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Kommana G, Hupfer M, Woodhouse JN, Grossart HP, Goldhammer T. Reduced greenhouse gas emissions from particulate organic matter degradation in iron-enriched sediments. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:1227-1244. [PMID: 38910491 DOI: 10.1039/d4em00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Iron (Fe) plays an important role in the biogeochemical cycling of carbon and nutrients in aquatic systems. Reactive Fe phases can interact with organic carbon and facilitate the removal of carbon from the biogeochemical cycle; however, this important ecosystem function is often strongly controlled by Fe availability. Due to pollution from lignite mining in the Lusatian province in Northeast Germany, large amounts of iron and sulfate are released into the fluvial-lacustrine system of the Spree River. It was hypothesized that the input of freshly precipitated iron oxyhydroxides from mining areas (e.g., ferrihydrite) alter the biodegradation of particulate organic matter (POM) in downstream lacustrine sediments. To investigate the Fe-dependent degradation of POM, slurries mimicking iron-polluted sediments (85 mg Fe per g, 116 mg Fe per g, and 149 mg Fe per g dry weight) were incubated with plankton or leaf POM under anoxic and oxic headspace conditions, and CO2 and CH4 emissions, water chemistry, and stable isotopes of dissolved inorganic carbon were measured. The experiments revealed that (i) with an increasing Fe content, the CO2 and CH4 emissions were gradually reduced, (ii) CO2 and CH4 production was higher during plankton degradation than during leaf decomposition, and (iii) under oxic conditions, CO2 production was higher and CH4 production was lower when compared to the treatments under anoxic conditions. These findings demonstrate that while benthic mineralization of fresh POM typically releases greenhouse gases into the water column, the availability of iron oxyhydroxides can contribute to reduced greenhouse gas emissions from sediments. This is of considerable relevance for future carbon budgets of similar mining-affected, iron-polluted fluvial-lacustrine river systems.
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Affiliation(s)
- Giulia Kommana
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Ecohydrology and Biogeochemistry, Mueggelseedamm 301, D-12587 Berlin, Germany.
- Brandenburg University of Technology Cottbus-Senftenberg, Department of Aquatic Ecology, Seestraße 45, D-15526 Bad Saarow, Germany
| | - Michael Hupfer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Ecohydrology and Biogeochemistry, Mueggelseedamm 301, D-12587 Berlin, Germany.
- Brandenburg University of Technology Cottbus-Senftenberg, Department of Aquatic Ecology, Seestraße 45, D-15526 Bad Saarow, Germany
| | - Jason Nicholas Woodhouse
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststraße 18, D-22609 Hamburg, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Plankton and Microbial Ecology, Zur Alten Fischerhuette 2, 16775 Stechlin, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Plankton and Microbial Ecology, Zur Alten Fischerhuette 2, 16775 Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany
| | - Tobias Goldhammer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Ecohydrology and Biogeochemistry, Mueggelseedamm 301, D-12587 Berlin, Germany.
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Weng X, Fu HM, Mao Z, Yan P, Xu XW, Shen Y, Chen YP. Fate of iron nanoparticles in anammox system: Dissolution, migration and transformation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119323. [PMID: 37852083 DOI: 10.1016/j.jenvman.2023.119323] [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: 08/13/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Iron nanoparticles (FeNPs) are commonly used in various industrial processes, leading to their release into the environment and eventual entrance into wastewater treatment plants (WWTPs). FeNPs undergo dissolution, migration, and transformation in WWTPs, which can potentially affect the stable operation of anaerobic ammonia oxidation (anammox) systems and may be discharged with wastewater or biomass. To better understand the fate of FeNPs in anammox systems, exposure experiments were conducted using anammox granular sludges (AnGS) and FeNPs. Results demonstrated that FeNPs released Fe2+ upon contact with water, with a portion being bound to functional groups in extracellular polymeric substances (EPS) and the rest entering the bacteria to form highly absorbable substances. A significant amount of FeNPs was observed to cover the surface of AnGS or aggregate and deposit at the bottom of the reactor, eventually converting into Fe3O4 and stably existing within the anammox system. The findings of this study clarify the fate of FeNPs in anammox systems and provide important insights into the stable operation of anammox systems under FeNPs exposure.
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Affiliation(s)
- Xun Weng
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Hui-Min Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - Zheng Mao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China; Chongqing Institute of Geology and Mineral Resources, Chongqing, 401120, China
| | - Peng Yan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Xiao-Wei Xu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China
| | - Yu Shen
- National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing, 400067, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing, 400045, China.
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Liu P, Zhang H, Fan Y, Xu D. Microbially Influenced Corrosion of Steel in Marine Environments: A Review from Mechanisms to Prevention. Microorganisms 2023; 11:2299. [PMID: 37764143 PMCID: PMC10535020 DOI: 10.3390/microorganisms11092299] [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: 08/02/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Microbially influenced corrosion (MIC) is a formidable challenge in the marine industry, resulting from intricate interactions among various biochemical reactions and microbial species. Many preventions used to mitigate biocorrosion fail due to ignorance of the MIC mechanisms. This review provides a summary of the current research on microbial corrosion in marine environments, including corrosive microbes and biocorrosion mechanisms. We also summarized current strategies for inhibiting MIC and proposed future research directions for MIC mechanisms and prevention. This review aims to comprehensively understand marine microbial corrosion and contribute to novel strategy developments for biocorrosion control in marine environments.
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Affiliation(s)
- Pan Liu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
| | - Haiting Zhang
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Yongqiang Fan
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
- College of Life and Health Sciences, Northeastern University, Shenyang 110819, China
| | - Dake Xu
- Shenyang National Laboratory for Materials Science, Northeastern University, Shenyang 110819, China
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Castillo J, Alom J, Gomez-Arias A, Cebekhulu S, Matu A, Cason E, Valverde A. Bacterial communities shift and influence in an acid mine drainage treatment using barium carbonate disperse alkaline substrate system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 885:163526. [PMID: 37116802 DOI: 10.1016/j.scitotenv.2023.163526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Chemical passive treatment systems used to remediate acid mine drainage has been evaluated based mainly on the reactivity of the chemical alkaline reagents, overlooking the activity of the microorganisms that proliferate in these artificial ecosystems. In this study, the bacterial communities of a unique passive treatment system known as BDAS (Barium carbonate Dispersed Alkaline Substrate) were investigated using 16S rRNA gene metagenomic sequencing combined with hydrochemical characterization of the AMD and phenotypic characterization of biogenic precipitates. According to the hydrochemical characterization, the water quality improved as the water progressed through the system, with a drastic increase in the pH (up to alkaline conditions) and total organic carbon, as well as the removal of main contaminants such as Ca2+, SO42-, Fe3+, Al3+, and Mn2+. These environmental changes resulted in an increase in bacterial diversity (richness) after the inlet and in the shift of the bacterial communities from chemoautotrophs (e.g., Ferrovum and Acidiphilum) to chemoheterotrophs (e.g., Brevundimonas and Geobacter). Some of these taxa harbour potential to immobilize metals, aiding in the treatment of the water. One of the mechanisms involved in the immobilization of metals is microbially induced calcium carbonate precipitation, which seems to occur spontaneously in BDAS. The production of biofilm was also observed in most parts of the system, except in the inlet, helping with the removal of metals. However, in the long run, the build-up of biofilm and precipitation of metals could clog (i.e., biofouling) the pores of the matrix, reducing the treatment efficiency. Potential human pathogens (e.g. Legionella) were also detected in BDAS indicating the need for a treatment step at the end of the system to remove pathogenic microorganisms. These findings present a new perspective of the bacterial communities and their effects (both positively and negatively) in a chemical passive treatment system.
