ping-pong mechanism with chief active species of hydroxyl radicals. The colorimetric detection of DA in human serum samples was performed based on SA@ZnPNS peroxidase-like activity. The linear range of DA detection was 0.1-40 μM, and the detection limit was 0.083 μM. This study provided a simple and practical method for the detection of DA and expanded the application of biosynthesized nanoparticles to biosensing fields.
Collapse
Affiliation(s)
- Jing Yang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, PR China; CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China
| | - Xiaofan Zhai
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China; Sanya Institute of Ocean Eco-Environmental Engineering, Zhenzhou Road, Sanya 572000, PR China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, No. 98 Daling Road, Nanning 530007, PR China.
| | - Xucheng Dong
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China
| | - Liuhui Zhao
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China; School of Bioengineering, Qilu University of Technology, No. 3501 Daxue Road, Jinan 250353, PR China
| | - Yu Zhang
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, PR China.
| | - Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, No. 6 Xianxialing Road, Qingdao 266061, PR China
| | - Jizhou Duan
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China; Sanya Institute of Ocean Eco-Environmental Engineering, Zhenzhou Road, Sanya 572000, PR China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, No. 98 Daling Road, Nanning 530007, PR China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, PR China
| | - Baorong Hou
- CAS Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, No. 7 Nanhai Road, Qingdao 266071, PR China; Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, No. 1 Wenhai Road, Qingdao 266235, PR China; Sanya Institute of Ocean Eco-Environmental Engineering, Zhenzhou Road, Sanya 572000, PR China; Institute of Marine Corrosion Protection, Guangxi Academy of Sciences, No. 98 Daling Road, Nanning 530007, PR China
| |
Collapse
|
44
|
Recent Applications and Strategies to Enhance Performance of Electrochemical Reduction of CO2 Gas into Value-Added Chemicals Catalyzed by Whole-Cell Biocatalysts. Processes (Basel) 2023. [DOI: 10.3390/pr11030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Carbon dioxide (CO2) is one of the major greenhouse gases that has been shown to cause global warming. Decreasing CO2 emissions plays an important role to minimize the impact of climate change. The utilization of CO2 gas as a cheap and sustainable source to produce higher value-added chemicals such as formic acid, methanol, methane, and acetic acid has been attracting much attention. The electrochemical reduction of CO2 catalyzed by whole-cell biocatalysts is a promising process for the production of value-added chemicals because it does not require costly enzyme purification steps and the supply of exogenous cofactors such as NADH. This study covered the recent applications of the diversity of microorganisms (pure cultures such as Shewanella oneidensis MR1, Sporomusa species, and Clostridium species and mixed cultures) as whole-cell biocatalysts to produce a wide range of value-added chemicals including methane, carboxylates (e.g., formate, acetate, butyrate, caproate), alcohols (e.g., ethanol, butanol), and bioplastics (e.g., Polyhydroxy butyrate). Remarkably, this study provided insights into the molecular levels of the proteins/enzymes (e.g., formate hydrogenases for CO2 reduction into formate and electron-transporting proteins such as c-type cytochromes) of microorganisms which are involved in the electrochemical reduction of CO2 into value-added chemicals for the suitable application of the microorganism in the chemical reduction of CO2 and enhancing the catalytic efficiency of the microorganisms toward the reaction. Moreover, this study provided some strategies to enhance the performance of the reduction of CO2 to produce value-added chemicals catalyzed by whole-cell biocatalysts.
