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Miyoshi SI, Amako K, Muraoka M, Morinaga H, Ueba S. Mobile genetic elements associated with utilization of dichloromethane and methanol as energy sources in Cupriavidus metallidurans. JOURNAL OF MICROORGANISM CONTROL 2024; 29:55-65. [PMID: 38880617 DOI: 10.4265/jmc.29.2_55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Cupriavidus metallidurans strain PD11 isolated from laboratory waste drainage can use C1 compounds, such as dichloromethane (DCM) and methanol, as a sole carbon and energy source. However, strain CH34 (a type-strain) cannot grow in the medium supplemented with DCM. In the present study, we aimed to unravel the genetic elements underlying the utilization of C1 compounds by strain PD11. The genome subtraction approach indicated that only strain PD11 had several genes highly homologous to those of Herminiimonas arsenicoxydans strain ULPAs1. Moreover, a series of polymerase chain reaction (PCR) to detect the orthologs of H. arsenicoxydans genes and the comparative study of the genomes of three strains revealed that the 87.9 kb DNA fragment corresponding to HEAR1959 to HEAR2054 might be horizontally transferred to strain PD11. The 87.9 kb DNA fragment identified was found to contain three genes whose products were putatively involved in the metabolism of formaldehyde, a common intermediate of DCM and methanol. In addition, reverse transcription PCR analysis showed that all three genes were significantly expressed when strain PD11 was cultivated in the presence of DCM or methanol. These findings suggest that strain PD11 can effectively utilize the C1 compounds because of transfer of the mobile genetic elements from other bacterial species, for instance, from H. arsenicoxydans.
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Affiliation(s)
- Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Keita Amako
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Mika Muraoka
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Hiroko Morinaga
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Saaya Ueba
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
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2
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Liu X, Roujeinikova A, Ottemann KM. FliL Functions in Diverse Microbes to Negatively Modulate Motor Output via Its N-Terminal Region. mBio 2023; 14:e0028323. [PMID: 36852985 PMCID: PMC10127578 DOI: 10.1128/mbio.00283-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
The flagellar motor protein FliL is conserved across many microbes, but its exact role has been obscured by varying fliL mutant phenotypes. We reanalyzed results from fliL studies and found they utilized alleles that differed in the amount of N- and C-terminal regions that were retained. Alleles that retain the N-terminal cytoplasmic and transmembrane helix (TM) regions in the absence of the C-terminal periplasmic domain result in loss of motility, while alleles that completely lack the N-terminal region, independent of the periplasmic domain, retain motility. We then tested this prediction in Helicobacter pylori fliL and found support for the idea. This analysis suggests that FliL function may be more conserved across bacteria than previously thought, that it is not essential for motility, and that the N-terminal region has the negative ability to regulate motor function. IMPORTANCE FliL is a protein found in the flagellar motor of bacteria, but what it does was not clear. To study FliL function, scientists often remove it and see what happens. Loss of FliL was thought to have different effects depending on the microbe. We uncovered, however, that part of the confusion arose because scientists inadvertently removed different parts of the protein. Our analysis and data suggest that leaving the N-terminal regions blocks motility, while fully removing FliL allows normal motility. This finding will help scientists understand FliL because it clarifies what needs to be removed to fully eliminate the protein, and also that the N-terminal region can block motility.