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Affiliation(s)
- J Castillo
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa.
| | - J Alom
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - A Gomez-Arias
- Department of Chemistry, University of the Free State, Bloemfontein, South Africa
| | - S Cebekhulu
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - A Matu
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa
| | - E Cason
- Department of Animal Sciences, University of the Free State, Bloemfontein, South Africa
| | - A Valverde
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), Consejo Superior de Investigaciones Científicas, Salamanca, Spain
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Han S, Tang R, Yang S, Xie CJ, Narsing Rao MP, Rensing C, Liu GH, Zhou SG. Geothrix oryzisoli sp. nov., a ferric iron-reducing bacterium isolated from paddy soil. Antonie Van Leeuwenhoek 2023; 116:477-486. [PMID: 36897496 DOI: 10.1007/s10482-023-01817-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/18/2023] [Indexed: 03/11/2023]
Abstract
An anaerobic, Gram-staining-negative, rod-shaped, Fe(III)-reducing strain, designated SG189T, was isolated from paddy soil in Fujian Province, China. Growth occurred at 20-35 ℃ (optimum 30 ℃), pH 6.5-8.0 (optimum 7.0) and 0-0.2% (w/v) NaCl (optimum 0%). The strain SG189T showed the highest 16S rRNA sequences similarities to the type strains of Geothrix fermentans DSM 14018T (98.9%), "Geothrix terrae" SG184T (99.0%) and "Geothrix alkalitolerans" SG263T (99.3%). ANI and dDDH values between strain SG189T and the most closely related Geothrix species were 86.5-87.1% and 31.5-32.9%, which lower than the cut-off values (ANI 95-96% and dDDH 70%) for prokaryotic species delineation. Further, genome-based phylogenomic trees constructed using 81 core genes (UBCG2) and 120 conserved genes (GTDB) showed that strain SG189T formed a clade with members of the genus Geothrix. The menaquinone was shown to be MK-8, and the major fatty acids were iso-C15:0 and iso-C13:0 3OH. The genomic DNA G + C content was 68.2%. Additionally, we found that strain SG189T possessed ability to reduce ferric iron, and strain SG189T could reduce 10 mM of ferric citrate in 10 days with lactate as the sole electron donor. Based on the observed physiological and biochemical properties, chemotaxonomic characteristics, ANI and dDDH values, SG189T represents a novel species of the genus Geothrix, for which the name Geothrix oryzisoli sp. nov. is proposed. The type strain is SG189T (= GDMCC 1.3408T = JCM 39324T).
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Affiliation(s)
- Shuang Han
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Rong Tang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Shang Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Cheng-Jie Xie
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Manik Prabhu Narsing Rao
- Programa de Doctorado en Ciencias Aplicadas, Universidad Autónoma de Chile, Talca, 3460000, Chile
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China
| | - Guo-Hong Liu
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, People's Republic of China.
| | - Shun-Gui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, People's Republic of China.
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Gios E, Mosley OE, Weaver L, Close M, Daughney C, Handley KM. Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles. ISME COMMUNICATIONS 2023; 3:13. [PMID: 36808147 PMCID: PMC9938205 DOI: 10.1038/s43705-023-00223-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/16/2023]
Abstract
Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford, UK
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Murray Close
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Chris Daughney
- GNS Science, Lower Hutt, New Zealand
- NIWA, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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7
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Ferrihydrite nanoparticles produced by Klebsiella oxytoca: Structure and properties dependence on the cultivation time. ADV POWDER TECHNOL 2022. [DOI: 10.1016/j.apt.2022.103692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Barkay T, Gu B. Demethylation─The Other Side of the Mercury Methylation Coin: A Critical Review. ACS ENVIRONMENTAL AU 2022; 2:77-97. [PMID: 37101582 PMCID: PMC10114901 DOI: 10.1021/acsenvironau.1c00022] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The public and environmental health consequences of mercury (Hg) methylation have drawn much attention and considerable research to Hg methylation processes and their dynamics in diverse environments and under a multitude of conditions. However, the net methylmercury (MeHg) concentration that accumulates in the environment is equally determined by the rate of MeHg degradation, a complex process mediated by a variety of biotic and abiotic mechanisms, about which our knowledge is limited. Here we review the current knowledge on MeHg degradation and its potential pathways and mechanisms. We describe detoxification by resistant microorganisms that employ the Hg resistance (mer) system to reductively break the carbon-mercury (C-Hg) bond producing methane (CH4) and inorganic mercuric Hg(II), which is then reduced by the mercuric reductase to elemental Hg(0). Very recent research has begun to elucidate a mechanism for the long-recognized mer-independent oxidative demethylation, likely involving some strains of anaerobic bacteria as well as aerobic methane-oxidizing bacteria, i.e., methanotrophs. In addition, photochemical and chemical demethylation processes are described, including the roles of dissolved organic matter (DOM) and free radicals as well as dark abiotic demethylation in the natural environment about which little is currently known. We focus on mechanisms and processes of demethylation and highlight the uncertainties and known effects of environmental factors leading to MeHg degradation. Finally, we suggest future research directions to further elucidate the chemical and biochemical mechanisms of biotic and abiotic demethylation and their significance in controlling net MeHg production in natural ecosystems.
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Affiliation(s)
- Tamar Barkay
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Perl SM, Celestian AJ, Cockell CS, Corsetti FA, Barge LM, Bottjer D, Filiberto J, Baxter BK, Kanik I, Potter-McIntyre S, Weber JM, Rodriguez LE, Melwani Daswani M. A Proposed Geobiology-Driven Nomenclature for Astrobiological In Situ Observations and Sample Analyses. ASTROBIOLOGY 2021; 21:954-967. [PMID: 34357788 PMCID: PMC8403179 DOI: 10.1089/ast.2020.2318] [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: 05/06/2023]
Abstract
As the exploration of Mars and other worlds for signs of life has increased, the need for a common nomenclature and consensus has become significantly important for proper identification of nonterrestrial/non-Earth biology, biogenic structures, and chemical processes generated from biological processes. The fact that Earth is our single data point for all life, diversity, and evolution means that there is an inherent bias toward life as we know it through our own planet's history. The search for life "as we don't know it" then brings this bias forward to decision-making regarding mission instruments and payloads. Understandably, this leads to several top-level scientific, theoretical, and philosophical questions regarding the definition of life and what it means for future life detection missions. How can we decide on how and where to detect known and unknown signs of life with a single biased data point? What features could act as universal biosignatures that support Darwinian evolution in the geological context of nonterrestrial time lines? The purpose of this article is to generate an improved nomenclature for terrestrial features that have mineral/microbial interactions within structures and to confirm which features can only exist from life (biotic), features that are modified by biological processes (biogenic), features that life does not affect (abiotic), and properties that can exist or not regardless of the presence of biology (abiogenic). These four categories are critical in understanding and deciphering future returned samples from Mars, signs of potential extinct/ancient and extant life on Mars, and in situ analyses from ocean worlds to distinguish and separate what physical structures and chemical patterns are due to life and which are not. Moreover, we discuss hypothetical detection and preservation environments for extant and extinct life, respectively. These proposed environments will take into account independent active and ancient in situ detection prospects by using previous planetary exploration studies and discuss the geobiological implications within an astrobiological context.
