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Ke C, Deng Y, Zhang S, Ren M, Liu B, He J, Wu R, Dang Z, Guo C. Sulfate availability drives the reductive transformation of schwertmannite by co-cultured iron- and sulfate-reducing bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167690. [PMID: 37820819 DOI: 10.1016/j.scitotenv.2023.167690] [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: 08/08/2023] [Revised: 09/14/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
Schwertmannite (Sch) is a highly bioavailable iron-hydroxysulfate mineral commonly found in acid mine drainage contaminated environment rich in sulfate (SO42-). Microbial-mediated Sch transformation has been well-studied, however, the understanding of how SO42- availability affects the microbial-mediated Sch transformation and the secondary minerals influence microbes is relatively limited. This study examined the effect of SO42- availability on the iron-reducing bacteria (FeRB) and SO42--reducing bacteria (SRB) consortium-mediated Sch transformation and the resulting secondary minerals in turn on bacteria. Increased SO42- accelerated the onset of microbial SO42- reduction, which significantly accelerated Sch reduction transformation. The extent of intermediate products such as lepidocrocite (22.1 % ~ 76.3 %, all treatments) and goethite (15.3 %, 10 mM SO42-, 5 d) formed by Sch transformation depended on SO42- concentrations. Vivianite, siderite and iron‑sulfur minerals (e.g., FeS and FeS2) were the dominant secondary minerals, in which the relative content of vivianite and siderite decreased while iron‑sulfur minerals increased with increasing SO42- concentration. Correspondingly, the abundance of FeRB and SRB was negatively and positively correlated with SO42- concentration, respectively; 1 mM SO42- promoted the cymA and omcA expression of FeRB, but 10 mM SO42- lowerd the cymA and omcA expression compared to the 1 mM SO42-; the dsr expression of SRB related linearly to the SO42- concentration. These secondary minerals accumulated on the cell surface to form cell encrustations, which limited the growth and gene expression of FeRB and SRB, and even inhibited the activity of SRB in the 10 mM SO42- treatment group. The 10 mM SO42- treatment group with low-intensity ultrasound effectively restored the SRB activity for reducing SO42- by disintegrating the cell-mineral aggregation, further indicating that cell encrustations limited the microbial metabolism. The results highlight the critical role that SO42- availability can play in controlling microbial transformation of mineral, and the influence of secondary minerals on microbial metabolism.
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Affiliation(s)
- Changdong Ke
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510535, China
| | - Yanping Deng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Siyu Zhang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Meihui Ren
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Bingcheng Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Jingyi He
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Renren Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Guangzhou 510535, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, South China University of Technology, Guangzhou 510006, China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, China; The Key Laboratory of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China.
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2
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Hilpmann S, Rossberg A, Steudtner R, Drobot B, Hübner R, Bok F, Prieur D, Bauters S, Kvashnina KO, Stumpf T, Cherkouk A. Presence of uranium(V) during uranium(VI) reduction by Desulfosporosinus hippei DSM 8344 T. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162593. [PMID: 36889400 DOI: 10.1016/j.scitotenv.2023.162593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Microbial U(VI) reduction influences uranium mobility in contaminated subsurface environments and can affect the disposal of high-level radioactive waste by transforming the water-soluble U(VI) to less mobile U(IV). The reduction of U(VI) by the sulfate-reducing bacterium Desulfosporosinus hippei DSM 8344T, a close phylogenetic relative to naturally occurring microorganism present in clay rock and bentonite, was investigated. D. hippei DSM 8344T showed a relatively fast removal of uranium from the supernatants in artificial Opalinus Clay pore water, but no removal in 30 mM bicarbonate solution. Combined speciation calculations and luminescence spectroscopic investigations showed the dependence of U(VI) reduction on the initial U(VI) species. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy showed uranium-containing aggregates on the cell surface and some membrane vesicles. By combining different spectroscopic techniques, including UV/Vis spectroscopy, as well as uranium M4-edge X-ray absorption near-edge structure recorded in high-energy-resolution fluorescence-detection mode and extended X-ray absorption fine structure analysis, the partial reduction of U(VI) could be verified, whereby the formed U(IV) product has an unknown structure. Furthermore, the U M4 HERFD-XANES showed the presence of U(V) during the process. These findings offer new insights into U(VI) reduction by sulfate-reducing bacteria and contribute to a comprehensive safety concept for a repository for high-level radioactive waste.