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Affiliation(s)
- Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
| | - Anna Roujeinikova
- Infection and Immunity Program, Department of Microbiology and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, California, USA
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3
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Biełło KA, Cabello P, Rodríguez-Caballero G, Sáez LP, Luque-Almagro VM, Roldán MD, Olaya-Abril A, Moreno-Vivián C. Proteomic Analysis of Arsenic Resistance during Cyanide Assimilation by Pseudomonas pseudoalcaligenes CECT 5344. Int J Mol Sci 2023; 24:ijms24087232. [PMID: 37108394 PMCID: PMC10138600 DOI: 10.3390/ijms24087232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Wastewater from mining and other industries usually contains arsenic and cyanide, two highly toxic pollutants, thereby creating the need to develop bioremediation strategies. Here, molecular mechanisms triggered by the simultaneous presence of cyanide and arsenite were analyzed by quantitative proteomics, complemented with qRT-PCR analysis and determination of analytes in the cyanide-assimilating bacterium Pseudomonas pseudoalcaligenes CECT 5344. Several proteins encoded by two ars gene clusters and other Ars-related proteins were up-regulated by arsenite, even during cyanide assimilation. Although some proteins encoded by the cio gene cluster responsible for cyanide-insensitive respiration decreased in the presence of arsenite, the nitrilase NitC required for cyanide assimilation was unaffected, thus allowing bacterial growth with cyanide and arsenic. Two complementary As-resistance mechanisms were developed in this bacterium, the extrusion of As(III) and its extracellular sequestration in biofilm, whose synthesis increased in the presence of arsenite, and the formation of organoarsenicals such as arseno-phosphoglycerate and methyl-As. Tetrahydrofolate metabolism was also stimulated by arsenite. In addition, the ArsH2 protein increased in the presence of arsenite or cyanide, suggesting its role in the protection from oxidative stress caused by both toxics. These results could be useful for the development of bioremediation strategies for industrial wastes co-contaminated with cyanide and arsenic.
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Affiliation(s)
- Karolina A Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Gema Rodríguez-Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Lara P Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
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4
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Ranganathan S, Sethi D, Kasivisweswaran S, Ramya L, Priyadarshini R, Yennamalli RM. Structural and functional mapping of ars gene cluster in Deinococcus indicus DR1. Comput Struct Biotechnol J 2022; 21:519-534. [PMID: 36618989 PMCID: PMC9807832 DOI: 10.1016/j.csbj.2022.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Deinococcus indicus DR1 is a novel Gram-negative bacterium, isolated from the Dadri wetlands in Uttar Pradesh, India. In addition to being radiation-resistant, the rod-shaped, red-pigmented organism shows extraordinary resistance to arsenic. The proteins of the corresponding ars gene cluster involved in arsenic extrusion in D. indicus DR1 have not yet been characterized. Additionally, how these proteins regulate each other providing arsenic resistance is still unclear. Here, we present a computational model of the operonic structure and the corresponding characterization of the six proteins of the ars gene cluster in D. indicus DR1. Additionally, we show the expression of the genes in the presence of arsenic using qRT-PCR. The ars gene cluster consists of two transcriptional regulators (ArsR1, ArsR2), two arsenate reductases (ArsC2, ArsC3), one metallophosphatase family protein (MPase), and a transmembrane arsenite efflux pump (ArsB). The transcriptional regulators are trans-acting repressors, and the reductases reduce arsenate (As5+) ions to arsenite (As3+) ions for favourable extrusion. The proteins modelled using RoseTTAFold, and their conformationally stable coordinates obtained after MD simulation indicate their various functional roles with respect to arsenic. Excluding ArsB, all the proteins belong to the α + β class of proteins. ArsB, being a membrane protein, is fully α-helical, with 12 transmembrane helices. The results show the degree of similarity or divergence of the mechanism utilized by these proteins of ars gene cluster in D. indicus DR1 to confer high levels of arsenic tolerance. This structural characterization study of the ars genes will enable new and deeper insights of arsenic tolerance.
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Affiliation(s)
- Shrivaishnavi Ranganathan
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu 613401, India
| | - Deepa Sethi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - Sandhya Kasivisweswaran
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
| | - L. Ramya
- Computational and Molecular Biophysics Laboratory, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu 613401, India
| | - Richa Priyadarshini
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India,Corresponding authors.
| | - Ragothaman M. Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, Tamil Nadu 613401, India,Corresponding authors.