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Affiliation(s)
- Scott M. Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Mineral Sciences, Natural History Museum of Los Angeles County, Los Angeles, California, USA
- Blue Marble Space Institute for Science, Seattle, Washington, USA
- Address correspondence to: Scott M. Perl, NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109, +USA
| | - Aaron J. Celestian
- Mineral Sciences, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Charles S. Cockell
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, Scotland
| | - Frank A. Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Laura M. Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Blue Marble Space Institute for Science, Seattle, Washington, USA
| | - David Bottjer
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | | | - Bonnie K. Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, Utah, USA
| | - Isik Kanik
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Sally Potter-McIntyre
- School of Earth Systems and Sustainability, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura E. Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Mohit Melwani Daswani
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Hassenkam T, Tsai EHR, Sørensen HO, Dalby KN, Mackenzie DMA, Holler M, Ferreira D, Grolimund D, Bruns S, Rosing MT. Direct evidence for eoarchean iron metabolism? GEOBIOLOGY 2021; 19:218-227. [PMID: 33624944 DOI: 10.1111/gbi.12432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/08/2020] [Accepted: 01/17/2021] [Indexed: 06/12/2023]
Abstract
Metasedimentary rocks from Isua, West Greenland (> 3,700 million years old) contain carbonaceous compounds, compatible with a biogenic origin (Hassenkam, Andersson, Dalby, Mackenzie, & Rosing, 2017; Ohtomo, Kakegawa, Ishida, Nagase, & Rosing, 2014; Rosing, 1999). The metamorphic mineral assemblage with garnet and quartz intergrowths contains layers of carbonaceous inclusions contiguous with carbon-rich sedimentary beds in the host rock. Previous studies (Hassenkam et al., 2017; Ohtomo et al., 2014; Rosing, 1999) on Isua rocks focused on testing the biogenic origin of the carbonaceous material, but here we searched for evidence which could provide new insights into the nature of the life that generated this carbonaceous material. We studied material trapped in inclusions armoured within quartz grains inside garnet porphyroblasts by non-destructive ptychographic X-ray nanotomography (PXCT). The 3D electron density maps generated by PXCT were correlated with maps from X-ray fluorescence tomography and micro-Raman spectroscopy. We found that the material trapped inside inclusions in the quartz grains consist of disordered carbon material encasing domains of iron-rich carbonaceous material. These results corroborate earlier claims (Hassenkam et al., 2017; Ohtomo et al., 2014; Rosing, 1999) for biogenic origins and are compatible with relics of metamorphosed biological material originally containing high iron/carbon ratios, comparable to ratios found in most extant organisms. These iron-rich domains represent the oldest evidence for organic iron complexes in the geologic record and are consistent with Fe-isotopic evidence for metabolic iron fractionation in > 3,700 Ma Isua banded iron formation (Czaja et al., 2013; Whitehouse & Fedo, 2007).
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Affiliation(s)
- Tue Hassenkam
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esther H R Tsai
- Paul Scherrer Institut, Villigen, Switzerland
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Henning O Sørensen
- Department of Chemistry, Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
- Department of Physics, Technical University of Denmark, Lyngby, Denmark
| | - Kim N Dalby
- Department of Chemistry, Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
- Haldor Topsøe A/S, Lyngby, Denmark
| | - David M A Mackenzie
- Department of Electronics and Nanoengineering, Aalto University, Aalto, Finland
| | | | | | | | - Stefan Bruns
- Helmholtz-Center Geesthacht, Centre for Materials and Coastal Research, Institute of Metallic Biomaterials, Geesthacht, Germany
| | - Minik T Rosing
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
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11
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Chmykhalo V, Belanova A, Belousova M, Butova V, Makarenko Y, Khrenkova V, Soldatov A, Zolotukhin P. Microbial-based magnetic nanoparticles production: a mini-review. Integr Biol (Camb) 2021; 13:98-107. [PMID: 33829272 DOI: 10.1093/intbio/zyab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/14/2022]
Abstract
The ever-increasing biomedical application of magnetic nanoparticles (MNPs) implies increasing demand in their scalable and high-throughput production, with finely tuned and well-controlled characteristics. One of the options to meet the demand is microbial production by nanoparticles-synthesizing bacteria. This approach has several benefits over the standard chemical synthesis methods, including improved homogeneity of synthesis, cost-effectiveness, safety and eco-friendliness. There are, however, specific challenges emanating from the nature of the approach that are to be accounted and resolved in each manufacturing instance. Most of the challenges can be resolved by proper selection of the producing organism and optimizing cell culture and nanoparticles extraction conditions. Other issues require development of proper continuous production equipment, medium usage optimization and precursor ions recycling. This mini-review focuses on the related topics in microbial synthesis of MNPs: producing organisms, culturing methods, nanoparticles characteristics tuning, nanoparticles yield and synthesis timeframe considerations, nanoparticles isolation as well as on the respective challenges and possible solutions.
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Affiliation(s)
- Victor Chmykhalo
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Anna Belanova
- Smart Materials International Research Centre, Southern Federal University, Rostov-on-Don, Russia
| | - Mariya Belousova
- English Language Department for Natural Sciences Faculties, Southern Federal University, Rostov-on-Don, Russia
| | - Vera Butova
- Smart Materials International Research Centre, Southern Federal University, Rostov-on-Don, Russia
| | | | - Vera Khrenkova
- Medical Consulting Department, Rostov-on-Don Pathological-Anatomical Bureau No. 1, Rostov-on-Don, Russia
| | - Alexander Soldatov
- Smart Materials International Research Centre, Southern Federal University, Rostov-on-Don, Russia
| | - Peter Zolotukhin
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
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12
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Dula S, Ajayeoba TA, Ijabadeniyi OA. Bacterial biofilm formation on stainless steel in the food processing environment and its health implications. Folia Microbiol (Praha) 2021; 66:293-302. [PMID: 33768506 DOI: 10.1007/s12223-021-00864-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/22/2021] [Indexed: 12/01/2022]
Abstract
Biofilm formation (BF) and production in the food processing industry (FPI) is a continual threat to food safety and quality. Various bacterial pathogens possess the ability to adhere and produce biofilms on stainless steel (SS) in the FPI due to flagella, curli, pili, fimbrial adhesins, extra polymeric substances, and surface proteins. The facilitating environmental conditions (temperature, pressure, variations in climatic conditions), SS properties (surface energy, hydrophobicity, surface roughness, topography), type of raw food materials, pre-processing, and processing conditions play a significant role in the enhancement of bacterial adhesion and favorable condition for BF. Furthermore, biofilm formers can tolerate different sanitizers and cleaning agents due to the constituents, concentration, contact time, bacterial cluster distribution, and composition of bacteria within the biofilm. Also, bacterial biofilms' ability to produce various endotoxins and exotoxins when consumed cause food infections and intoxications with serious health implications. It is thus crucial to understand BF's repercussions and develop effective interventions against these phenomena that make persistent pathogens difficult to remove in the food processing environment.
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Affiliation(s)
- Stanley Dula
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa
| | - Titilayo Adenike Ajayeoba
- Department of Biotechnology and Food Science, Durban University of Technology, Durban, South Africa. .,Department of Microbiology, Faculty of Science, Adeleke University, Ede, Nigeria.
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13
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Gan C, Wu R, Luo Y, Song J, Luo D, Li B, Yang Y, Xu M. Visualizing and Isolating Iron-Reducing Microorganisms at the Single-Cell Level. Appl Environ Microbiol 2021; 87:e02192-20. [PMID: 33158896 PMCID: PMC7848898 DOI: 10.1128/aem.02192-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/03/2020] [Indexed: 01/06/2023] Open
Abstract
Iron-reducing microorganisms (FeRM) play key roles in many natural and engineering processes. Visualizing and isolating FeRM from multispecies samples are essential to understand the in situ location and geochemical role of FeRM. Here, we visualized FeRM by a "turn-on" Fe2+-specific fluorescent chemodosimeter (FSFC) with high sensitivity, selectivity, and stability. This FSFC could selectively identify and locate active FeRM from either pure culture, coculture of different bacteria, or sediment-containing samples. Fluorescent intensity of the FSFC could be used as an indicator of Fe2+ concentration in bacterial cultures. By combining the use of the FSFC with that of a single-cell sorter, we obtained three FSFC-labeled cells from an enriched consortium, and all of them were subsequently shown to be capable of iron reduction; two unlabeled cells were shown to have no iron-reducing capability, further confirming the feasibility of the FSFC.IMPORTANCE Visualization and isolation of FeRM from samples containing multiple species are commonly needed by researchers from different disciplines, such as environmental microbiology, environmental sciences, and geochemistry. However, no available method has been reported. In this study, we provide a method to visualize FeRM and evaluate their activity even at the single-cell level. When this approach is combined with use of a single-cell sorter, FeRM can also be isolated from samples containing multiple species. This method can be used as a powerful tool to uncover the in situ or ex situ role of FeRM and their interactions with ambient microbes or chemicals.