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Affiliation(s)
- Stephan Hilpmann
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - André Rossberg
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany; Rossendorf Beamline (BM20-ROBL), European Synchrotron Radiation Facility, Grenoble, France
| | - Robin Steudtner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Björn Drobot
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - René Hübner
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Dresden, Germany
| | - Frank Bok
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Damien Prieur
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany; Rossendorf Beamline (BM20-ROBL), European Synchrotron Radiation Facility, Grenoble, France
| | - Stephen Bauters
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany; Rossendorf Beamline (BM20-ROBL), European Synchrotron Radiation Facility, Grenoble, France
| | - Kristina O Kvashnina
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany; Rossendorf Beamline (BM20-ROBL), European Synchrotron Radiation Facility, Grenoble, France
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstraße 400, 01328 Dresden, Germany.
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Zarei M, Fatemi F, Ghasemi R, Mir-Derikvand M, Hosseinpour H, Samani TR. The effect of not-anaerobicization and discolored bacteria on uranium reduction by Shewanella sp. RCRI7. Appl Radiat Isot 2023; 192:110551. [PMID: 36508960 DOI: 10.1016/j.apradiso.2022.110551] [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: 04/23/2022] [Revised: 10/04/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
Shewanella sp. RCRI7 is a native strain capable of reducing uranium in anaerobic conditions. In order to employ this bacterium for the bioremediation, the mutual effects of uranium and the bacteria are studied in two different approaches. The optimal settings for the bacterial proliferation capacity and uranium reduction without anaerobicization of the environment, as well as the related effects of bioremediation and bacterial color under uranium-reducing conditions, have been investigated in this study. Uranium reduction procedure was analyzed using XRD, spectrophotometry and ICP-AES. In addition, the uranium's effect on the population of the first-generation of the bacteria as well as the color and growth of the second-generation were investigated using neobar lam and CFU (Colony Forming Unit), respectively. Uranium toxicity reduced the population of non-anaerobicized bacteria more than the anaerobicized bacteria after one day of incubation, while the amount of uranium extracted by the bacteria was almost the same. In both situations, the bacteria were able to reduce uranium after two weeks of incubation. In addition to the cell counts, uranium toxicity disrupts the growth and development of healthy second-generation anaerobicized bacteria, as created creamy-colored colonies grow slower than red-colored colonies. Furthermore, due to malfunctioning cytochromes, unlike red bacteria, creamy-colored bacteria were unable to extract the optimum amount of uranium. This study reveals that reduced uranium can be produced in a deprived environment without anaerobicization. Creamy-colored Shewanella can remove soluble uranium, however the most effective bacteria have red cytochromes. These findings represent a big step forward in the industrialization of uranium bioremediation.
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Affiliation(s)
- Mahsa Zarei
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Faezeh Fatemi
- Nuclear Fuel Cycle Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
| | - Razieh Ghasemi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Mir-Derikvand
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
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Then A, Ewald J, Söllner N, Cooper RE, Küsel K, Ibrahim B, Schuster S. Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211553. [PMID: 35620008 PMCID: PMC9115035 DOI: 10.1098/rsos.211553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe3+)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe2+)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe2+-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe3+-reducing/Fe2+-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe3+ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe2+ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe3+ reduction rate than longer periods.
