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Li C, Zhang C, Yu T, Ma X, Yang Y, Liu X, Hou Q, Li B, Lin K, Yang Z, Wang L. Identification of soil parent materials in naturally high background areas based on machine learning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162684. [PMID: 36894078 DOI: 10.1016/j.scitotenv.2023.162684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Recently, farmlands with high geological background of Cd derived from carbonate rock (CA) and black shale areas (BA) have received wide attention. However, although both CA and BA belong to high geological background areas, the mobility of soil Cd differs significantly between them. In addition to the difficulty in reaching the parent material in deep soil, it is challenging to perform land use planning in high geological background areas. This study attempts to determine the key soil geochemical parameters related to the spatial patterns of lithology and the main factors influencing the geochemical behavior of soil Cd, and ultimately uses them and machine-learning methods to identify CA and BA. In total, 10,814 and 4323 surface soil samples were collected from CA and BA, respectively. Hot spot analysis revealed that soil properties and soil Cd were significantly correlated with the underlying bedrock, except for TOC and S. Further research confirmed that the concentration and mobility of Cd in high geological background areas were mainly affected by pH and Mn. The soil parent materials were then predicted using artificial neural network (ANN), random forest (RF) and support vector machine (SVM) models. The ANN and RF models showed higher Kappa coefficients and overall accuracies than those of the SVM model, suggesting that ANNs and RF have the potential to predict soil parent materials from soil data, which might help in ensuring safe land use and coordinating activities in high geological background areas.
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Affiliation(s)
- Cheng Li
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Chaosheng Zhang
- School of Geography, Archaeology & Irish Studies, National University of Ireland, University Road, Galway H91 CF50, Ireland
| | - Tao Yu
- School of Science, China University of Geosciences, Beijing 100083, PR China
| | - Xudong Ma
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Yeyu Yang
- Key Laboratory of Karst Dynamics, MNR&GZAR, Institute of Krast Geology, CAGS, Guilin 541004, China
| | - Xu Liu
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Qingye Hou
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Bo Li
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Kun Lin
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China
| | - Zhongfang Yang
- School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, PR China.
| | - Lei Wang
- Guangxi Bureau of Geology & Mineral Prospecting & Exploitation, Nanning 530023, PR China
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2
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Potysz A. Microbial influence and dynamics of metallurgical waste dissolution in a landfill and recovery context: A multi-phase experimental approach and geochemical model. CHEMOSPHERE 2023; 311:136964. [PMID: 36419268 DOI: 10.1016/j.chemosphere.2022.136964] [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: 12/31/2021] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
The effects of abiotic and biotic dissolution on metallurgical wastes (slag and matte) were examined combining a multi-phase experimental approach with a solution renewal and geochemical model. The conditions studied included the exposure of solid wastes to water, a growth medium, and heterotrophic siderophore-producing bacterium Pseudomonas fluorescens. Quantification of the dissolution was performed by tracking the element release, whereas immobilization processes were predicted by applying a geochemical model and scanning electron microscopic observations. The results demonstrated that the phase composition of these wastes subjected to (bio)dissolution was linked to the behavior of Pseudomonas fluorescens, with the deteriorative dissolution effects varying between slag and matte. The contribution level of the bacteria to the mobilization of the elements exhibited the following order: Cu > Pb > Zn; however, the entrapment of these elements in biomass affected the amount of metals released. Copper-bearing sulfides and metallic lead-bearing phases were specifically found to be highly susceptible to (bio)dissolution. Moreover, the bacteria contribution to the Zn release from sphalerite played less of an important role compared to its abiotic mobilization. Overall, this study underlines the important role of bacteria at the interface where wastes are exposed to weathering, resulting in accelerated dissolution. The application of bacteria to Co and Mo recovery is an important approach to the detoxification of landfilled wastes.
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Affiliation(s)
- Anna Potysz
- University of Wroclaw, Faculty of Earth Sciences and Environmental Management, Institute of Geological Sciences, Cybulskiego 30, 50-205, Wrocław, Poland.
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3
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Gaylarde C, Little B. Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153193. [PMID: 35122860 DOI: 10.1016/j.scitotenv.2022.153193] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.
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Affiliation(s)
- Christine Gaylarde
- Department of Microbiology and Plant Biology, Oklahoma University, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Brenda Little
- BJ Little Corrosion Consulting, LLC, 6528 Alakoko Drive, Diamondhead, MS 39525, USA.