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Affiliation(s)
- Cuifen Gan
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Rongrong Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yeshen Luo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jianhua Song
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Dizhou Luo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Bei Li
- The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, CAS, Changchun, China
- Hooke Instruments Ltd., Changchun, China
| | - Yonggang Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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14
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Ziadi I, El-Bassi L, Bousselmi L, Akrout H. Characterization of the biofilm grown on 304L stainless steel in urban wastewaters: extracellular polymeric substances (EPS) and bacterial consortia. BIOFOULING 2020; 36:977-989. [PMID: 33086880 DOI: 10.1080/08927014.2020.1836163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Characterization of the biofilm growing on stainless steel (SS) in untreated (UTUWW) and treated (TUWW) urban wastewaters was performed. In both media, the first phase of biofilm growth was aerobic, when the genera Caldimonas, Caulobacter, Terriglobus and Edaphobacter (iron oxidizing bacteria [IOB]) and the genera Bacillus, Sulfurimonas, Syntrophobacter and Desulfobacter (sulfur oxidizing bacteria [SOB]) were identified. In the second phase, established after immersion for 7 days, the high amount of EPS inhibited the access of oxygen and promoted the growth of anaerobic bacteria, which were the genus Shewanella (iron-reducing bacterium [IRB]) and the genera Desulfovirga, Desulfovibrio, Desulfuromusa, Desulfococcus, and Desulfosarcina (sulfate-reducing bacteria [SRB]). Electrochemical measurements showed that in the first stage, the aerobic bacteria and the high amount of EPS delayed the cathodic reduction of oxygen. However, in the second stage, EPS and the anaerobic bacteria promoted anodic dissolution.
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Affiliation(s)
- Islem Ziadi
- Laboratory of Wastewaters and Environment, Centre of Water Researches and Technologies (CERTE), Soliman, Tunisia
- National Institute of Applied Sciences and Technology (INSAT), Carthage University, Tunis, Tunisia
| | - Leila El-Bassi
- Laboratory of Wastewaters and Environment, Centre of Water Researches and Technologies (CERTE), Soliman, Tunisia
| | - Latifa Bousselmi
- Laboratory of Wastewaters and Environment, Centre of Water Researches and Technologies (CERTE), Soliman, Tunisia
| | - Hanene Akrout
- Laboratory of Wastewaters and Environment, Centre of Water Researches and Technologies (CERTE), Soliman, Tunisia
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15
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Mustapha NA, Toya S, Maeda T. Effect of Aso limonite on anaerobic digestion of waste sewage sludge. AMB Express 2020; 10:74. [PMID: 32300904 PMCID: PMC7162999 DOI: 10.1186/s13568-020-01010-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/07/2020] [Indexed: 11/23/2022] Open
Abstract
The effect of Aso volcanic limonite was explored in anaerobic digestion using waste sewage sludge (WSS). In this study, methane and hydrogen sulfide were remarkably inhibited when Aso limonite was mixed with WSS as well as a significant reduction of ammonia. Although pH was lowered after adding Aso limonite, methane was still inhibited in neutralized pH condition at 7.0. Hydrolysis stage was not influenced by Aso limonite as supported by the result that a high protease activity was still detected in the presence of the material. However, acidogenesis stage was affected by Aso limonite as indicated by the different productions of organic acids. Acetic acid, was accumulated in the presence of Aso limonite due to the inhibition of methane production, except in the highest concentration of Aso limonite which the production of acetate may be inhibited. Besides, the production of propionate and butyrate reduced in accordance to the increased concentration of Aso limonite. In addition, Archaeal activity (methanogens) in WSS with Aso limonite was low in agreement with the low methane production. Thus, these results indicate that Aso limonite influences the acidogenesis and methanogenesis processes, by which the productions of methane and ammonia were inhibited. On the other hand, in the contactless of Aso limonite during the anaerobic digestion of WSS (Aso limonite was placed in the area of headspace in the vial), Aso limonite had the adsorptive ability for hydrogen sulfide from WSS, but not for methane. This contactless system of Aso limonite may be a practical means to remove hydrogen sulfide without inhibiting methane production as an important bioenergy source.
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16
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Maggiori C, Stromberg J, Blanco Y, Goordial J, Cloutis E, García-Villadangos M, Parro V, Whyte L. The Limits, Capabilities, and Potential for Life Detection with MinION Sequencing in a Paleochannel Mars Analog. ASTROBIOLOGY 2020; 20:375-393. [PMID: 31976742 DOI: 10.1089/ast.2018.1964] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
No instrument capable of direct life detection has been included on a mission payload to Mars since NASA's Viking missions in the 1970s. This prevents us from discovering whether life is or ever was present on Mars. DNA is an ideal target biosignature since it is unambiguous, nonspecific, and readily detectable with nanopore sequencing. Here, we present a proof-of-concept utilization of the Oxford Nanopore Technologies (ONT) MinION sequencer for direct life detection and show how it can complement results from established space mission instruments. We used nanopore sequencing data from the MinION to detect and characterize the microbial life in a set of paleochannels near Hanksville, UT, with supporting data from X-ray diffraction, reflectance spectroscopy, Raman spectroscopy, and Life Detector Chip (LDChip) microarray immunoassay analyses. These paleochannels are analogs to martian sinuous ridges. The MinION-generated metagenomes reveal a rich microbial community dominated by bacteria and containing radioresistant, psychrophilic, and halophilic taxa. With spectral data and LDChip immunoassays, these metagenomes were linked to the surrounding Mars analog environment and potential metabolisms (e.g., methane production and perchlorate reduction). This shows a high degree of synergy between these techniques for detecting and characterizing biosignatures. We also resolved a prospective lower limit of ∼0.001 ng of DNA required for successful sequencing. This work represents the first determination of the MinION's DNA detection limits beyond ONT recommendations and the first whole metagenome analysis of a sinuous ridge analog.
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Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
| | | | - Yolanda Blanco
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Jacqueline Goordial
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine
| | - Edward Cloutis
- Department of Geography, Faculty of Science, University of Winnipeg, Winnipeg, Canada
| | | | - Victor Parro
- Department of Molecular Evolution, Centro de Astrobiología (INTA-CSIC), Madrid, Spain
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Quebec, Canada
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17
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Zhao G, Li E, Li J, Liu F, Liu F, Xu M. Goethite Hinders Azo Dye Bioreduction by Blocking Terminal Reductive Sites on the Outer Membrane of Shewanella decolorationis S12. Front Microbiol 2019; 10:1452. [PMID: 31293561 PMCID: PMC6604703 DOI: 10.3389/fmicb.2019.01452] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/11/2019] [Indexed: 01/21/2023] Open
Abstract
Iron (hydr)oxides are the most ubiquitous Fe(III)-containing minerals in the near-surface environments and can regulate organic pollutant biotransformation by participating in bacterial extracellular electron transfer under anaerobic conditions. Mechanisms described so far are based on their redox properties in bacterial extracellular respiration. Here, we find that goethite, a typical iron (hydr)oxide, inhibits the bioreduction of different polar azo dyes by Shewanella decolorationis S12 not through electron competition, but by the contact of its surface Fe(III) with the bacterial outer surface. Through the combined results of attenuated total reflectance (ATR) Fourier transform infrared spectroscopy, two-dimensional correlation spectroscopy, and confocal laser scanning microscope, we found that the outer membrane proteins MtrC and OmcA of strain S12 are key binding sites for goethite surface. Meanwhile, they were identified as the important reductive terminals for azo dyes. These results suggest that goethite may block the terminal reductive sites of azo dyes on the bacterial outer membrane to inhibit their bioreduction. This discovered role of goethite in bioreduction provides new insight into the microbial transformation processes of organic pollutants in iron (hydr)oxide-containing environments.