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5
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Bhardwaj A. Understanding the diversified microbial operon framework coupled to arsenic transformation and expulsion. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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DeVore CL, Rodriguez-Freire L, Villa N, Soleimanifar M, Gonzalez-Estrella J, Ali AMS, Lezama-Pacheco J, Ducheneaux C, Cerrato JM. Mobilization of As, Fe, and Mn from Contaminated Sediment in Aerobic and Anaerobic Conditions: Chemical or Microbiological Triggers? ACS EARTH & SPACE CHEMISTRY 2022; 6:1644-1654. [PMID: 36238447 PMCID: PMC9555341 DOI: 10.1021/acsearthspacechem.1c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We integrated aqueous chemistry, spectroscopy, and microbiology techniques to identify chemical and microbial processes affecting the release of arsenic (As), iron (Fe), and manganese (Mn) from contaminated sediments exposed to aerobic and anaerobic conditions. The sediments were collected from Cheyenne River Sioux Tribal lands in South Dakota, which has dealt with mining legacy for several decades. The range of concentrations of total As measured from contaminated sediments was 96 to 259 mg kg-1, which co-occurs with Fe (21 000-22 005 mg kg-1) and Mn (682-703 mg kg-1). The transition from aerobic to anaerobic redox conditions yielded the highest microbial diversity, and the release of the highest concentrations of As, Fe, and Mn in batch experiments reacted with an exogenous electron donor (glucose). The reduction of As was confirmed by XANES analyses when transitioning from aerobic to anaerobic conditions. In contrast, the releases of As, Fe and Mn after a reaction with phosphate was at least 1 order of magnitude lower compared with experiments amended with glucose. Our results indicate that mine waste sediments amended with an exogenous electron donor trigger microbial reductive dissolution caused by anaerobic respiration. These dissolution processes can affect metal mobilization in systems transitioning from aerobic to anaerobic conditions in redox gradients. Our results are relevant for natural systems, for surface and groundwater exchange, or other systems in which metal cycling is influenced by chemical and biological processes.
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Affiliation(s)
- Cherie L DeVore
- Department of Civil, Construction & Environmental Engineering, MSC01 1070, University of New Mexico, Albuquerque, New Mexico 87131, United States; Department of Earth Systems Science, Stanford University, Stanford, California 94305, United States
| | - Lucia Rodriguez-Freire
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Noelani Villa
- Department of Civil, Construction & Environmental Engineering, MSC01 1070, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Maedeh Soleimanifar
- Department of Civil & Environmental Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Jorge Gonzalez-Estrella
- Department of Civil, Construction & Environmental Engineering, MSC01 1070, University of New Mexico, Albuquerque, New Mexico 87131, United States; School of Civil and Environmental Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Abdul Mehdi S Ali
- Department of Earth and Planetary Sciences, MSC03 2040, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Juan Lezama-Pacheco
- Department of Earth Systems Science, Stanford University, Stanford, California 94305, United States
| | - Carlyle Ducheneaux
- Department of Environment and Natural Resources, Cheyenne River Sioux Tribe, Eagle Butte, South Dakota 57625, United States
| | - José M Cerrato
- Department of Civil, Construction & Environmental Engineering, MSC01 1070, University of New Mexico, Albuquerque, New Mexico 87131, United States
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7
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Lee J, Levin DE. Differential metabolism of arsenicals regulates Fps1-mediated arsenite transport. J Cell Biol 2022; 221:212996. [PMID: 35139143 PMCID: PMC8932518 DOI: 10.1083/jcb.202109034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 01/21/2023] Open
Abstract
Arsenic is an environmental toxin that exists mainly as pentavalent arsenate and trivalent arsenite. Both forms activate the yeast SAPK Hog1 but with different consequences. We describe a mechanism by which cells distinguish between these arsenicals through one-step metabolism to differentially regulate the bidirectional glycerol channel Fps1, an adventitious port for arsenite. Cells exposed to arsenate reduce it to thiol-reactive arsenite, which modifies a set of cysteine residues in target proteins, whereas cells exposed to arsenite metabolize it to methylarsenite, which modifies an additional set of cysteine residues. Hog1 becomes arsenylated, which prevents it from closing Fps1. However, this block is overcome in cells exposed to arsenite through methylarsenylation of Acr3, an arsenite efflux pump that we found also regulates Fps1 directly. This adaptation allows cells to restrict arsenite entry through Fps1 and also allows its exit when produced from arsenate exposure. These results have broad implications for understanding how SAPKs activated by diverse stressors can drive stress-specific outputs.