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4
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McMillan HM, Kuehn MJ. The extracellular vesicle generation paradox: a bacterial point of view. EMBO J 2021; 40:e108174. [PMID: 34636061 PMCID: PMC8561641 DOI: 10.15252/embj.2021108174] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
All bacteria produce secreted vesicles that carry out a variety of important biological functions. These extracellular vesicles can improve adaptation and survival by relieving bacterial stress and eliminating toxic compounds, as well as by facilitating membrane remodeling and ameliorating inhospitable environments. However, vesicle production comes with a price. It is energetically costly and, in the case of colonizing pathogens, it elicits host immune responses, which reduce bacterial viability. This raises an interesting paradox regarding why bacteria produce vesicles and begs the question as to whether the benefits of producing vesicles outweigh their costs. In this review, we discuss the various advantages and disadvantages associated with Gram-negative and Gram-positive bacterial vesicle production and offer perspective on the ultimate score. We also highlight questions needed to advance the field in determining the role for vesicles in bacterial survival, interkingdom communication, and virulence.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and MicrobiologyDuke UniversityDurhamNCUSA
| | - Meta J Kuehn
- Department of BiochemistryDuke UniversityDurhamNCUSA
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5
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Singh KN, Narzary D. Heavy metal tolerance of bacterial isolates associated with overburden strata of an opencast coal mine of Assam (India). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:63111-63126. [PMID: 34218386 DOI: 10.1007/s11356-021-15153-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/23/2021] [Indexed: 05/21/2023]
Abstract
Coal overburden strata (OBS) vary in thickness, geochemical composition, and physical properties from stratum to stratum. Here, we enumerated the cultivable bacterial diversity and their distribution in different OBS taken from the opencast mining of Tikok colliery, Assam. The pH of the coal OBS ranged from 2.46 to 7.93, but 73% of the OBS was acidic. The OBS samples were mostly of shale types except for a few that were sandstone, mudstone, and red soil. The bacterial CFUs per gram OBS samples were highly diverse ranging from 52 to 57.4×104. A total of 79 bacterial pure culture isolates belonging to 19 genera, 12 family, and 3 phyla (Actinobacteria, Firmicutes, and Proteobacteria) were recovered in nutrient agar plates. Firmicutes appeared dominant over the others. All the isolates were screened for heavy metal tolerance in broth culture augmented with five different metals (Ni2+, Cu2+, Cr6+, As3+, and Cd2+) separately. The number of isolates that showed tolerance was 95% for Cr6+, 69.6% for Ni2+, 50.6% each for As3+ and Cu2+, and 7.6% for Cd2+. The bacterial isolates with high metal tolerance, i.e., 5 to 12 mM could be promising for bioremediation of Ni2+, Cu2+, Cr6+, and As3+ from the sites contaminated with these heavy metals.
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Affiliation(s)
- Khomdram Niren Singh
- Microbiology and Molecular Systematics Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, 781014, India
| | - Diganta Narzary
- Microbiology and Molecular Systematics Laboratory, Department of Botany, Gauhati University, Guwahati, Assam, 781014, India.
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6
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McMillan HM, Rogers N, Wadle A, Hsu-Kim H, Wiesner MR, Kuehn MJ, Hendren CO. Microbial vesicle-mediated communication: convergence to understand interactions within and between domains of life. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2021; 23:664-677. [PMID: 33899070 DOI: 10.1039/d1em00022e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
All cells produce extracellular vesicles (EVs). These biological packages contain complex mixtures of molecular cargo and have a variety of functions, including interkingdom communication. Recent discoveries highlight the roles microbial EVs may play in the environment with respect to interactions with plants as well as nutrient cycling. These studies have also identified molecules present within EVs and associated with EV surfaces that contribute to these functions. In parallel, studies of engineered nanomaterials have developed methods to track and model small particle behavior in complex systems and measure the relative importance of various surface features on transport and function. While studies of EV behavior in complex environmental conditions have not yet employed transdisciplinary approaches, it is increasingly clear that expertise from disparate fields will be critical to understand the role of EVs in these systems. Here, we outline how the convergence of biology, soil geochemistry, and colloid science can both develop and address questions surrounding the basic principles governing EV-mediated interkingdom interactions.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas Rogers
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Austin Wadle
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Mark R Wiesner
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Meta J Kuehn
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA and Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Christine Ogilvie Hendren
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA and Department of Geological and Environmental Sciences, Appalachian State University, Boone, NC 28608, USA.
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7
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Jung P, Baumann K, Emrich D, Springer A, Felde VJ, Dultz S, Baum C, Frank M, Büdel B, Leinweber P. Lichens Bite the Dust - A Bioweathering Scenario in the Atacama Desert. iScience 2020; 23:101647. [PMID: 33103085 PMCID: PMC7578742 DOI: 10.1016/j.isci.2020.101647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/25/2020] [Accepted: 10/01/2020] [Indexed: 11/23/2022] Open
Abstract
Bioweathering mediated by microorganisms plays a significant role in biogeochemical cycles on global scales over geological timescales. Single processes induced by specific taxa have been described but could rarely be demonstrated for complex communities that dominate whole landscapes. The recently discovered grit crust of the coastal Atacama Desert, which is a transitional community between a cryptogamic ground cover and a rock-bound lithic assemblage, offers the unique chance to elucidate various bioweathering processes that occur simultaneously. Here, we present a bioweathering scenario of this biocenosis including processes such as penetration of the lithomatrix, microbial responses to wet-dry cycles, alkalinolysis, enzyme activity, and mineral re-localization. Frequently occurring fog, for example, led to a volume increase of microorganisms and the lithomatrix. This, together with pH shifts and dust accumulation, consequently results in biophysical breakdown and the formation of a terrestrial protopedon, an initial stage of pedogenesis fueled by the grit crust.