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Affiliation(s)
- Gang Zhao
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Enze Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jianjun Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Feifei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Fei Liu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
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18
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Zhang WH, Sun RB, Xu L, Liang JN, Zhou J. Assessment of bacterial communities in Cu-contaminated soil immobilized by a one-time application of micro-/nano-hydroxyapatite and phytoremediation for 3 years. CHEMOSPHERE 2019; 223:240-249. [PMID: 30784731 DOI: 10.1016/j.chemosphere.2019.02.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/30/2019] [Accepted: 02/10/2019] [Indexed: 05/21/2023]
Abstract
Heavy metals contamination of soil has been considered as a global environmental problem, and consequently various soil amendments have been widely used in immobilization. Previous studies have reported that micro-/nano-hydroxyapatite (MHA/NHA) as a novel chemical material could alleviate soil acidity and reduce the bioavailability of heavy metals. However, the mechanism of soil microorganism responding to the application of MHA/NHA is little studied. Presently, an in-situ field experiment was conducted to determine the effects of MHA/NHA and the other three traditional amendments including alkali slag (AS), lime (L) and apatite (AP) on soil copper (Cu) bioavailability and dominate bacterial population. The results showed that the application of MHA/NHA effectively increased soil pH and decreased soil available Cu content, and showed the highest increasing effects on the activities of urease, catalase and acid phosphatase. Compared with the control, MHA/NHA significantly changed the soil bacterial community structure and increased the bacterial abundance and diversity. Besides, analysis of the dominate population showed that the application of MHA/NHA decreased the relative abundance of acidophiles and the indicator of soil degradation. Additionally, the relative abundance of potential plant growth promoting bacteria increased with the addition of MHA/NHA, which was confirmed by the characteristics (the ability of producing indole acetic acid and siderophore) of bacterial strains. These results suggested that these dominate bacterial populations with significant changes may be regarded as the biomarkers for the recovery of soil ecological environment, which provides a theoretical basis for the ecological evaluation of MHA/NHA.
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Affiliation(s)
- Wen-Hui Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China
| | - Rui-Bo Sun
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Lei Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China
| | - Jia-Ni Liang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China
| | - Jing Zhou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Science, Nanjing, 210008, China; National Engineering and Technology Research Center for Red Soil Improvement, Red Soil Ecological Experiment Station, Chinese Academy of Sciences, Liujiazhan Plantation, Yingtan, 335211, China; Jiangxi Engineering Research Center of Eco-Remediation of Heavy Metal Pollution, Jiangxi Academy of Science, Nanchang, 330096, China.
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19
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Lebedev N, Stroud RM, Yates MD, Tender LM. Spatially Resolved Chemical Analysis of Geobacter sulfurreducens Cell Surface. ACS NANO 2019; 13:4834-4842. [PMID: 30943001 DOI: 10.1021/acsnano.9b02032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Geobacter sulfurreducens is of interest for the highest efficiency of power generation and extremely long extracellular electron transfer (EET) between the bacterium and electrodes. Despite more than 15 years of intensive molecular biological research, there is still no clear answer which molecules are responsible for these processes. In the present work, we look at the problem from another (atomic) perspective and identify the location and shape of the compounds that are known to be conductive, particularly those containing Fe atoms. By using highly sophisticated energy dispersive X-ray spectroscopy combined with high-angle annular dark-field transmission electron microscopy enabling detection, identification, and localization of chemical compounds on the surface at nearly atomic spatial resolution, we analyze Fe spatial distribution within the G. sulfurreducens community. We discover the presence of small Fe-containing particles on the surface of the bacterium cells. The size of the particles (diameter 5.6 nm) is highly reproducible and comparable with the size of a single protein. The particles cover about 2% of the cell surface, which is similar to that expected for molecular conductors responsible for electron transfer through the bacterium cell wall. We find that G. sulfurreducens filaments ("bacterial molecular wires") also contain Fe atoms in their bundles. We observe that the bacterium enable changing the distance between the Fe-containing bundles in the filaments from separated to attached (the latter is needed for the efficient electron transfer between the Fe-containing particles), depending on the bacterium metabolic activity and attachment to extracellular substrates. These results are consistent with the recently published research about the role of Fe atoms in protein molecular conductance ( Phys. Chem. Chem. Phys. , 2018 , 20 , 14072 - 14081 ) and show what type of Fe-containing particles are involved in the bacterial extracellular communication. They can be used for the design and construction of artificial biomolecular wires and bioinorganic interfaces.
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Affiliation(s)
- Nikolai Lebedev
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Rhonda M Stroud
- Materials Science and Technology Division , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
| | - Leonard Martin Tender
- Center for Bio/Molecular Science and Engineering , U.S. Naval Research Laboratory , Washington , DC 20375 , United States
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20
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Zeng Y, Wang H, Guo C, Wan J, Fan C, Reinfelder JR, Lu G, Wu F, Huang W, Dang Z. Schwertmannite transformation via direct or indirect electron transfer by a sulfate reducing enrichment culture. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:738-748. [PMID: 30031307 DOI: 10.1016/j.envpol.2018.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
Understanding the mechanism of the microbial transformation of Fe(III)-oxyhydroxysulfate minerals is of considerable interest, because this transformation plays an important role in controlling the behaviour of toxic metals from acid mine drainage (AMD). In this study, we examined a sulfate reducing enrichment culture from AMD-contaminated sediments and predicted the possible pathway of electron transfer when incubated with schwertmannite, a common Fe(III)-oxyhydroxysulfate occurring in the AMD environment. Experiments were designed to distinguish the mechanisms by which bacteria facilitate direct (i.e., bacteria allowed to adhere to the mineral) or indirect (i.e., bacteria separated from the mineral by dialysis bag) electron transfer to reduce the mineral. The effects of adding anthraquinone-2,6-disulfonate (AQDS) as an exogenous electron shuttle were also investigated. Vivianite was detected as the main product of schwertmannite transformation. Reduction of sulfate and iron were more pronounced in direct treatments, while more non-reductive dissolution were observed in indirect treatments. The addition of AQDS lead to the production of more dissolved Fe2+ over 20 d than in the absence of AQDS. Microbial community composition differed in direct and indirect treatments, while the addition of AQDS did not significantly affect the community structure in each treatment. After incubation for 20 d, the growth of Desulfovibrio exceeded that of the originally dominant Citrobacter in direct treatments, while an unknown genus most closely related to Citrobacter within Enterobacteriaceae was predominant in indirect treatments. This monodominant community in indirect treatments was assumed not to transfer electron directly to schwertmannite but to rely on shuttling mechanism. PICRUSt results implied that bacteria in indirect treatment have potential to produce shuttling compounds or complexing agents. The absence of dsr genes and the putative fermentative process suggested that the Enterobacteriaceae might indirectly facilitate the dissolution and transformation of schwertmannite.
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Affiliation(s)
- Yufei Zeng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Han Wang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Jingjing Wan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Cong Fan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China
| | - Fengchang Wu
- State Environmental Protection Key Laboratory of Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing, 100012, PR China
| | - Weilin Huang
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China.