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Affiliation(s)
- Andre Then
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Natalie Söllner
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Rebecca E. Cooper
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bashar Ibrahim
- Centre for Applied Mathematics and Bioinformatics, and Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
- European Virus Bioinformatics Center, Leutragraben 1 07743 Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias-Schleiden-Institute, University of Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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5
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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6
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Zarei M, Mir-Derikvand M, Hosseinpour H, Samani TR, Ghasemi R, Fatemi F. U (VI) tolerance affects Shewanella sp. RCRI7 biological responses: growth, morphology and bioreduction ability. Arch Microbiol 2021; 204:81. [PMID: 34958431 DOI: 10.1007/s00203-021-02716-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 10/30/2021] [Accepted: 11/19/2021] [Indexed: 11/27/2022]
Abstract
Native Shewanella sp. RCRI7 is recently counted as an operative bacterium in the uranium bio-reduction. The aim of this study was to investigate the effects of uranium tolerance on the morphology and population of RCRI7, following its potential removal capacity in different time intervals. In this research, the bacterial growth and uranium removal kinetic were evaluated in aerobic TSB medium, uranium-reducing condition (URC), aerobic uranium-containing (AUC) and anaerobic uranium-free (AUF) solution, following evaluations of omcAB gene expressions. In addition, spectrophotometry analyses were performed in URC confirming the bio-reduction mechanism. It was found that the bacteria can grow efficiently in the presence of 0.5 mM uranium anaerobically, unlike AUC and AUF solutions. Since the bacterium's adsorption capacity is quickly saturated, it can be deduced that uranium reduction should be dominant as incubation times proceed up to 84 h in URC. In 92 h incubation, the adsorbed uranium containing unreduced and reduced (U (IV) monomeric), was released to the solution due to either increased pH or bacterial death. In AUC and AUF, improper conditions lead to the reduced bacterial size (coccus-shape formation) and increased bacterial aggregations; however, membrane vesicles produced by the bacteria avoid the uranium incrustation in AUC. In overall, this study implies that Shewanella sp. RCRI7 are well tolerated by uranium under anaerobic conditions and the amount of regenerated uranium increases over time in the reduced form.
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Affiliation(s)
- Mahsa Zarei
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Mohammad Mir-Derikvand
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | | | | | - Razieh Ghasemi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Faezeh Fatemi
- Nuclear Fuel Cycle Research School, Nuclear Science and Technology Research Institute, Tehran, Iran.
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7
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McMillan HM, Kuehn MJ. The extracellular vesicle generation paradox: a bacterial point of view. EMBO J 2021; 40:e108174. [PMID: 34636061 PMCID: PMC8561641 DOI: 10.15252/embj.2021108174] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
All bacteria produce secreted vesicles that carry out a variety of important biological functions. These extracellular vesicles can improve adaptation and survival by relieving bacterial stress and eliminating toxic compounds, as well as by facilitating membrane remodeling and ameliorating inhospitable environments. However, vesicle production comes with a price. It is energetically costly and, in the case of colonizing pathogens, it elicits host immune responses, which reduce bacterial viability. This raises an interesting paradox regarding why bacteria produce vesicles and begs the question as to whether the benefits of producing vesicles outweigh their costs. In this review, we discuss the various advantages and disadvantages associated with Gram-negative and Gram-positive bacterial vesicle production and offer perspective on the ultimate score. We also highlight questions needed to advance the field in determining the role for vesicles in bacterial survival, interkingdom communication, and virulence.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and MicrobiologyDuke UniversityDurhamNCUSA
| | - Meta J Kuehn
- Department of BiochemistryDuke UniversityDurhamNCUSA
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8
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McMillan HM, Rogers N, Wadle A, Hsu-Kim H, Wiesner MR, Kuehn MJ, Hendren CO. Microbial vesicle-mediated communication: convergence to understand interactions within and between domains of life. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:664-677. [PMID: 33899070 DOI: 10.1039/d1em00022e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
All cells produce extracellular vesicles (EVs). These biological packages contain complex mixtures of molecular cargo and have a variety of functions, including interkingdom communication. Recent discoveries highlight the roles microbial EVs may play in the environment with respect to interactions with plants as well as nutrient cycling. These studies have also identified molecules present within EVs and associated with EV surfaces that contribute to these functions. In parallel, studies of engineered nanomaterials have developed methods to track and model small particle behavior in complex systems and measure the relative importance of various surface features on transport and function. While studies of EV behavior in complex environmental conditions have not yet employed transdisciplinary approaches, it is increasingly clear that expertise from disparate fields will be critical to understand the role of EVs in these systems. Here, we outline how the convergence of biology, soil geochemistry, and colloid science can both develop and address questions surrounding the basic principles governing EV-mediated interkingdom interactions.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Rogers
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Austin Wadle
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Meta J Kuehn
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA and Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Christine Ogilvie Hendren
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA and Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC 28608, USA.