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Affiliation(s)
- Patrick Jung
- Applied Logistics and Polymer Sciences, University of Applied Sciences Kaiserslautern, Carl-Schurz-Straße 10-16, 66953 Pirmasens, Germany
| | - Karen Baumann
- Faculty of Agricultural and Environmental Science, Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18051 Rostock, Germany
| | - Dina Emrich
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Applied Vegetation Ecology, Tennenbacher Str. 4, 79106 Freiburg, Germany
| | - Armin Springer
- Medical Biology and Electron Microscopy Centre, University Medicine Rostock, Strempelstraße 14, 18057 Rostock, Germany
- Department Life, Light and Matter, University of Rostock, 18051 Rostock, Germany
| | - Vincent J.M.N.L. Felde
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Nordbahnhofstr. 1a, 37213 Witzenhausen, Germany
| | - Stefan Dultz
- Institute of Soil Science, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Christel Baum
- Faculty of Agricultural and Environmental Science, Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18051 Rostock, Germany
| | - Marcus Frank
- Medical Biology and Electron Microscopy Centre, University Medicine Rostock, Strempelstraße 14, 18057 Rostock, Germany
- Department Life, Light and Matter, University of Rostock, 18051 Rostock, Germany
| | - Burkhard Büdel
- Plant Ecology and Systematics, University of Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
| | - Peter Leinweber
- Faculty of Agricultural and Environmental Science, Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18051 Rostock, Germany
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8
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Samuels T, Bryce C, Landenmark H, Marie‐Loudon C, Nicholson N, Stevens AH, Cockell C. Microbial Weathering of Minerals and Rocks in Natural Environments. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/9781119413332.ch3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Romaniuk K, Golec P, Dziewit L. Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. Front Microbiol 2018; 9:3144. [PMID: 30619210 PMCID: PMC6305408 DOI: 10.3389/fmicb.2018.03144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Piotr Golec
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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10
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Wang YL, Wang Q, Yuan R, Sheng XF, He LY. Isolation and characterization of mineral-dissolving bacteria from different levels of altered mica schist surfaces and the adjacent soil. World J Microbiol Biotechnol 2018; 35:2. [PMID: 30536084 DOI: 10.1007/s11274-018-2573-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 12/03/2018] [Indexed: 10/27/2022]
Abstract
Microorganisms play important role in mineral weathering. However, little is known about rock-associated mineral-dissolving bacteria. In this study, 129 bacterial isolates were obtained from the less and more weathered mica schist surfaces and the adjacent soil and characterized for mineral dissolving activity, population, and the linkage of rock weathering level and distribution of the bacteria. Among the 129 isolates, 112 isolates could dissolve biotite. The relative abundance of the highly effective Fe solubilizers was significantly higher on the more altered rock surface (89.6%) than in the soil (51.2%) and on the less altered rock surface (22.5%), while the relative abundance of the highly effective Si solubilizers was significantly higher in the soil (65.9%) than on the more (41.7%) and less (12.5%) altered rock surfaces. Furthermore, 17.5-42.5%, 87.5%, and 60.9-90.2% of the highly effective acid- and siderophore-producing isolates were obtained in the less and more weathered rocks and the soil, respectively. The mineral-dissolving bacteria belonged to 18 genera and Burkholderia, Bacillus, and Paenibacillus were the dominant and highly effective mineral-dissolving bacteria. Phylogenetic analysis found 2, 9, and 5 bacterial species in the highly effective mineral-dissolving bacteria on the less and more altered rock surfaces and in the soil, respectively. The results showed the abundant and diverse mineral-dissolving bacterial populations on the more weathered rock surfaces. The results also suggested distinct mineral-dissolving activities and mechanisms of the bacteria and highlighted the possibility for the development of bacterial inocula for plant nutrition improvement in silicate mineral-rich soils.