Collapse
|
45
|
Deng X, Okamoto A. Direct extracellular electron transfer to an indium tin doped oxide electrode via heme redox reactions in Desulfovibrio ferrophilus IS5. Electrochim Acta 2023. [DOI: 10.1016/j.electacta.2023.142293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
46
|
Zhao J, Li F, Kong S, Chen T, Song H, Wang Z. Elongated Riboflavin-Producing Shewanella oneidensis in a Hybrid Biofilm Boosts Extracellular Electron Transfer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206622. [PMID: 36710254 PMCID: PMC10037984 DOI: 10.1002/advs.202206622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Shewanella oneidensis is able to carry out extracellular electron transfer (EET), although its EET efficiency is largely limited by low flavin concentrations, poor biofilm forming-ability, and weak biofilm conductivity. After identifying an important role for riboflavin (RF) in EET via in vitro experiments, the synthesis of RF is directed to 837.74 ± 11.42 µm in S. oneidensis. Molecular dynamics simulation reveals RF as a cofactor that binds strongly to the outer membrane cytochrome MtrC, which is correspondingly further overexpressed to enhance EET. Then the cell division inhibitor sulA, which dramatically enhanced the thickness and biomass of biofilm increased by 155% and 77%, respectively, is overexpressed. To reduce reaction overpotential due to biofilm thickness, a spider-web-like hybrid biofilm comprising RF, multiwalled carbon nanotubes (MWCNTs), and graphene oxide (GO) with adsorption-optimized elongated S. oneidensis, achieve a 77.83-fold increase in power (3736 mW m-2 ) relative to MR-1 and dramatically reduce the charge-transfer resistance and boosted biofilm electroactivity. This work provides an elegant paradigm to boost EET based on a synthetic biology strategy and materials science strategy, opens up further opportunities for other electrogenic bacteria.
Collapse
Affiliation(s)
- Juntao Zhao
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Feng Li
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Shutian Kong
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Tao Chen
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Hao Song
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic BiologyTianjin UniversityTianjin300072P. R. China
- Key Laboratory of Systems Bioengineering (Ministry of Education)Tianjin UniversityTianjin300072P. R. China
- School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072P. R. China
| |
Collapse
|
47
|
Liu YN, Lv ZT, Lv WL, Liu DF, Liu XW. Label-Free Optical Imaging of the Electron Transfer in Single Live Microbial Cells. NANO LETTERS 2023; 23:558-566. [PMID: 36594792 DOI: 10.1021/acs.nanolett.2c04018] [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: 06/17/2023]
Abstract
Measurement of electron transfer at the single-particle or -cell level is crucial to the in situ study of basic chemical and biological processes. However, it remains challenging to directly probe the microbial extracellular electron transfer process due to the weakness of signals and the lack of techniques. Here, we present a label-free and noninvasive imaging method that is able to measure the electron transfer in microbial cells. We measured the extracellular electron transfer processes by imaging the redox reaction of c-type outer membrane cytochromes in microbial cells using a plasmonic imaging technique, and obtained the electrochemical activity parameters (formal potential and number of electrons transferred) of multiple individual microbial cells, allowing for unveiling ample heterogeneities in electron transfer at the single-cell level. We anticipate that this method will contribute to the study of electron transfer in various biological and chemical processes.
Collapse
Affiliation(s)
- Yi-Nan Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Zhen-Ting Lv
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Wen-Li Lv
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Dong-Feng Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
| | - Xian-Wei Liu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei230026, China
- Department of Applied Chemistry, University of Science and Technology of China, Hefei230026, China
| |
Collapse
|
48
|
Yu C, Zhu X, Mohamed A, Dai K, Cai P, Liu S, Huang Q, Xing B. Enhanced Cr(VI) bioreduction by biochar: Insight into the persistent free radicals mediated extracellular electron transfer. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:129927. [PMID: 36152545 DOI: 10.1016/j.jhazmat.2022.129927] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/14/2022] [Accepted: 09/04/2022] [Indexed: 05/22/2023]
Abstract
Biochar can act as a shuttle to accelerate the extracellular electron transfer (EET) by exoelectrogens. However, it is poorly understood how the persistent free radicals (PFRs) in biochar affected EET and the redox reaction. Herein, the effects of the biochar and chitosan modified biochar (CBC) on the Cr(VI) bioreduction by Shewanella oneidensis MR-1 (MR-1) was investigated. Kinetic study indicated that the Cr(VI) bioreduction rate constant by MR-1 was increased by 1.8-33.7 folds in the presence of biochar, and by 2.7-60.2 folds in the presence of CBC, respectively. Moreover, Cr(VI) bioreduction rates increased with the decreasing pH. Results suggested that the electrostatic attraction between Cr(VI) and redox-active particles could accelerate the EET by c-cytochrome due to the promotion of the Cr(VI) migration from aqueous phase to biochar or CBC. Electron paramagnetic resonance analysis suggested that the PFRs affected the electron transfer from the ·O2- generated by MR-1 to Cr(VI) and accelerate the Cr(VI) bioreduction. Remarkably, in the presence of PFRs, this electron shuttling process was dependent on the non-metal-reducing respiratory pathway. Our results offer new insights that free radicals may be widely involved in the EET and strongly impact on the redox reaction in the environment.