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21
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Fakra SC, Luef B, Castelle CJ, Mullin SW, Williams KH, Marcus MA, Schichnes D, Banfield JF. Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:503-512. [PMID: 26371540 DOI: 10.1021/acs.est.5b01409] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accurate mapping of the composition and structure of minerals and associated biological materials is critical in geomicrobiology and environmental research. Here, we have developed an apparatus that allows the correlation of cryogenic transmission electron microscopy (cryo-TEM) and synchrotron hard X-ray microprobe (SHXM) data sets to precisely determine the distribution, valence state, and structure of selenium in biofilms sampled from a contaminated aquifer near Rifle, CO. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms is ∼25-300 nm red amorphous Se0 aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for the microbial dissimilatory reduction of Se(VI) to Se(IV) to Se0. Extended X-ray absorption fine-structure spectroscopy showed red amorphous Se0 with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. Complementary scanning transmission X-ray microscopy revealed that these aggregates are strongly associated with a protein-rich biofilm matrix. These findings have important implications for predicting the stability and mobility of Se bioremediation products and understanding of Se biogeochemical cycling. The approach, involving the correlation of cryo-SHXM and cryo-TEM data sets from the same specimen area, is broadly applicable to biological and environmental samples.
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Affiliation(s)
- Sirine C Fakra
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Birgit Luef
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Cindy J Castelle
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Sean W Mullin
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Kenneth H Williams
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Matthew A Marcus
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Denise Schichnes
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
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22
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Rozas EE, Mendes MA, Nascimento CAO, Espinosa DCR, Oliveira R, Oliveira G, Custodio MR. Bioleaching of electronic waste using bacteria isolated from the marine sponge Hymeniacidon heliophila (Porifera). JOURNAL OF HAZARDOUS MATERIALS 2017; 329:120-130. [PMID: 28131039 DOI: 10.1016/j.jhazmat.2017.01.037] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/13/2017] [Accepted: 01/20/2017] [Indexed: 06/06/2023]
Abstract
The bacteria isolated from Hymeniacidon heliophila sponge cells showed bioleaching activity. The most active strain, Hyhel-1, identified as Bacillus sp., was selected for bioleaching tests under two different temperatures, 30°C and 40°C, showing rod-shaped cells and filamentous growth, respectively. At 30°C, the bacteria secreted substances which linked to the leached copper, and at 40°C metallic nanoparticles were produced inside the cells. In addition, infrared analysis detected COOH groups and linear peptides in the tested bacteria at both temperatures. The Hyhel-1 strain in presence of electronic waste (e-waste) induced the formation of crust, which could be observed due to bacteria growing on the e-waste fragment. SEM-EDS measurements showed that the bacterial net surface was composed mostly of iron (16.1% w/w), while a higher concentration of copper was observed in the supernatant (1.7% w/w) and in the precipitated (49.8% w/w). The substances linked to copper in the supernatant were sequenced by MALDI-TOF-ms/ms and identified as macrocyclic surfactin-like peptides, similar to the basic sequence of Iturin, a lipopeptide from Bacillus subtilis. Finally, the results showed that Hyhel-1 is a bioleaching bacteria and cooper nanoparticles producer and that this bacteria could be used as a copper recovery tool from electronic waste.
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Affiliation(s)
- Enrique E Rozas
- LSCP, Chemical Engineering Department, University of São Paulo (USP), Brazil.
| | - Maria A Mendes
- LSCP, Chemical Engineering Department, University of São Paulo (USP), Brazil
| | | | - Denise C R Espinosa
- LAREX, Chemical Engineering Department, University of São Paulo (USP), Brazil
| | | | | | - Marcio R Custodio
- Departamento de Fisiologia Geral, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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23
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Ferreira MR, Dantas JM, Salgueiro CA. Molecular interactions between Geobacter sulfurreducens triheme cytochromes and the electron acceptor Fe(iii) citrate studied by NMR. Dalton Trans 2017; 46:2350-2359. [DOI: 10.1039/c6dt04129a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular interactions betweenGeobacter sulfurreducenstriheme cytochromes and Fe(iii) citrate.
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Affiliation(s)
- Marisa R. Ferreira
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Joana M. Dantas
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
| | - Carlos A. Salgueiro
- UCIBIO-Requimte
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade NOVA de Lisboa
- 2829-516 Caparica
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24
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Abstract
Soft x-ray spectromicroscopy techniques have seen great amount of development in the recent years, and with the development of new diffraction limited synchrotron source, many new nanoscale and mesoscale characterization opportunities of applied materials are foreseen. In this perspective, the authors present some examples that illustrate the capabilities of spectromicroscopy techniques, namely, 2D and 3D spatially resolved chemical quantification, surface and bulk sensitive measurements, and polarization dependent measurements as applied to iron oxide nanoparticulate materials of biological, geological, and other origins.
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25
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Son HA, Choi SK, Jeong ES, Kim B, Kim HT, Sung WM, Kim JW. Microbial Activation of Bacillus subtilis-Immobilized Microgel Particles for Enhanced Oil Recovery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8909-8915. [PMID: 27506231 DOI: 10.1021/acs.langmuir.6b02010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Microbially enhanced oil recovery involves the use of microorganisms to extract oil remaining in reservoirs. Here, we report fabrication of microgel particles with immobilized Bacillus subtilis for application to microbially enhanced oil recovery. Using B. subtilis isolated from oil-contaminated soils in Myanmar, we evaluated the ability of this microbe to reduce the interfacial tension at the oil-water interface via production of biosurfactant molecules, eventually yielding excellent emulsification across a broad range of the medium pH and ionic strength. To safely deliver B. subtilis into a permeable porous medium, in this study, these bacteria were physically immobilized in a hydrogel mesh of microgel particles. In a core flooding experiment, in which the microgel particles were injected into a column packed with silica beads, we found that these particles significantly increased oil recovery in a concentration-dependent manner. This result shows that a mesh of microgel particles encapsulating biosurfactant-producing microorganisms holds promise for recovery of oil from porous media.
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Affiliation(s)
- Han Am Son
- Korea Institute of Geoscience and Mineral Resources , Daejeon 34132, Republic of Korea
- Department of Natural Resources and Environmental Engineering, Hanyang University , Seoul 04763, Republic of Korea
| | | | | | | | - Hyun Tae Kim
- Korea Institute of Geoscience and Mineral Resources , Daejeon 34132, Republic of Korea
| | - Won Mo Sung
- Department of Natural Resources and Environmental Engineering, Hanyang University , Seoul 04763, Republic of Korea
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26
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Lu X, Liu Y, Johs A, Zhao L, Wang T, Yang Z, Lin H, Elias DA, Pierce EM, Liang L, Barkay T, Gu B. Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4366-73. [PMID: 27019098 DOI: 10.1021/acs.est.6b00401] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Microbial methylation and demethylation are two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems. Although mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjiensis Bem. Here we report, for the first time, that the strain G. bemidjiensis Bem can mediate a suite of Hg transformations, including Hg(II) reduction, Hg(0) oxidation, MeHg production and degradation under anoxic conditions. Results suggest that G. bemidjiensis utilizes a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) as the major reaction product, possibly due to the presence of genes encoding homologues of an organomercurial lyase (MerB) and a mercuric reductase (MerA). In addition, the cells can strongly sorb Hg(II) and MeHg, reduce or oxidize Hg, resulting in both time and concentration-dependent Hg species transformations. Moderate concentrations (10-500 μM) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of Hg methylation and demethylation among anaerobic bacteria, thereby influencing net MeHg production in anoxic water and sediments.