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Affiliation(s)
- Yuan Li Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qi Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Rui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xia Fang Sheng
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Lin Yan He
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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11
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Włodarczyk A, Lirski M, Fogtman A, Koblowska M, Bidziński G, Matlakowska R. The Oxidative Metabolism of Fossil Hydrocarbons and Sulfide Minerals by the Lithobiontic Microbial Community Inhabiting Deep Subterrestrial Kupferschiefer Black Shale. Front Microbiol 2018; 9:972. [PMID: 29867875 PMCID: PMC5962744 DOI: 10.3389/fmicb.2018.00972] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
Black shales are one of the largest reservoirs of fossil organic carbon and inorganic reduced sulfur on Earth. It is assumed that microorganisms play an important role in the transformations of these sedimentary rocks and contribute to the return of organic carbon and inorganic sulfur to the global geochemical cycles. An outcrop of deep subterrestrial ~256-million-year-old Kupferschiefer black shale was studied to define the metabolic processes of the deep biosphere important in transformations of organic carbon and inorganic reduced sulfur compounds. This outcrop was created during mining activity 12 years ago and since then it has been exposed to the activity of oxygen and microorganisms. The microbial processes were described based on metagenome and metaproteome studies as well as on the geochemistry of the rock. The microorganisms inhabiting the subterrestrial black shale were dominated by bacterial genera such as Pseudomonas, Limnobacter, Yonghaparkia, Thiobacillus, Bradyrhizobium, and Sulfuricaulis. This study on black shale was the first to detect archaea and fungi, represented by Nitrososphaera and Aspergillus genera, respectively. The enzymatic oxidation of fossil aliphatic and aromatic hydrocarbons was mediated mostly by chemoorganotrophic bacteria, but also by archaea and fungi. The dissimilative enzymatic oxidation of primary reduced sulfur compounds was performed by chemolithotrophic bacteria. The geochemical consequences of microbial activity were the oxidation and dehydrogenation of kerogen, as well as oxidation of sulfide minerals.
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Affiliation(s)
- Agnieszka Włodarczyk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Koblowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | | | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
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12
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Wang Q, Zhang Z, Zhu Y, He L, Sheng X. Impact of poxB, pta, and ackA genes on mineral-weathering of Enterobacter cloacae S71. J Basic Microbiol 2018; 58:633-642. [PMID: 29732559 DOI: 10.1002/jobm.201800013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/17/2018] [Accepted: 04/12/2018] [Indexed: 11/11/2022]
Abstract
In this study, biotite weathering behaviors were compared between mineral-weathering bacteria Enterobacter cloacae S71, mutant strains created by the deletion of poxB, pta, and ackA genes involved in acetate formation, and their complemented strains. Compared to strain S71, a decrease in bacterial growth was observed during the early and middle stages for the mutant ΔpoxB and at the middle and later stages for the mutants Δpta and ΔackA. Dissolved Al and Fe concentrations were lower during the early stage for strain ΔpoxB, at the early or middle stage for strain Δpta, and at the middle and later stages and throughout the weathering process for strain ΔackA, compared to strain S71. Acetate production was depressed during the early stage for strain ΔpoxB, at the early and middle stages for strain Δpta, and throughout the weathering process for strain ΔackA. Overall, the ackA gene exhibited a larger impact on dissolved Fe and acetate concentrations than both the poxB and pta genes. Reduced bacterial growth and lower dissolved Al, Fe, and acetate concentrations recovered by the complemented strains. These results show that strain S71 promoted mineral weathering through the production of acetic acid with distinctive impacts by the genes involved in acetate.
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Affiliation(s)
- Qi Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Zhendong Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Ying Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Linyan He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, PR China
| | - Xiafang Sheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, PR China
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13
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Barthen R, Karimzadeh L, Gründig M, Grenzer J, Lippold H, Franke K, Lippmann-Pipke J. Glutamic acid leaching of synthetic covellite - A model system combining experimental data and geochemical modeling. CHEMOSPHERE 2018; 196:368-376. [PMID: 29316462 DOI: 10.1016/j.chemosphere.2017.12.138] [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: 12/21/2016] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
For Kupferschiefer mining established pyrometallurgical and acidic bioleaching methods face numerous problems. This is due to the finely grained and dispersed distribution of the copper minerals, the complex mineralogy, comparably low copper content, and the possibly high carbonate and organic content in this ore. Leaching at neutral pH seemed worth a try: At neutral pH the abundant carbonates do not need to be dissolved and therewith would not consume excessive amounts of provided acids. Certainly, copper solubility at neutral pH is reduced compared to an acidic environment; however, if copper complexing ligands would be supplied abundantly, copper contents in the mobile phase could easily reach the required economic level. We set up a model system to study the effect of parameters such as pH, microorganisms, microbial metabolites, and organic ligands on covellite leaching to get a better understanding of the processes in copper leaching at pH ≥ 6. With this model system we could show that glutamic acid and the microbial siderophore desferrioxamine B promote covellite dissolution. Both experimental and modeling data showed that pH is an important parameter in covellite dissolution. An increase of pH from 6 to 9 could elevate copper extraction in the presence of glutamic acid by a factor of five. These results have implications for both development of a biotechnological process regarding metal extraction from Kupferschiefer, and for the interaction of bacterial metabolites with the lithosphere and potential mobilization of heavy metals in alkaline environments.
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Affiliation(s)
- R Barthen
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Dresden, Germany
| | - L Karimzadeh
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Leipzig, Germany
| | - M Gründig
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Leipzig, Germany
| | - J Grenzer
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Ion Beam Physics and Materials Research, Dresden, Germany
| | - H Lippold
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Leipzig, Germany.
| | - K Franke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Leipzig, Germany
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14
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Goes KCGPD, Lovato GM, Andrade DS. Composition of bacterial community in enrichment cultures of shale by-products from Irati Formation, Brazil. Braz J Microbiol 2018; 49:742-748. [PMID: 29551640 PMCID: PMC6175702 DOI: 10.1016/j.bjm.2017.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 12/05/2017] [Accepted: 12/27/2017] [Indexed: 01/20/2023] Open
Abstract
We examined microbial communities from enriched fine and retorted shale particles using sequencing of V4 variable region of 16S rRNA. High number of microbial genera was found in both enriched shale by-products that were dominate by Actinobacteria, Firmicutes and Proteobacteria, showing differences due to microbial colonization after the pyrolysis process.