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Zlatkov N, Nadeem A, Uhlin BE, Wai SN. Eco-evolutionary feedbacks mediated by bacterial membrane vesicles. FEMS Microbiol Rev 2021; 45:fuaa047. [PMID: 32926132 PMCID: PMC7968517 DOI: 10.1093/femsre/fuaa047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial membrane vesicles (BMVs) are spherical extracellular organelles whose cargo is enclosed by a biological membrane. The cargo can be delivered to distant parts of a given habitat in a protected and concentrated manner. This review presents current knowledge about BMVs in the context of bacterial eco-evolutionary dynamics among different environments and hosts. BMVs may play an important role in establishing and stabilizing bacterial communities in such environments; for example, bacterial populations may benefit from BMVs to delay the negative effect of certain evolutionary trade-offs that can result in deleterious phenotypes. BMVs can also perform ecosystem engineering by serving as detergents, mediators in biochemical cycles, components of different biofilms, substrates for cross-feeding, defense systems against different dangers and enzyme-delivery mechanisms that can change substrate availability. BMVs further contribute to bacteria as mediators in different interactions, with either other bacterial species or their hosts. In short, BMVs extend and deliver phenotypic traits that can have ecological and evolutionary value to both their producers and the ecosystem as a whole.
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Affiliation(s)
- Nikola Zlatkov
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Aftab Nadeem
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, SE-90187 Umeå, Sweden
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10
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Mansor M, Xu J. Benefits at the nanoscale: a review of nanoparticle-enabled processes favouring microbial growth and functionality. Environ Microbiol 2020; 22:3633-3649. [PMID: 32705763 DOI: 10.1111/1462-2920.15174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/29/2022]
Abstract
Nanoparticles are ubiquitous and co-occur with microbial life in every environment on Earth. Interactions between microbes and nanoparticles impact the biogeochemical cycles via accelerating various reaction rates and enabling biological processes at the smallest scales. Distinct from microbe-mineral interactions at large, microbe-nanoparticle interactions may involve higher levels of active recognition and utilization of the reactive, changeable, and thereby 'moldable' nano-sized inorganic phases by microbes, which has been given minimal attention in previous reviews. Here we have compiled the various cases of microbe-nanoparticle interactions with clear and potential benefits to the microbial cells and communities. Specifically, we discussed (i) the high bioavailabilities of nanoparticles due to increased specific surface areas and size-dependent solubility, with a focus on environmentally-relevant iron(III) (oxyhydr)oxides and pyrite, (ii) microbial utilization of nanoparticles as 'nano-tools' for electron transfer, chemotaxis, and storage units, and (iii) speculated benefits of precipitating 'moldable' nanoparticles in extracellular biomineralization. We further discussed emergent questions concerning cellular level responses to nanoparticle-associated cues, and the factors that affect nanoparticles' bioavailabilities beyond size-dependent effects. We end the review by proposing a framework towards more quantitative approaches and by highlighting promising techniques to guide future research in this exciting field.
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Affiliation(s)
- Muammar Mansor
- Geomicrobiology, Center for Applied Geoscience, University of Tuebingen, Tuebingen, 72076, Germany
| | - Jie Xu
- Department of Geological Sciences, the University of Texas at El Paso, El Paso, Texas, 79968, USA
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11
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Chandramohan A, Duprat E, Remusat L, Zirah S, Lombard C, Kish A. Novel Mechanism for Surface Layer Shedding and Regenerating in Bacteria Exposed to Metal-Contaminated Conditions. Front Microbiol 2019; 9:3210. [PMID: 30697196 PMCID: PMC6341005 DOI: 10.3389/fmicb.2018.03210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
Surface layers (S-layers) are components of the cell walls throughout the Bacteria and the Archaea that provide protection for microorganisms against diverse environmental stresses, including metal stress. We have previously characterized the process by which S-layers serve as a nucleation site for metal mineralization in an archaeon for which the S-layer represents the only cell wall component. Here, we test the hypothesis originally proposed in cyanobacteria that a “shedding” mechanism exists for replacing S-layers that have become mineral-encrusted, using Lysinibacillus sp. TchIII 20n38, metallotolerant gram-positive bacterium, as a model organism. We characterize for the first time a mechanism for resistance to metals through S-layer shedding and regeneration. S-layers nucleate the formation of Fe-mineral on the cell surface, depending on physiological state of the cells and metal exposure times, leading to the encrustation of the S-layer and changes in the cell morphology as observed by scanning electron microscopy. Using Nanoscale Secondary Ion Mass Spectrometry, we show that mineral-encrusted S-layers are shed by the bacterial cells after a period of latency (2 days under the conditions tested) in a heterogeneous fashion likely reflecting natural variations in metal stress resistance. The emerging cells regenerate new S-layers as part of their cell wall structure. Given the wide diversity of S-layer bearing prokaryotes, S-layer shedding may represent an important mechanism for microbial survival in metal-contaminated environments.