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Affiliation(s)
- Xia Lu
- School of Nuclear Science and Technology, Lanzhou University , Lanzhou, China
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Yurong Liu
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing, China
| | - Alexander Johs
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Linduo Zhao
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Tieshan Wang
- School of Nuclear Science and Technology, Lanzhou University , Lanzhou, China
| | - Ziming Yang
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Hui Lin
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Eric M Pierce
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Liyuan Liang
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, New Jersey 08901, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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27
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Oikonomou CM, Chang YW, Jensen GJ. A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 2016; 14:205-20. [PMID: 26923112 PMCID: PMC5551487 DOI: 10.1038/nrmicro.2016.7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
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Affiliation(s)
- Catherine M Oikonomou
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Yi-Wei Chang
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
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28
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Hurley KR, Ring HL, Kang H, Klein ND, Haynes CL. Characterization of Magnetic Nanoparticles in Biological Matrices. Anal Chem 2015; 87:11611-9. [DOI: 10.1021/acs.analchem.5b02229] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Katie R. Hurley
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Hattie L. Ring
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
- Center
for Magnetic Resonance Research, University of Minnesota, 2021 Sixth
Street SE, Minneapolis, Minnesota 55455, United States
| | - Hyunho Kang
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Nathan D. Klein
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christy L. Haynes
- Department
of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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29
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Yu W, Xu L, Graham N, Qu J. Contribution of Fe3O4 nanoparticles to the fouling of ultrafiltration with coagulation pre-treatment. Sci Rep 2015; 5:13067. [PMID: 26268589 PMCID: PMC4535038 DOI: 10.1038/srep13067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
A coagulation (FeCl3)-ultrafiltration process was used to treat two different raw waters with/without the presence of Fe3O4 nanoparticle contaminants. The existence of Fe3O4 nanoparticles in the raw water was found to increase both irreversible and reversible membrane fouling. The trans-membrane pressure (TMP) increase was similar in the early stages of the membrane runs for both raw waters, while it increased rapidly after about 15 days in the raw water with Fe3O4 nanoparticles, suggesting the involvement of biological effects. Enhanced microbial activity with the presence of Fe3O4 nanoparticles was evident from the measured concentrations of extracellular polymeric substances (EPS) and deoxyribonucleic acid (DNA), and fluorescence intensities. It is speculated that Fe3O4 nanoparticles accumulated in the cake layer and increased bacterial growth. Associated with the bacterial growth is the production of EPS which enhances the bonding with, and between, the coagulant flocs; EPS together with smaller sizes of the nano-scale primary particles of the Fe3O4-CUF cake layer, led to the formation of a lower porosity, more resilient cake layer and membrane pore blockage.
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Affiliation(s)
- Wenzheng Yu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Lei Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Centre for Water Resources Research (CWRR), School of Civil, Structural and Environmental Engineering, University College Dublin, Newstead Building, Belfield, Dublin 4, Ireland
| | - Nigel Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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30
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Tian C, Wang C, Tian Y, Wu X, Xiao B. Vertical distribution of Fe and Fe(III)-reducing bacteria in the sediments of Lake Donghu, China. Can J Microbiol 2015; 61:575-83. [PMID: 26156094 DOI: 10.1139/cjm-2015-0129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In lake sediments, iron (Fe) is the most versatile element, and the redox cycling of Fe has a wide influence on the biogeochemical cycling of organic and inorganic substances. The aim of the present study was to analyze the vertical distribution of Fe and Fe(III)-reducing bacteria (FeRB) in the surface sediment (30 cm) of Lake Donghu, China. At the 3 sites we surveyed, FeRB and Fe(II)-oxidizing bacteria (FeOB) coexisted in anoxic sediments. Geobacter-related FeRB accounted for 5%-31% of the total Bacteria, while Gallionella-related FeOB accounted for only 0.1%-1.3%. A significant correlation between the relative abundance of poorly crystalline Fe and Geobacter spp. suggested that poorly crystalline Fe favored microbial Fe(III) reduction. Poorly crystalline Fe and Geobacter spp. were significantly associated with solid-phase Fe(II) and total inorganic phosphorus levels. Pore water Fe(II) concentrations negatively correlated with NO3(-) at all sites. We concluded that Geobacter spp. were abundant in the sediments of Lake Donghu, and the redox of Fe might participate in the cycling of nitrogen and phosphorus in sediments. These observations provided insight into the roles of microbial Fe cycling in lake sediments.
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Affiliation(s)
- Cuicui Tian
- a Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China.,b University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chunbo Wang
- a Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China.,b University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingying Tian
- a Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China.,b University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xingqiang Wu
- a Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
| | - Bangding Xiao
- a Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
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31
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Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 2015; 523:208-11. [PMID: 26083755 DOI: 10.1038/nature14486] [Citation(s) in RCA: 669] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/10/2015] [Indexed: 02/04/2023]
Abstract
A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.
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32
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High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy. PLoS One 2015; 10:e0126404. [PMID: 26018431 PMCID: PMC4446341 DOI: 10.1371/journal.pone.0126404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/01/2015] [Indexed: 11/21/2022] Open
Abstract
The study of the interaction of bacteria with surfaces requires the detection of specific bacterial groups with high spatial resolution. Here, we describe a method to rapidly and efficiently add nanogold particles to oligonucleotide probes, which target bacterial ribosomal RNA. These nanogold-labeled probes are then used in an in situ hybridization procedure that ensures both cellular integrity and high specificity. Electron microscopy subsequently enables the visualization of specific cells with high local precision on complex surface structures. This method will contribute to an increased understanding of how bacteria interact with surface structures on a sub-micron scale.
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33
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Dual Roles of Capsular Extracellular Polymeric Substances in Photocatalytic Inactivation of Escherichia coli: Comparison of E. coli BW25113 and Isogenic Mutants. Appl Environ Microbiol 2015; 81:5174-83. [PMID: 26002903 DOI: 10.1128/aem.00775-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/19/2015] [Indexed: 12/11/2022] Open
Abstract
The dual roles of capsular extracellular polymeric substances (EPS) in the photocatalytic inactivation of bacteria were demonstrated in a TiO2-UVA system, by comparing wild-type Escherichia coli strain BW25113 and isogenic mutants with upregulated and downregulated production of capsular EPS. In a partition system in which direct contact between bacterial cells and TiO2 particles was inhibited, an increase in the amount of EPS was associated with increased bacterial resistance to photocatalytic inactivation. In contrast, when bacterial cells were in direct contact with TiO2 particles, an increase in the amount of capsular EPS decreased cell viability during photocatalytic treatment. Taken together, these results suggest that although capsular EPS can protect bacterial cells by consuming photogenerated reactive species, it also facilitates photocatalytic inactivation of bacteria by promoting the adhesion of TiO2 particles to the cell surface. Fluorescence microscopy and scanning electron microscopy analyses further confirmed that high capsular EPS density led to more TiO2 particles attaching to cells and forming bacterium-TiO2 aggregates. Calculations of interaction energy, represented by extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) potential, suggested that the presence of capsular EPS enhances the attachment of TiO2 particles to bacterial cells via acid-base interactions. Consideration of these mechanisms is critical for understanding bacterium-nanoparticle interactions and the photocatalytic inactivation of bacteria.
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34
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Merkley ED, Wrighton KC, Castelle CJ, Anderson BJ, Wilkins MJ, Shah V, Arbour T, Brown JN, Singer SW, Smith RD, Lipton MS. Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis. J Proteome Res 2015; 14:1361-75. [PMID: 25496566 DOI: 10.1021/pr500983v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of G. bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.