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Affiliation(s)
- Jongmin Lee
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA
| | - David E Levin
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA.,Department of Microbiology, Boston University School of Medicine, Boston, MA
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8
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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9
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Leiva-Aravena E, Vera MA, Nerenberg R, Leiva ED, Vargas IT. Biofilm formation of Ancylobacter sp. TS-1 on different granular materials and its ability for chemolithoautotrophic As(III)-oxidation at high concentrations. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126733. [PMID: 34339991 DOI: 10.1016/j.jhazmat.2021.126733] [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: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
The oxidation of arsenic (As) is a key step in its removal from water, and biological oxidation may provide a cost-effective and sustainable method. The biofilm-formation ability of Ancylobacter sp. TS-1, a novel chemolithoautotrophic As oxidizer, was studied for four materials: polypropylene, graphite, sand, and zeolite. After seven days under batch mixotrophic conditions, with high concentrations of As(III) (225 mg·L-1), biofilm formation was detected on all materials except for polypropylene. The results demonstrate As(III)-oxidation of TS-1 biofilms and suggest that the number of active cells was similar for graphite, sand, and zeolite. However, the biofilm biomass follows the specific surface area of each material: 7.0, 2.4, and 0.4 mg VSS·cm-3 for zeolite, sand, and graphite, respectively. Therefore, the observed biofilm-biomass differences were probably associated with different amounts of EPS and inert biomass. Lastly, As(III)-oxidation kinetics were assessed for the biofilms formed on graphite and zeolite under chemolithoautotrophic conditions. The normalized oxidation rate for biofilms formed on these materials was 3.6 and 1.0 mg·L-1·h-1·cm-3, resulting among the highest reported values for As(III)-oxidizing biofilms operated at high-As(III) concentrations. Our findings suggest that biofilm reactors based on Ancylobacter sp. TS-1 are highly promising for their utilization in As(III)-oxidation pre-treatment of high-As(III) polluted waters.
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Affiliation(s)
- Enzo Leiva-Aravena
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; CEDEUS, Centro de Desarrollo Urbano Sustentable, Chile
| | - Mario A Vera
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; Instituto de Ingeniería Biológica y Médica, Facultades de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences Notre Dame, University of Notre Dame, Notre Dame, IN, United States
| | - Eduardo D Leiva
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; Departamento de Química Inorgánica, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ignacio T Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile; CEDEUS, Centro de Desarrollo Urbano Sustentable, Chile.
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10
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Ghosh S, Pramanik S. Structural diversity, functional aspects and future therapeutic applications of human gut microbiome. Arch Microbiol 2021; 203:5281-5308. [PMID: 34405262 PMCID: PMC8370661 DOI: 10.1007/s00203-021-02516-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.
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Affiliation(s)
- Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India.
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute, i-8 Sector-C, East Kolkata Township, Kolkata, 700107, India
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11
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Barra Caracciolo A, Terenzi V. Rhizosphere Microbial Communities and Heavy Metals. Microorganisms 2021; 9:microorganisms9071462. [PMID: 34361898 PMCID: PMC8307176 DOI: 10.3390/microorganisms9071462] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022] Open
Abstract
The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants’ functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.
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12
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Biological characterization of Bacillus flexus strain SSAI1 transforming highly toxic arsenite to less toxic arsenate mediated by periplasmic arsenite oxidase enzyme encoded by aioAB genes. Biometals 2021; 34:895-907. [PMID: 33956287 DOI: 10.1007/s10534-021-00316-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022]
Abstract
Bacillus flexus strain SSAI1 isolated from agro-industry waste, Tuem, Goa, India displayed high arsenite resistance as minimal inhibitory concentration was 25 mM in mineral salts medium. This bacterial strain exposed to 10 mM arsenite demonstrated rapid arsenite oxidation and internalization of 7 mM arsenate within 24 h. The Fourier transformed infrared (FTIR) spectroscopy of cells exposed to arsenite revealed important functional groups on the cell surface interacting with arsenite. Furthermore, scanning electron microscopy combined with electron dispersive X-ray spectroscopy (SEM-EDAX) of cells exposed to arsenite revealed clumping of cells with no surface adsorption of arsenite. Transmission electron microscopy coupled with electron dispersive X-ray spectroscopic (TEM-EDAX) analysis of arsenite exposed cells clearly demonstrated ultra-structural changes and intracellular accumulation of arsenic. Whole-genome sequence analysis of this bacterial strain interestingly revealed the presence of large number of metal(loid) resistance genes, including aioAB genes encoding arsenite oxidase responsible for the oxidation of highly toxic arsenite to less toxic arsenate. Enzyme assay further confirmed that arsenite oxidase is a periplasmic enzyme. The genome of strain SSAI1 also carried glpF, aioS and aioE genes conferring resistance to arsenite. Therefore, multi-metal(loid) resistant arsenite oxidizing Bacillus flexus strain SSAI1 has potential to bioremediate arsenite contaminated environmental sites and is the first report of its kind.
