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Mazzoli R, Pescarolo S, Gilli G, Gilardi G, Valetti F. Hydrogen production pathways in Clostridia and their improvement by metabolic engineering. Biotechnol Adv 2024; 73:108379. [PMID: 38754796 DOI: 10.1016/j.biotechadv.2024.108379] [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: 12/04/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024]
Abstract
Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.
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Affiliation(s)
- Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
| | - Simone Pescarolo
- Biology applied to the environment, Laboratories of microbiology and ecotoxicology, Ecobioqual, Environment Park. Via Livorno 60, 10144 Torino, Italy
| | - Giorgio Gilli
- Department of Sciences of Public Health and Pediatrics, School of Medicine, University of Torino, Via Santena 5 bis, 10126 Torino, Italy
| | - Gianfranco Gilardi
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Valetti
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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2
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González E, Vera F, Scott F, Guerrero C, Bolívar JM, Aroca G, Muñoz JÁ, Ladero M, Santos VE. Acidophilic heterotrophs: basic aspects and technological applications. Front Microbiol 2024; 15:1374800. [PMID: 38827148 PMCID: PMC11141062 DOI: 10.3389/fmicb.2024.1374800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/04/2024] [Indexed: 06/04/2024] Open
Abstract
Acidophiles comprise a group of microorganisms adapted to live in acidic environments. Despite acidophiles are usually associated with an autotrophic metabolism, more than 80 microorganisms capable of utilizing organic matter have been isolated from natural and man-made environments. The ability to reduce soluble and insoluble iron compounds has been described for many of these species and may be harnessed to develop new or improved mining processes when oxidative bioleaching is ineffective. Similarly, as these microorganisms grow in highly acidic media and the chances of contamination are reduced by the low pH, they may be employed to implement robust fermentation processes. By conducting an extensive literature review, this work presents an updated view of basic aspects and technological applications in biomining, bioremediation, fermentation processes aimed at biopolymers production, microbial electrochemical systems, and the potential use of extremozymes.
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Affiliation(s)
- Ernesto González
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Fernando Vera
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Felipe Scott
- Faculty of Engineering and Applied Sciences, Universidad de Los Andes, Santiago, Chile
| | - Cecilia Guerrero
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Juan M. Bolívar
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Germán Aroca
- School of Biochemical Engineering, Faculty of Engineering, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jesús Ángel Muñoz
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Ladero
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
| | - Victoria E. Santos
- Department of Chemical and Materials Engineering, Faculty of Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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Xiu W, Gai R, Chen S, Ren C, Lloyd JR, Bassil NM, Nixon SL, Polya DA, Hou S, Guo H. Ammonium-Enhanced Arsenic Mobilization from Aquifer Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38317381 DOI: 10.1021/acs.est.3c09640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Ammonium-related pathways are important for groundwater arsenic (As) enrichment, especially via microbial Fe(III) reduction coupled with anaerobic ammonium oxidation; however, the key pathways (and microorganisms) underpinning ammonium-induced Fe(III) reduction and their contributions to As mobilization in groundwater are still unknown. To address this gap, aquifer sediments hosting high As groundwater from the western Hetao Basin were incubated with 15N-labeled ammonium and external organic carbon sources (including glucose, lactate, and lactate/acetate). Decreases in ammonium concentrations were positively correlated with increases in the total produced Fe(II) (Fe(II)tot) and released As. The molar ratios of Fe(II)tot to oxidized ammonium ranged from 3.1 to 3.7 for all incubations, and the δ15N values of N2 from the headspace increased in 15N-labeled ammonium-treated series, suggesting N2 as the key end product of ammonium oxidation. The addition of ammonium increased the As release by 16.1% to 49.6%, which was more pronounced when copresented with organic electron donors. Genome-resolved metagenomic analyses (326 good-quality MAGs) suggested that ammonium-induced Fe(III) reduction in this system required syntrophic metabolic interactions between bacterial Fe(III) reduction and archaeal ammonium oxidation. The current results highlight the significance of syntrophic ammonium-stimulated Fe(III) reduction in driving As mobilization, which is underestimated in high As groundwater.
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Affiliation(s)
- Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, PR China
- MWR Key Laboratory of Groundwater Conservation and School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Ruixuan Gai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
- Institute of Earth sciences, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cui Ren
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
- MWR Key Laboratory of Groundwater Conservation and School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Jonathan R Lloyd
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Naji M Bassil
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Sophie L Nixon
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, U.K
| | - David A Polya
- Williamson Research Centre for Molecular Environmental Science, School of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Shengwei Hou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Department of Ocean Science & Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
- MWR Key Laboratory of Groundwater Conservation and School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
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Gregory SP, Mackie JRM, Barnett MJ. Radioactive waste microbiology: predicting microbial survival and activity in changing extreme environments. FEMS Microbiol Rev 2024; 48:fuae001. [PMID: 38216518 PMCID: PMC10853057 DOI: 10.1093/femsre/fuae001] [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: 07/31/2023] [Revised: 12/01/2023] [Accepted: 01/11/2024] [Indexed: 01/14/2024] Open
Abstract
The potential for microbial activity to occur within the engineered barrier system (EBS) of a geological disposal facility (GDF) for radioactive waste is acknowledged by waste management organizations as it could affect many aspects of the safety functions of a GDF. Microorganisms within an EBS will be exposed to changing temperature, pH, radiation, salinity, saturation, and availability of nutrient and energy sources, which can limit microbial survival and activity. Some of the limiting conditions are incorporated into GDF designs for safety reasons, including the high pH of cementitious repositories, the limited pore space of bentonite-based repositories, or the high salinity of GDFs in evaporitic geologies. Other environmental conditions such as elevated radiation, temperature, and desiccation, arise as a result of the presence of high heat generating waste (HHGW). Here, we present a comprehensive review of how environmental conditions in the EBS may limit microbial activity, covering HHGW and lower heat generating waste (LHGW) in a range of geological environments. We present data from the literature on the currently recognized limits to life for each of the environmental conditions described above, and nutrient availability to establish the potential for life in these environments. Using examples where each variable has been modelled for a particular GDF, we outline the times and locations when that variable can be expected to limit microbial activity. Finally, we show how this information for multiple variables can be used to improve our understanding of the potential for microbial activity to occur within the EBS of a GDF and, more broadly, to understand microbial life in changing environments exposed to multiple extreme conditions.