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Affiliation(s)
- Archjana Chandramohan
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, IRD UMR 206, Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS UMR 7590, IRD UMR 206, Paris, France
| | - Severine Zirah
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Carine Lombard
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
| | - Adrienne Kish
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS UMR 7245, Paris, France
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Modulation of calcium carbonate precipitation by exopolysaccharide in Bacillus sp. JH7. Appl Microbiol Biotechnol 2017. [DOI: 10.1007/s00253-017-8372-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Preservation of Archaeal Surface Layer Structure During Mineralization. Sci Rep 2016; 6:26152. [PMID: 27221593 PMCID: PMC4879539 DOI: 10.1038/srep26152] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/21/2016] [Indexed: 12/18/2022] Open
Abstract
Proteinaceous surface layers (S-layers) are highly ordered, crystalline structures commonly found in prokaryotic cell envelopes that augment their structural stability and modify interactions with metals in the environment. While mineral formation associated with S-layers has previously been noted, the mechanisms were unconstrained. Using Sulfolobus acidocaldarius a hyperthermophilic archaeon native to metal-enriched environments and possessing a cell envelope composed only of a S-layer and a lipid cell membrane, we describe a passive process of iron phosphate nucleation and growth within the S-layer of cells and cell-free S-layer "ghosts" during incubation in a Fe-rich medium, independently of metabolic activity. This process followed five steps: (1) initial formation of mineral patches associated with S-layer; (2) patch expansion; (3) patch connection; (4) formation of a continuous mineral encrusted layer at the cell surface; (5) early stages of S-layer fossilization via growth of the extracellular mineralized layer and the mineralization of cytosolic face of the cell membrane. At more advanced stages of encrustation, encrusted outer membrane vesicles are formed, likely in an attempt to remove damaged S-layer proteins. The S-layer structure remains strikingly well preserved even upon the final step of encrustation, offering potential biosignatures to be looked for in the fossil record.
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14
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Toyofuku M, Tashiro Y, Hasegawa Y, Kurosawa M, Nomura N. Bacterial membrane vesicles, an overlooked environmental colloid: Biology, environmental perspectives and applications. Adv Colloid Interface Sci 2015; 226:65-77. [PMID: 26422802 DOI: 10.1016/j.cis.2015.08.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022]
Abstract
Phospholipid vesicles play important roles in biological systems. Bacteria are one of the most abundant organisms on Earth, and bacterial membrane vesicles (MVs) were first observed 50 years ago. Many bacteria release MVs to the environment that mainly consist of the cell membrane and typically range from 20 to 400 nm in size. Bacterial MVs are involved in several biological functions, such as delivery of cargo, virulence and gene transfer. MVs can be isolated from laboratory culture and directly from the environment, indicating their high abundance in and impact on ecosystems. Many colloidal particles in the environment ranging in size from 1 nm to 1 μm have been reported but not characterized at the molecular level, and MVs remain to be explored. Hence, MVs can be considered terra incognita in environmental colloid research. Although MV biogenesis and biological roles are yet to be fully understood, the accumulation of knowledge has opened new avenues for their applications. Via genetic engineering, the MV yield can be greatly increased, and the components of MVs can be tailored. Recent studies have demonstrated that MVs have promising potential for applications such as drug delivery systems and nanobiocatalysts. For instance, MV vaccines have been extensively studied and have already been approved in Europe. Recent MV studies have evoked great interest in the fields of biology and biotechnology, but fundamental questions, such as their transport in the environment or physicochemical features of MVs, remain to be addressed. In this review, we present the current understanding of bacterial MVs and environmental perspectives and further introduce their applications.