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Wang Y, Zhang C, Yu X, Ge Y. Arsenite Oxidation by Dunaliella salina is Affected by External Phosphate Concentration. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 105:868-873. [PMID: 33211134 DOI: 10.1007/s00128-020-03045-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/09/2020] [Indexed: 06/11/2023]
Abstract
Arsenic (As) contamination in terrestrial and aquatic environments is a well-known global environmental problem. The biooxidation of arsenite [As(III)] and subsequent arsenate [As(V)] removal have increasingly been used for remediation of As-polluted groundwater. However, little is known about As(III) oxidation by microalgae, especially those from saltwater environments. In this study, we investigated As(III) toxicity and oxidation in the marine microalga Dunaliella salina in the presence of different phosphate concentrations. The results of the As(III) toxicity experiments showed that D. salina was tolerant to As(III) (5.4 ± 0.31 mg As L-1 at 72 h of culture). The As(V) percentage in the P-enriched (11.2 mg L-1) medium was 7.2-fold greater than in the P-deficient one after 24-h exposure, indicating As(III) oxidation by D. salina was more pronounced with increased phosphate levels. Treatment of As(III) with and without 2,4-dinitrophenol (DNP) on the algal cells showed that As(III) oxidation occurred mainly on the cell surface and in the cytoplasm of D. salina. The results of this study suggest that transformation of As(III) into As(V) may be an important pathway of detoxification in D. salina and that phosphate plays a key role in this oxidation process.
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Affiliation(s)
- Ya Wang
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Chunhua Zhang
- Demonstration Laboratory of Element and Life Science Research, Laboratory Centre of Life Science, College of Life Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiangyang Yu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology, Nanjing, 210014, China
- Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ying Ge
- Jiangsu Provincial Key Laboratory of Marine Biology, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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14
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Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F. Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2. Microb Genom 2020; 6:mgen000447. [PMID: 33034553 PMCID: PMC7660254 DOI: 10.1099/mgen.0.000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/14/2020] [Indexed: 11/30/2022] Open
Abstract
Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was previously observed that after exposure to arsenite, when grown in a biofilm, some strains of Thiomonas bacteria develop variants that are more resistant to arsenic. Here, we identified the mechanisms involved in the emergence of such variants in biofilms. We found that the percentage of variants generated increased in the presence of high concentrations of arsenite (5.33 mM), especially in the detached cells after growth under biofilm-forming conditions. Analysis of gene expression in the parent strain CB2 revealed that genes involved in DNA repair were upregulated in the conditions where variants were observed. Finally, we assessed the phenotypes and genomes of the subsequent variants generated to evaluate the number of mutations compared to the parent strain. We determined that multiple point mutations accumulated after exposure to arsenite when cells were grown under biofilm conditions. Some of these mutations were found in what is referred to as ICE19, a genomic island (GI) carrying arsenic-resistance genes, also harbouring characteristics of an integrative and conjugative element (ICE). The mutations likely favoured the excision and duplication of this GI. This research aids in understanding how Thiomonas bacteria adapt to highly toxic environments, and, more generally, provides a window to bacterial genome evolution in extreme environments.