Collapse
Affiliation(s)
- Cheng Yu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xiaoxi Zhu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Abdelkader Mohamed
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China; Soil and Water Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Abou Zaabl 13759, Egypt
| | - Ke Dai
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China; State Environmental Protection Key Laboratory of Soil Health and Green Remediation, Wuhan 430070, PR China.
| | - Peng Cai
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shilin Liu
- College of Food Science and Technology, Huazhong Agricultural University, Key Laboratory of Environment Correlative Dietology, Ministry of Education, Wuhan 430070, PR China
| | - Qiaoyun Huang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA 01003, United States
| |
Collapse
|
49
|
In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent. THE ISME JOURNAL 2023; 17:12-20. [PMID: 36151459 PMCID: PMC9751133 DOI: 10.1038/s41396-022-01316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022]
Abstract
Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.
Collapse
|
50
|
Zhu X, Dou F, Long M, Wang X, Liu W, Li F, Liu T, Wu Y. Electron shuttle-dependent biofilm formation and biocurrent generation: Concentration effects and mechanistic insights. Front Microbiol 2023; 14:1070800. [PMID: 36937307 PMCID: PMC10016380 DOI: 10.3389/fmicb.2023.1070800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction Electron shuttles (ESs) play a key role in extracellular electron transfer (EET) in Shewanella oneidensis MR-1. However, the quantification relationship between ES concentration, biofilm formation, and biocurrent generation has not been clarified. Methods In this study, 9,10-anthraquinone-2-sulfonic acid (AQS)-mediated EET and biofilm formation were evaluated at different AQS concentrations in bioelectrochemical systems (BESs) with S. oneidensis MR-1. Results and discussion Both the biofilm biomass (9- to 17-fold) and biocurrent (21- to 80-fold) were substantially enhanced by exogenous AQS, suggesting the dual ability of AQS to promote both biofilm formation and electron shuttling. Nevertheless, biofilms barely grew without the addition of exogenous AQS, revealing that biofilm formation by S. oneidensis MR-1 is highly dependent on electron shuttling. The biofilm growth was delayed in a BES of 2,000 μM AQS, which is probably because the redundant AQS in the bulk solution acted as a soluble electron acceptor and delayed biofilm formation. In addition, the maximum biocurrent density in BESs with different concentrations of AQS was fitted to the Michaelis-Menten equation (R 2 = 0.97), demonstrating that microbial-catalyzed ES bio-reduction is the key limiting factor of the maximum biocurrent density in BESs. This study provided a fundamental understanding of ES-mediated EET, which could be beneficial for the enrichment of electroactive biofilms, the rapid start-up of microbial fuel cells (MFCs), and the design of BESs for wastewater treatment.
Collapse
Affiliation(s)
- Xiao Zhu
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Dou
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Mingliang Long
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
| | - Xinxin Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
| | - Wei Liu
- College of Materials and Energy, South China Agricultural University, Guangzhou, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Yundang Wu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Yundang Wu
| |
Collapse
|