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Affiliation(s)
- Masanori Toyofuku
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Yosuke Tashiro
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Shizuoka 432-8561, Japan
| | - Yusuke Hasegawa
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Hamamatsu, Shizuoka 432-8561, Japan
| | - Masaharu Kurosawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Nobuhiko Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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15
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Schwechheimer C, Kuehn MJ. Outer-membrane vesicles from Gram-negative bacteria: biogenesis and functions. Nat Rev Microbiol 2015; 13:605-19. [PMID: 26373371 PMCID: PMC5308417 DOI: 10.1038/nrmicro3525] [Citation(s) in RCA: 1128] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Outer-membrane vesicles (OMVs) are spherical buds of the outer membrane filled with periplasmic content and are commonly produced by Gram-negative bacteria. The production of OMVs allows bacteria to interact with their environment, and OMVs have been found to mediate diverse functions, including promoting pathogenesis, enabling bacterial survival during stress conditions and regulating microbial interactions within bacterial communities. Additionally, because of this functional versatility, researchers have begun to explore OMVs as a platform for bioengineering applications. In this Review, we discuss recent advances in the study of OMVs, focusing on new insights into the mechanisms of biogenesis and the functions of these vesicles.
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Affiliation(s)
- Carmen Schwechheimer
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Meta J Kuehn
- Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA
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Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. Fe biomineralization mirrors individual metabolic activity in a nitrate-dependent Fe(II)-oxidizer. Front Microbiol 2015; 6:879. [PMID: 26441847 PMCID: PMC4562303 DOI: 10.3389/fmicb.2015.00879] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022] Open
Abstract
Microbial biomineralization sometimes leads to periplasmic encrustation, which is predicted to enhance microorganism preservation in the fossil record. Mineral precipitation within the periplasm is, however, thought to induce death, as a result of permeability loss preventing nutrient and waste transit across the cell wall. This hypothesis had, however, never been investigated down to the single cell level. Here, we cultured the nitrate reducing Fe(II) oxidizing bacteria Acidovorax sp. strain BoFeN1 that have been previously shown to promote the precipitation of a diversity of Fe minerals (lepidocrocite, goethite, Fe phosphate) encrusting the periplasm. We investigated the connection of Fe biomineralization with carbon assimilation at the single cell level, using a combination of electron microscopy and Nano-Secondary Ion Mass Spectrometry. Our analyses revealed strong individual heterogeneities of Fe biomineralization. Noteworthy, a small proportion of cells remaining free of any precipitate persisted even at advanced stages of biomineralization. Using pulse chase experiments with (13)C-acetate, we provide evidence of individual phenotypic heterogeneities of carbon assimilation, correlated with the level of Fe biomineralization. Whereas non- and moderately encrusted cells were able to assimilate acetate, higher levels of periplasmic encrustation prevented any carbon incorporation. Carbon assimilation only depended on the level of Fe encrustation and not on the nature of Fe minerals precipitated in the cell wall. Carbon assimilation decreased exponentially with increasing cell-associated Fe content. Persistence of a small proportion of non-mineralized and metabolically active cells might constitute a survival strategy in highly ferruginous environments. Eventually, our results suggest that periplasmic Fe biomineralization may provide a signature of individual metabolic status, which could be looked for in the fossil record and in modern environmental samples.
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Affiliation(s)
- Jennyfer Miot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Laurent Remusat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Elodie Duprat
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Adriana Gonzalez
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
| | - Sylvain Pont
- Département des Collections, Muséum National d’Histoire NaturelleParis, France
| | - Mélanie Poinsot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’Histoire Naturelle, Université Pierre et Marie Curie – Sorbonne Universités, CNRS UMR 7590, IRD 206Paris, France
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