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Affiliation(s)
- Kelle C. Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa, Kāneʻohe, HI, USA
| | - Stephanie Fouteau
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Aline Huber
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Martina Peres
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Hugo Varet
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
- Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756, IP CNRS), Institut Pasteur, Paris, France
| | - Caroline Proux
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Julien Deschamps
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rachel Torchet
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Stephane Cruveiller
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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15
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Shi K, Wang Q, Wang G. Microbial Oxidation of Arsenite: Regulation, Chemotaxis, Phosphate Metabolism and Energy Generation. Front Microbiol 2020; 11:569282. [PMID: 33072028 PMCID: PMC7533571 DOI: 10.3389/fmicb.2020.569282] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
Arsenic (As) is a metalloid that occurs widely in the environment. The biological oxidation of arsenite [As(III)] to arsenate [As(V)] is considered a strategy to reduce arsenic toxicity and provide energy. In recent years, research interests in microbial As(III) oxidation have been growing, and related new achievements have been revealed. This review focuses on the highlighting of the novel regulatory mechanisms of bacterial As(III) oxidation, the physiological relevance of different arsenic sensing systems and functional relationship between microbial As(III) oxidation and those of chemotaxis, phosphate uptake, carbon metabolism and energy generation. The implication to environmental bioremediation applications of As(III)-oxidizing strains, the knowledge gaps and perspectives are also discussed.
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Affiliation(s)
- Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Wang
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
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17
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Barral-Fraga L, Barral MT, MacNeill KL, Martiñá-Prieto D, Morin S, Rodríguez-Castro MC, Tuulaikhuu BA, Guasch H. Biotic and Abiotic Factors Influencing Arsenic Biogeochemistry and Toxicity in Fluvial Ecosystems: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17072331. [PMID: 32235625 PMCID: PMC7177459 DOI: 10.3390/ijerph17072331] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 01/20/2023]
Abstract
This review is focused on the biogeochemistry of arsenic in freshwaters and, especially, on the key role that benthic microalgae and prokaryotic communities from biofilms play together in through speciation, distribution, and cycling. These microorganisms incorporate the dominant iAs (inorganic arsenic) form and may transform it to other arsenic forms through metabolic or detoxifying processes. These transformations have a big impact on the environmental behavior of arsenic because different chemical forms exhibit differences in mobility and toxicity. Moreover, exposure to toxicants may alter the physiology and structure of biofilms, leading to changes in ecosystem function and trophic relations. In this review we also explain how microorganisms (i.e., biofilms) can influence the effects of arsenic exposure on other key constituents of aquatic ecosystems such as fish. At the end, we present two real cases of fluvial systems with different origins of arsenic exposure (natural vs. anthropogenic) that have improved our comprehension of arsenic biogeochemistry and toxicity in freshwaters, the Pampean streams (Argentina) and the Anllóns River (Galicia, Spain). We finish with a briefly discussion of what we consider as future research needs on this topic. This work especially contributes to the general understanding of biofilms influencing arsenic biogeochemistry and highlights the strong impact of nutrient availability on arsenic toxicity for freshwater (micro) organisms.
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Affiliation(s)
- Laura Barral-Fraga
- Grup de recerca en Ecologia aquàtica continental (GRECO), Departament de Ciències Ambientals, Universitat de Girona, 17071 Girona, Spain;
- LDAR24—Laboratoire Départemental d’Analyse et de Recherche du Département de la Dordogne, 24660 Coulounieix-Chamiers, Périgueux, France
- Correspondence:
| | - María Teresa Barral
- Instituto CRETUS, Departmento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.T.B.); (D.M.-P.)
| | - Keeley L. MacNeill
- Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA;
| | - Diego Martiñá-Prieto
- Instituto CRETUS, Departmento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.T.B.); (D.M.-P.)