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Affiliation(s)
- Simon P Gregory
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Jessica R M Mackie
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
| | - Megan J Barnett
- British Geological Survey, Nicker Hill, Keyworth, Nottingham NG12 5GG, United Kingdom
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Bhattacharyya S, Bhattarai N, Pfannenstiel DM, Wilkins B, Singh A, Harshey RM. A heritable iron memory enables decision-making in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2309082120. [PMID: 37988472 PMCID: PMC10691332 DOI: 10.1073/pnas.2309082120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/12/2023] [Indexed: 11/23/2023] Open
Abstract
The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when Escherichia coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This "iron" memory preexists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, which tracks with its iron memory, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We demonstrate that cellular iron levels also track with biofilm formation and antibiotic tolerance, suggesting that iron memory may impact other physiologies.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Nabin Bhattarai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Dylan M. Pfannenstiel
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Brady Wilkins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE19716
| | - Rasika M. Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
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Yadav S, Sadhotra C, Patil SA. Retracted: The bidirectional extracellular electron transfer process aids iron cycling by Geoalkalibacter halelectricus in a highly saline-alkaline condition. Appl Environ Microbiol 2023:e0060923. [PMID: 37681980 DOI: 10.1128/aem.00609-23] [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: 04/12/2023] [Accepted: 07/16/2023] [Indexed: 09/09/2023] Open
Abstract
Bidirectional extracellular electron transfer (EET) is crucial to upholding microbial metabolism with insoluble electron acceptors or donors in anoxic environments. Investigating bidirectional EET-capable microorganisms is desired to understand the cell-cell and microbe-mineral interactions and their role in mineral cycling besides leveraging their energy generation and conversion, biosensing, and bio-battery applications. Here, we report on iron cycling by haloalkaliphilic Geoalkalibacter halelectricus via bidirectional EET under haloalkaline conditions. It efficiently reduces Fe3+ oxide (Fe2O3) to Fe0 at a 0.75 ± 0.08 mM/mgprotein/d rate linked to acetate oxidation via outward EET and oxidizes Fe0 to Fe3+ at a 0.24 ± 0.03 mM/mgprotein/d rate via inward EET to reduce fumarate. Bioelectrochemical cultivation confirmed its outward and inward EET capabilities. It produced 895 ± 23 µA/cm2 current by linking acetate oxidation to anode reduction via outward EET and reduced fumarate by drawing electrons from the cathode (‒2.5 ± 0.3 µA/cm2) via inward EET. The cyclic voltammograms of G. halelectricus biofilms revealed redox moieties with different formal potentials, suggesting the involvement of different membrane components in bidirectional EET. The cyclic voltammetry and GC-MS analysis of the cell-free spent medium revealed the lack of soluble redox mediators, suggesting direct electron transfer by G. halelecctricus in achieving bidirectional EET. By reporting on the first haloalkaliphilic bacterium capable of oxidizing and reducing insoluble Fe0 and Fe3+ oxide, respectively, this study advances the limited understanding of the metabolic capabilities of extremophiles to respire on insoluble electron acceptors or donors via bidirectional EET and invokes the possible role of G. halelectricus in iron cycling in barely studied haloalkaline environments. IMPORTANCE Bidirectional extracellular electron transfer (EET) appears to be a key microbial metabolic process in anoxic environments that are depleted in soluble electron donor and acceptor molecules. Though it is an ecologically important and applied microbial phenomenon, it has been reported with a few microorganisms, mostly from nonextreme environments. Moreover, direct electron transfer-based bidirectional EET is studied for very few microorganisms with electrodes in engineered systems and barely with the natural insoluble electron acceptor and donor molecules in anoxic conditions. This study advances the understanding of extremophilic microbial taxa capable of bidirectional EET and its role in barely investigated Fe cycling in highly saline-alkaline environments. It also offers research opportunities for understanding the membrane components involved in the bidirectional EET of G. halelectricus. The high rate of Fe3+ oxide reduction activity by G. halelectricus suggests its possible use as a biocatalyst in the anaerobic iron bioleaching process under neutral-alkaline pH conditions.
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Affiliation(s)
- Sukrampal Yadav
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali) , Knowledge City, Punjab, India
| | - Chetan Sadhotra
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali) , Knowledge City, Punjab, India
| | - Sunil A Patil
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali (IISER Mohali) , Knowledge City, Punjab, India
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Bhattacharyya S, Bhattarai N, Pfannenstiel DM, Wilkins B, Singh A, Harshey RM. Iron Memory in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541523. [PMID: 37609133 PMCID: PMC10441380 DOI: 10.1101/2023.05.19.541523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when E. coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Nabin Bhattarai
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Dylan M. Pfannenstiel
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Brady Wilkins
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Abhyudai Singh
- Electrical & Computer Engineering, University of Delaware, Newark, DE 19716
| | - Rasika M. Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
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