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Affiliation(s)
- Kelly Campos Guerra Pinheiro de Goes
- Universidade Estadual de Londrina, Centro de Ciências Biológicas, Departamento de Biologia Geral, Londrina, PR, Brazil; Instituto Agronômico do Paraná (IAPAR), Londrina, PR, Brazil
| | | | - Diva S Andrade
- Instituto Agronômico do Paraná (IAPAR), Londrina, PR, Brazil.
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15
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Meyer-Dombard DR, Casar CP, Simon AG, Cardace D, Schrenk MO, Arcilla CA. Biofilm formation and potential for iron cycling in serpentinization-influenced groundwater of the Zambales and Coast Range ophiolites. Extremophiles 2018; 22:407-431. [PMID: 29450709 DOI: 10.1007/s00792-018-1005-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 02/05/2018] [Indexed: 02/01/2023]
Abstract
Terrestrial serpentinizing systems harbor microbial subsurface life. Passive or active microbially mediated iron transformations at alkaline conditions in deep biosphere serpentinizing ecosystems are understudied. We explore these processes in the Zambales (Philippines) and Coast Range (CA, USA) ophiolites, and associated surface ecosystems by probing the relevance of samples acquired at the surface to in situ, subsurface ecosystems, and the nature of microbe-mineral associations in the subsurface. In this pilot study, we use microcosm experiments and batch culturing directed at iron redox transformations to confirm thermodynamically based predictions that iron transformations may be important in subsurface serpentinizing ecosystems. Biofilms formed on rock cores from the Zambales ophiolite on surface and in-pit associations, confirming that organisms from serpentinizing systems can form biofilms in subsurface environments. Analysis by XPS and FTIR confirmed that enrichment culturing utilizing ferric iron growth substrates produced reduced, magnetic solids containing siderite, spinels, and FeO minerals. Microcosms and enrichment cultures supported organisms whose near relatives participate in iron redox transformations. Further, a potential 'principal' microbial community common to solid samples in serpentinizing systems was identified. These results indicate collectively that iron redox transformations should be more thoroughly and universally considered when assessing the function of terrestrial subsurface ecosystems driven by serpentinization.
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Affiliation(s)
- D'Arcy R Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA.
| | - Caitlin P Casar
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Alexander G Simon
- Department of Earth and Environmental Sciences, University of Illinois at Chicago, m/c 186, 845 W. Taylor St., Chicago, IL, 60515, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, IL, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Carlo A Arcilla
- National Institute of Geological Sciences, University of the Philippines, Diliman, Quezon City, Philippines
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16
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Xi J, Wei M, Tang B. Differences in weathering pattern, stress resistance and community structure of culturable rock-weathering bacteria between altered rocks and soils. RSC Adv 2018; 8:14201-14211. [PMID: 35540768 PMCID: PMC9079951 DOI: 10.1039/c8ra01268g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 03/24/2018] [Indexed: 12/04/2022] Open
Abstract
In this study, we isolated and characterized rock-weathering bacteria from the surfaces of less and more altered tuffs, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in these rocks and soils. Using a moderate-nutrition medium, we obtained 150 isolates from the rocks and soils. The rock-weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, and Fe released from tuff under aerobic conditions. Based on the potential of the bacterial influence on the element releases, the isolates could be grouped into highly, moderately, and least effective element solubilizers, respectively. Significantly more highly effective Al and Fe solubilizers were observed in the altered rocks, while the soils had more highly effective Si solubilizers. Furthermore, more isolates from the altered rocks significantly acidified the culture medium in the rock weathering process. Dynamic changes in the element release showed the distinct element releasing patterns of three selected isolates. More isolates from the altered rocks could grow at 4 °C or at 55 °C or at pH 4. Some isolates from the altered rocks could grow at pH 10 and with 10–15% (w/v) NaCl. The altered rocks and the soils existed in diverse and different highly weathering-specific culturable rock-weathering community structures. The changes in the culturable weathering communities between the altered rocks and the soils were attributable not only to major bacterial groups but also to a change in the minor population structure. Rock-weathering bacteria from the surfaces of less and more altered tuffs were isolated and characterized, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in the rocks and soils.![]()
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Affiliation(s)
- Jun Xi
- College of Life Science
- Bengbu Medical College
- Bengbu 233030
- P. R. China
| | - Meili Wei
- College of Life Science
- Bengbu Medical College
- Bengbu 233030
- P. R. China
| | - Bikui Tang
- College of Life Science
- Bengbu Medical College
- Bengbu 233030
- P. R. China
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17
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Stasiuk R, Włodarczyk A, Karcz P, Janas M, Skłodowska A, Matlakowska R. Bacterial weathering of fossil organic matter and organic carbon mobilization from subterrestrial Kupferschiefer black shale: long-term laboratory studies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:459-466. [PMID: 28618204 DOI: 10.1111/1758-2229.12559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/01/2017] [Accepted: 06/08/2017] [Indexed: 06/07/2023]
Abstract