| | - Soizic Morin
- INRAE—Institut National de Recherche en Agriculture, Alimentation et Environnement, UR EABX—Equipe ECOVEA, 33612 Cestas Cedex, France;
| | - María Carolina Rodríguez-Castro
- INEDES—Instituto de Ecología y Desarrollo Sustentable (UNLu-CONICET), Universidad Nacional de Luján, 6700 Buenos Aires, Argentina;
- CONICET—Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1425FQB CABA, Argentina
| | - Baigal-Amar Tuulaikhuu
- School of Agroecology, Mongolian University of Life Sciences, Khoroo 11, Ulaanbaatar 17024, Mongolia;
| | - Helena Guasch
- Grup de recerca en Ecologia aquàtica continental (GRECO), Departament de Ciències Ambientals, Universitat de Girona, 17071 Girona, Spain;
- CEAB—Centre d’Estudis Avançats de Blanes, CSIC, Blanes, 17300 Girona, Spain
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18
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Cheng L, Min D, Liu DF, Li WW, Yu HQ. Sensing and Approaching Toxic Arsenate by Shewanella putrefaciens CN-32. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14604-14611. [PMID: 31747260 DOI: 10.1021/acs.est.9b05890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although arsenic at a high concentration imposes strong selective pressure on microbes, various microbes have been found to grow in As-rich environments. So far, little is known about how microbes can sense and move toward arsenate in the environment, and the underlying molecular mechanisms have not been revealed. Here, we report the chemotaxis response toward arsenate (As(V)) by Shewanella putrefaciens CN-32, a model dissimilatory metal-reducing bacterium (DMRB), and elucidate the mechanisms. We find that S. putrefaciens CN-32 exhibits a chemotactic behavior toward As(V) and diverse electron acceptors. To sense As(V), S. putrefaciens CN-32 requires functional arsenate respiratory reductase but does not depend on its metal-reducing-like respiratory pathway. We observe that such a sense is governed by an energy taxis mechanism and mediated by several methyl-accepting chemotaxis proteins (MCPs), rather than a specific MCP. Moreover, we reveal that the chemotactic signal transduction pathway is conserved in Shewanella, and histidine kinase and flagella-mediated motility are essential for taxis toward As(V). This work reverses the conventional view about arsenic as a chemotactic inhibitor to microbes by revealing the positive chemotaxis of Shewanella to As(V).
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19
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Han YH, Yin DX, Jia MR, Wang SS, Chen Y, Rathinasabapathi B, Chen DL, Ma LQ. Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:1178-1189. [PMID: 31470481 DOI: 10.1016/j.scitotenv.2019.07.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.
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Affiliation(s)
- Yong-He Han
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, China
| | - Dai-Xia Yin
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Meng-Ru Jia
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shan-Shan Wang
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China
| | - Yanshan Chen
- School of the Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Deng-Long Chen
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; Innovative Center for Eco-Friendly Polymeric Materials, Quanzhou, Fujian 362801, China.
| | - Lena Q Ma
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States.
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20
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Rahman Z, Thomas L, Singh VP. Study of As-resistant bacteria from Nadia, India and a survey of two As resistance-related proteins. J Basic Microbiol 2019; 60:47-57. [PMID: 31680284 DOI: 10.1002/jobm.201900373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/30/2019] [Accepted: 10/11/2019] [Indexed: 11/07/2022]
Abstract
The present investigation deals with the characterisation of three As-resistant bacteria, Bacillus aryabhattai strain VPS1, Bacillus licheniformis strain VPS6 and Sporosarcina thermotolerans strain VPS7 isolated from the rhizosphere of a contaminated paddy field in Chakdaha, Nadia, West Bengal, India. Two strains, VPS6 and VPS7 showed ureolytic activity, which can be used for microbial-induced calcite precipitation of As as a bioremediation option. However, As reduction and oxidation capacities were not reported in any of these bacteria. A phylogenetic tree of 16S ribosomal RNA gene sequences was constructed for all three bacterial isolates, including different species of As-resistant Bacillus and Sporosarcina. Furthermore, literature survey and genome mining were employed to explore the diversity of As resistance-related proteins, arsenite S-adenosylmethyltransferase (ArsM) and arsenical pump membrane protein (ArsB) among different bacteria, and the phylogenetic relatedness was studied to understand the distribution and evolution of their amino acid sequences. ArsB was predominantly present in a wide variety of bacteria (347 taxa); however, ArsM was reported in comparatively fewer isolates (109 taxa). There were a total of 60 similar taxa that contained both ArsM and ArsB. Both proteins were most abundantly present in phylum Proteobacteria. Overall, this investigation enumerates As-resistant bacteria to understand the As metabolism in the environment, and the phylogenetic analysis of As resistance-related proteins helps in understanding the functional relationship in different bacteria for their role in As mobility in the environment.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, India.,Department of Botany, University of Delhi, Delhi, India