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Affiliation(s)
- Eric D Merkley
- Signature Sciences and Technology Division, and ‡Biological Sciences Division, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
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35
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Ma S, Zhou K, Yang K, Lin D. Heteroagglomeration of oxide nanoparticles with algal cells: effects of particle type, ionic strength and pH. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:932-939. [PMID: 25495243 DOI: 10.1021/es504730k] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Discharged oxide nanoparticles (NPs) have been shown toxic to unicellular algae, yet the research on heteroagglomeration between NPs and cells as an important precondition of the toxicity is scarce. This study for the first time investigated heteroagglomerations between various NPs and algal cells (Chlorella pyrenoidosa) and analyzed influencing factors including pH and ionic strength (IS) through cosettling experiment, transmission electron microscopic (TEM) observation, and Derjaguin–Landau–Verwey–Overbeek (DLVO) calculation. The examined NPs included anatase and rutile TiO2, microporous and spherical SiO2, and α-form and β-form Al2O3. The results of cosettling experiments coincided well with the TEM observations, whereas the DLVO theory could only partly explain the NP–cell heteroagglomerations. The NP–cell heteroagglomeration for rutile TiO2 and β-form Al2O3 was weak and insensitive to pH or IS. Preferential heteroagglomeration occurred at low pH or high IS for microporous SiO2, while marked heteroagglomeration only occurred under the neutral and low IS condition for anatase TiO2. The heteroagglomeration for spherical SiO2 was insensitive to pH but increased with increasing IS, while the heteroagglomeration for α-form Al2O3 occurred at low pH and irrelevant to IS. The work will shed new light on the bionano interfacial interaction and help to understand biological effects of NPs.
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36
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Chaturongakul S, Ounjai P. Phage-host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front Microbiol 2014; 5:442. [PMID: 25191318 PMCID: PMC4138488 DOI: 10.3389/fmicb.2014.00442] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/04/2014] [Indexed: 01/21/2023] Open
Abstract
Complex interactions between bacteriophages and their bacterial hosts play significant roles in shaping the structure of environmental microbial communities, not only by genetic transduction but also by modification of bacterial gene expression patterns. Survival of phages solely depends on their ability to infect their bacterial hosts, most importantly during phage entry. Successful dynamic adaptation of bacteriophages when facing selective pressures, such as host adaptation and resistance, dictates their abundance and diversification. Co-evolution of the phage tail fibers and bacterial receptors determine bacterial host ranges, mechanisms of phage entry, and other infection parameters. This review summarizes the current knowledge about the physical interactions between tailed bacteriophages and bacterial pathogens (e.g., Salmonella enterica and Pseudomonas aeruginosa) and the influences of the phage on host gene expression. Understanding these interactions can offer insights into phage-host dynamics and suggest novel strategies for the design of bacterial pathogen biological controls.
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Affiliation(s)
- Soraya Chaturongakul
- Department of Microbiology, Faculty of Science, Mahidol University Bangkok, Thailand ; Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University Bangkok, Thailand
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37
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Comolli LR, Banfield JF. Inter-species interconnections in acid mine drainage microbial communities. Front Microbiol 2014; 5:367. [PMID: 25120533 PMCID: PMC4110969 DOI: 10.3389/fmicb.2014.00367] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/01/2014] [Indexed: 02/04/2023] Open
Abstract
Metagenomic studies are revolutionizing our understanding of microbes in the biosphere. They have uncovered numerous proteins of unknown function in tens of essentially unstudied lineages that lack cultivated representatives. Notably, few of these microorganisms have been visualized, and even fewer have been described ultra-structurally in their essentially intact, physiologically relevant states. Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. Ultrastructural findings indicate the importance of microbial interconnectedness via a range of mechanisms, including direct cytoplasmic bridges and pervasive pili. The data also suggest a variety of biological structures associated with cell-cell interfaces that lack explanation. Some may play roles in inter-species interactions. Interdependences amongst the archaea may have confounded prior isolation efforts. Overall, the findings underline knowledge gaps related to archaeal cell components and highlight the likely importance of co-evolution in shaping microbial lineages.
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Affiliation(s)
- Luis R Comolli
- Structural Biology and Imaging Department, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jill F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA
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38
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Pereira L, Mehboob F, Stams AJM, Mota MM, Rijnaarts HHM, Alves MM. Metallic nanoparticles: microbial synthesis and unique properties for biotechnological applications, bioavailability and biotransformation. Crit Rev Biotechnol 2013; 35:114-28. [DOI: 10.3109/07388551.2013.819484] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Antimicrobial activity of metals: mechanisms, molecular targets and applications. Nat Rev Microbiol 2013; 11:371-84. [PMID: 23669886 DOI: 10.1038/nrmicro3028] [Citation(s) in RCA: 1331] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metals have been used as antimicrobial agents since antiquity, but throughout most of history their modes of action have remained unclear. Recent studies indicate that different metals cause discrete and distinct types of injuries to microbial cells as a result of oxidative stress, protein dysfunction or membrane damage. Here, we describe the chemical and toxicological principles that underlie the antimicrobial activity of metals and discuss the preferences of metal atoms for specific microbial targets. Interdisciplinary research is advancing not only our understanding of metal toxicity but also the design of metal-based compounds for use as antimicrobial agents and alternatives to antibiotics.
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Zachara JM, Long PE, Bargar J, Davis JA, Fox P, Fredrickson JK, Freshley MD, Konopka AE, Liu C, McKinley JP, Rockhold ML, Williams KH, Yabusaki SB. Persistence of uranium groundwater plumes: contrasting mechanisms at two DOE sites in the groundwater-river interaction zone. JOURNAL OF CONTAMINANT HYDROLOGY 2013; 147:45-72. [PMID: 23500840 DOI: 10.1016/j.jconhyd.2013.02.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 01/10/2013] [Accepted: 02/06/2013] [Indexed: 05/22/2023]
Abstract
We examine subsurface uranium (U) plumes at two U.S. Department of Energy sites that are located near large river systems and are influenced by groundwater-river hydrologic interaction. Following surface excavation of contaminated materials, both sites were projected to naturally flush remnant uranium contamination to levels below regulatory limits (e.g., 30 μg/L or 0.126 μmol/L; U.S. EPA drinking water standard), with 10 years projected for the Hanford 300 Area (Columbia River) and 12 years for the Rifle site (Colorado River). The rate of observed uranium decrease was much lower than expected at both sites. While uncertainty remains, a comparison of current understanding suggests that the two sites have common, but also different mechanisms controlling plume persistence. At the Hanford 300 A, the persistent source is adsorbed U(VI) in the vadose zone that is released to the aquifer during spring water table excursions. The release of U(VI) from the vadose zone and its transport within the oxic, coarse-textured aquifer sediments is dominated by kinetically-limited surface complexation. Modeling implies that annual plume discharge volumes to the Columbia River are small (<one pore volume). At the Rifle site, slow oxidation of naturally reduced, contaminant U(IV) in the saturated zone and a continuous influx of U(VI) from natural, up-gradient sources influence plume persistence. Rate-limited mass transfer and surface complexation also control U(VI) migration velocity in the sub-oxic Rifle groundwater. Flux of U(VI) from the vadose zone at the Rifle site may be locally important, but it is not the dominant process that sustains the plume. A wide range in microbiologic functional diversity exists at both sites. Strains of Geobacter and other metal reducing bacteria are present at low natural abundance that are capable of enzymatic U(VI) reduction in localized zones of accumulated detrital organic carbon or after organic carbon amendment. Major differences between the sites include the geochemical nature of residual, contaminant U; the rates of current kinetic processes (both biotic and abiotic) influencing U(VI) solid-liquid distribution; the presence of detrital organic matter and the resulting spatial heterogeneity in microbially-driven redox properties; and the magnitude of groundwater hydrologic dynamics controlled by river-stage fluctuations, geologic structures, and aquifer hydraulic properties. The comparative analysis of these sites provides important guidance to the characterization, understanding, modeling, and remediation of groundwater contaminant plumes influenced by surface water interaction that are common world-wide.
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Affiliation(s)
- John M Zachara
- Pacific Northwest National Laboratory, Richland, WA 99354, USA.
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