A large part of the organic carbon present in the lithosphere is trapped in fossil organic matter deposited in sedimentary rocks. Only specialized microorganisms are able to degrade it contributing to the return of the carbon to the global cycle. The role of bacteria in this process is not yet completely understood. In the present laboratory studies, subterrestrial organic-rich ∼256-million-year-old Kupferschiefer black shale was exposed to the activity of an indigenous consortium of lithobiontic bacteria for 365 days under aerobic conditions. An interdisciplinary research approach was applied, consisting of a detailed comparison of the chemical composition of extractable bitumens as well as resistant to extraction kerogen of the unweathered black shale to that of the bioweathered and chemically weathered, identification of mobilized organic compounds and spectrometry-based determination of proteomic composition of the bacterial biofilm. The oxidative bioweathering of bitumens and kerogen was confirmed. The mobilization of organic carbon in the form of oxidized organic compounds, such as monohydroxy and dihydroxy alcohols, aldehydes, monocarboxylic and dicarboxylic acids and esters due to the microbial activity, was documented. The enzymes crucial for the aerobic metabolism of aliphatic and aromatic hydrocarbons such as monooxygenases and dehydrogenases were identified in the epilithic biofilm inhabiting the black shale.
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Affiliation(s)
- Robert Stasiuk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Agnieszka Włodarczyk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Przemysław Karcz
- Polish Geological Institute National Research Institute, Wrocław, 53-122, Poland
| | - Marcin Janas
- Polish Geological Institute National Research Institute, Warsaw, 00-975, Poland
| | - Aleksandra Skłodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, 02-096, Poland
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18
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Podolich O, Zaets I, Kukharenko O, Orlovska I, Reva O, Khirunenko L, Sosnin M, Haidak A, Shpylova S, Rohutskyy I, Kharina A, Skoryk М, Kremenskoy M, Klymchuk D, Demets R, de Vera JP, Kozyrovska N. The First Space-Related Study of a Kombucha Multimicrobial Cellulose-Forming Community: Preparatory Laboratory Experiments. ORIGINS LIFE EVOL B 2017; 47:169-185. [PMID: 27025932 DOI: 10.1007/s11084-016-9483-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/31/2015] [Indexed: 12/18/2022]
Abstract
Biofilm-forming microbial communities are known as the most robust assemblages that can survive in harsh environments. Biofilm-associated microorganisms display greatly increased resistance to physical and chemical adverse conditions, and they are expected to be the first form of life on Earth or anywhere else. Biological molecules synthesized by biofilm -protected microbiomes may serve as markers of the nucleoprotein life. We offer a new experimental model, a kombucha multimicrobial culture (KMC), to assess a structural integrity of a widespread microbial polymer - cellulose - as a biosignature of bacteria-producers for the multipurpose international project "BIOlogical and Mars Experiment (BIOMEX)", which aims to study the vitality of pro- and eukaryotic organisms and the stability of organic biomolecules in contact with minerals to analyze the detectability of life markers in the context of a planetary background. In this study, we aimed to substantiate the detectability of mineralized cellulose with spectroscopy and to study the KMC macrocolony phenotype stability under adverse conditions (UV, excess of inorganics etc.). Cellulose matrix of the KMC macrocolony has been mineralized in the mineral-water interface under assistance of KMC-members. Effect of bioleached ions on the cellulose matrix has been visible, and the FT-IR spectrum proved changes in cellulose structure. However, the specific cellulose band vibration, confirming the presence of β(1,4)-linkages between monomers, has not been quenched by secondary minerals formed on the surface of pellicle. The cellulose-based KMC macrocolony phenotype was in a dependence on extracellular matrix components (ionome, viriome, extracellular membrane vesicles), which provided its integrity and rigidness in a certain extent under impact of stressful factors.
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Affiliation(s)
- O Podolich
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine.
| | - I Zaets
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine
| | - O Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine
| | - I Orlovska
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine
| | - O Reva
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | | | - M Sosnin
- Institute of Physics of NASU, Kyiv, Ukraine
| | - A Haidak
- Institute of Biology, Kyiv National Taras Shevchenko University, Kyiv, Ukraine
| | - S Shpylova
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine
| | | | - A Kharina
- Institute of Biology, Kyiv National Taras Shevchenko University, Kyiv, Ukraine
| | | | | | - D Klymchuk
- Institute of Botany of NASU, Kyiv, Ukraine
| | - R Demets
- ESA/ESTEC, Noordwijk, The Netherlands
| | - J-P de Vera
- German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Berlin, Germany
| | - N Kozyrovska
- Institute of Molecular Biology and Genetics of NASU, Acad. Zabolotnoho str., 150, 03680, Kyiv, Ukraine
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19
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Origin of the El Dragón Selenium Mineralization, Quijarro Province, Potosí, Bolivia. MINERALS 2017. [DOI: 10.3390/min7050068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Mühling M, Poehlein A, Stuhr A, Voitel M, Daniel R, Schlömann M. Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH. Front Microbiol 2016; 7:2082. [PMID: 28066396 PMCID: PMC5178258 DOI: 10.3389/fmicb.2016.02082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/08/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus "Ferrovum" and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of "Ferrovum" and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis.
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Affiliation(s)
- Martin Mühling
- Institute of Biological Sciences, Technische Universität Bergakademie Freiberg Freiberg, Germany
| | - Anja Poehlein
- Georg-August-University Göttingen, Genomic and Applied Microbiology and Göttingen Genomics, Laboratory Göttingen, Germany
| | - Anna Stuhr
- Institute of Biological Sciences, Technische Universität Bergakademie Freiberg Freiberg, Germany
| | - Matthias Voitel
- Institute of Biological Sciences, Technische Universität Bergakademie Freiberg Freiberg, Germany
| | - Rolf Daniel
- Georg-August-University Göttingen, Genomic and Applied Microbiology and Göttingen Genomics, Laboratory Göttingen, Germany
| | - Michael Schlömann
- Institute of Biological Sciences, Technische Universität Bergakademie Freiberg Freiberg, Germany
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21
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Microorganisms meet solid minerals: interactions and biotechnological applications. Appl Microbiol Biotechnol 2016; 100:6935-46. [DOI: 10.1007/s00253-016-7678-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 06/08/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
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22
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Włodarczyk A, Szymańska A, Skłodowska A, Matlakowska R. Determination of factors responsible for the bioweathering of copper minerals from organic-rich copper-bearing Kupferschiefer black shale. CHEMOSPHERE 2016; 148:416-425. [PMID: 26835647 DOI: 10.1016/j.chemosphere.2016.01.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/07/2016] [Accepted: 01/15/2016] [Indexed: 06/05/2023]
Abstract
The aim of this study was to investigate the bioweathering of copper minerals present in the alkaline, copper-bearing and organic-rich Kupferschiefer black shale through the action of a consortium of indigenous lithobiontic, heterotrophic, neutrophilic bacteria isolated from this sedimentary rock. The involvement of microorganisms in the direct/enzymatic bioweathering of fossil organic matter of the rock was confirmed. As a result of bacterial activity, a spectrum of various organic compounds such as urea and phosphoric acid tributyl ester were released from the rock. These compounds indirectly act on the copper minerals occurring in the rock and cause them to weather. This process was reflected in the mobilization of copper, iron and sulfur and in changes in the appearance of copper minerals observed under reflected light. The potential role of identified enzymes in biodegradation of fossil organic matter and role of organic compounds released from black shale as a result of this process in copper minerals weathering was discussed. The presented results provide a new insight into the role of chemical compounds released by bacteria during fossil organic matter bioweathering potentially important in the cycling of copper and iron deposited in the sedimentary rock. The originality of the described phenomenon lies in the fact that the bioweathering of fossil organic matter and, consequently, of copper minerals occur simultaneously in the same environment, without any additional sources of energy, electrons and carbon.
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Affiliation(s)
- Agnieszka Włodarczyk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Agata Szymańska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Aleksandra Skłodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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23
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Ullrich SR, Poehlein A, Tischler JS, González C, Ossandon FJ, Daniel R, Holmes DS, Schlömann M, Mühling M. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PLoS One 2016; 11:e0146832. [PMID: 26808278 PMCID: PMC4725956 DOI: 10.1371/journal.pone.0146832] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/22/2015] [Indexed: 02/07/2023] Open
Abstract
Background Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce. Objective In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12. Phylogeny and Lifestyle The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in “Ferrovum” strain JA12. Therefore, the results of the present study extend our understanding of the genus “Ferrovum” and provide a comprehensive framework for future comparative genome and metagenome studies.
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Affiliation(s)
- Sophie R. Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
| | - Anja Poehlein
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - Judith S. Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Carolina González
- Center for System Biotechnology, Bio-Computing Division and Applied Genetics Division, Fraunhofer Chile Research Foundation, Avenida Mariano Sánchez Fontecilla 310, Santiago, Chile, and Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482, and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Francisco J. Ossandon
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Rolf Daniel
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
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24
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Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, Schlüter A, Pühler A, Bartosik D. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Front Microbiol 2015; 6:152. [PMID: 26074880 PMCID: PMC4447125 DOI: 10.3389/fmicb.2015.00152] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/09/2015] [Indexed: 12/31/2022] Open
Abstract
The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland). It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m) Lubin mine were taken and 20 bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e., they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Adam Pyzik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Magdalena Szuplewska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Sebastian Mielnicki
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw Warsaw, Poland
| | - Daniel Wibberg
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, Center for Biotechnology (CeBiTec), Bielefeld University Bielefeld, Germany
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw Warsaw, Poland
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25
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Włodarczyk A, Stasiuk R, Skłodowska A, Matlakowska R. Extracellular compounds produced by bacterial consortium promoting elements mobilization from polymetallic Kupferschiefer black shale (Fore-Sudetic Monocline, Poland). CHEMOSPHERE 2015; 122:273-279. [PMID: 25522852 DOI: 10.1016/j.chemosphere.2014.11.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 11/18/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Culture experiments employing Fe-deficient medium showed that a consortium of indigenous microorganisms isolated from Kupferschiefer black shale produced a mixture of extracellular compounds containing siderophores which could form complexes with a wide range of elements and were able to mediate element mobilization from polymetallic black shale. The mobilization of a diverse array of elements including a number of essential trace elements (Co, Cu, Mn, Mo, Zn) and toxic species (As) was shown. Since the bacteria used in this study were originally obtained from a subsurface copper deposit, these results highlight the potential importance of extracellular compounds in biogeochemical cycles of elements in underground environment and their ecological significance in promoting the uptake of essential trace metals and resistance to toxic elements.
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Affiliation(s)
- Agnieszka Włodarczyk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Robert Stasiuk
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Aleksandra Skłodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Renata Matlakowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Li J, Sun W, Wang S, Sun Z, Lin S, Peng X. Bacteria diversity, distribution and insight into their role in S and Fe biogeochemical cycling during black shale weathering. Environ Microbiol 2014; 16:3533-47. [DOI: 10.1111/1462-2920.12536] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 06/09/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Jiwei Li
- Sanya Institute of Deep-Sea Science and Engineering; Chinese Academy of Sciences; Sanya 572000 China
| | - Weimin Sun
- Department of Environmental Science; Rutgers University; New Brunswick NJ 08901 USA
| | - Shiming Wang
- Faculty of Geosciences and Environmental Engineering; Southwest Jiaotong University; Chengdu 610031 China
| | - Zhilei Sun
- Department of Marine Mineral Resources; Qingdao Institute of Marine Geology; Qingdao 266071 China
| | - Sixiang Lin
- Faculty of Geosciences and Environmental Engineering; Southwest Jiaotong University; Chengdu 610031 China
| | - Xiaotong Peng
- Sanya Institute of Deep-Sea Science and Engineering; Chinese Academy of Sciences; Sanya 572000 China
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Rajpert L, Skłodowska A, Matlakowska R. Biotransformation of copper from Kupferschiefer black shale (Fore-Sudetic Monocline, Poland) by yeast Rhodotorula mucilaginosa LM9. CHEMOSPHERE 2013; 91:1257-1265. [PMID: 23490182 DOI: 10.1016/j.chemosphere.2013.02.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/06/2013] [Accepted: 02/07/2013] [Indexed: 06/01/2023]
Abstract
This study describes the yeast Rhodotorula mucilaginosa strain LM9 isolated from copper-bearing, organic-rich Kupferschiefer black shale and its role in copper biotransformation. Strain LM9 exhibited great ability to simultaneously mobilize and immobilize copper from this sedimentary rock. In addition, it showed considerable resistance to copper and high uptake of this metal. Moreover, malic and oxalic acid as well as siderophore (rhodotorulic acid) produced by this strain enhanced its resistance by promoting the mobilization and complexation of copper from black shale. These processes, characterized here under laboratory conditions, are assumed to play a role in copper cycling in black shale as well as in the adaptation of strain LM9 to the conditions prevailing in its natural mine habitat. The findings of this study indicate that yeast strain LM9 might be used for the recovery of copper particularly from alkaline or slightly neutral ores in a non-chemical environmentally-friendly procedure.
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Affiliation(s)
- Liwia Rajpert
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Manning AJ, Kuehn MJ. Functional advantages conferred by extracellular prokaryotic membrane vesicles. J Mol Microbiol Biotechnol 2013; 23:131-41. [PMID: 23615201 DOI: 10.1159/000346548] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The absence of subcellular organelles is a characteristic typically used to distinguish prokaryotic from eukaryotic cells. But recent discoveries do not support this dogma. Over the past 50 years, researchers have begun to appreciate and characterize Gram-negative bacterial outer membrane-derived vesicles and Gram-positive and archaeal membrane vesicles. These extracellular, membrane-bound organelles can perform a variety of functions, including binding and delivery of DNA, transport of virulence factors, protection of the cell from outer membrane targeting antimicrobials and ridding the cell of toxic envelope proteins. Here, we review the contributions of these extracellular organelles to prokaryotic physiology and compare these with the contributions of the bacterial interior membrane-bound organelles responsible for harvesting light energy and for generating magnetic crystals of heavy metals. Understanding the roles of these multifunctional extracellular vesicle organelles as microbial tools will help us to better realize the diverse interactions that occur in our polymicrobial world.
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Affiliation(s)
- Andrew J Manning
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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