| | - Lebin Thomas
- Department of Botany, University of Delhi, Delhi, India.,Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Ved P Singh
- Department of Botany, University of Delhi, Delhi, India
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21
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Qiao Z, Huang J, Cao Y, Shi K, Wang G. Genetics and proteomics analyses reveal the roles of PhoB1 and PhoB2 regulators in bacterial responses to arsenite and phosphate. Res Microbiol 2019; 170:263-271. [PMID: 31279088 DOI: 10.1016/j.resmic.2019.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 11/25/2022]
Abstract
In bacteria, phosphate (Pi) stress response is governed by the two-component regulatory system, sensor kinase PhoR and its cognate response regulatory protein PhoB. The arsenite [As(III)]-oxidizing bacterium Agrobacterium tumefaciens GW4 contains two phoB genes, phoB1 and phoB2. phoB1 is adjacent to As(III)-oxidizing genes, however, the functions of PhoB1 and PhoB2 remain unclear. Here, phoB1 and phoB2 were each deleted in-frame, and proteomics, qRT-PCR and protein-DNA interaction were performed. We found that (1) phoB1 and phoB2 were both upregulated under low Pi conditions and phoB1 was induced by As(III), but phoB2 was not; (2) deletion of phoB1 reduced As(III)-oxidizing efficiency and protein-DNA interaction analysis showed PhoB1 could interact with aioXSR promoter to regulate As(III) oxidation; (3) deletions of phoB1 or phoB2 both reduced exopolysaccharides (EPS) synthesis; and (4) PhoB1 influenced Pi uptake, As(III) oxidation, EPS synthesis, TCA cycle, energy production and stress response with As(III), and PhoB2 was associated with Pi uptake and EPS synthesis in low Pi conditions. These results showed PhoB1 and PhoB2 were both involved in Pi acquisition, PhoB1 was more important with As(III) and PhoB2 played a major role without As(III). Strain GW4 uses these two regulators to survive under low Pi and arsenic-rich environments.
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Affiliation(s)
- Zixu Qiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Jing Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Yajing Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.
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22
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Cavalca L, Zecchin S, Zaccheo P, Abbas B, Rotiroti M, Bonomi T, Muyzer G. Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy. Front Microbiol 2019; 10:1480. [PMID: 31312188 PMCID: PMC6614289 DOI: 10.3389/fmicb.2019.01480] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/13/2019] [Indexed: 11/13/2022] Open
Abstract
Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidation of arsenite, in combination with arsenate-adsorbing materials, could be employed for metalloid removal.
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Affiliation(s)
- Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Sarah Zecchin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Patrizia Zaccheo
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milan, Italy
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Marco Rotiroti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Tullia Bonomi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Rahman Z, Singh VP. The relative impact of toxic heavy metals (THMs) (arsenic (As), cadmium (Cd), chromium (Cr)(VI), mercury (Hg), and lead (Pb)) on the total environment: an overview. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:419. [PMID: 31177337 DOI: 10.1007/s10661-019-7528-7] [Citation(s) in RCA: 457] [Impact Index Per Article: 91.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/08/2019] [Indexed: 05/18/2023]
Abstract
Certain five heavy metals viz. arsenic (As), cadmium (Cd), chromium (Cr)(VI), mercury (Hg), and lead (Pb) are non-threshold toxins and can exert toxic effects at very low concentrations. These heavy metals are known as most problematic heavy metals and as toxic heavy metals (THMs). Several industrial activities and some natural processes are responsible for their high contamination in the environment. In recent years, high concentrations of heavy metals in different natural systems including atmosphere, pedosphere, hydrosphere, and biosphere have become a global issue. These THMs have severe deteriorating effects on various microorganisms, plants, and animals. Human exposure to the THMs may evoke serious health injuries and impairments in the body, and even certain extremities can cause death. In all these perspectives, this review provides a comprehensive account of the relative impact of the THMs As, Cd, Cr(VI), Hg, and Pb on our total environment.
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Affiliation(s)
- Zeeshanur Rahman
- Department of Botany, Zakir Husain Delhi College, University of Delhi, Delhi, 110002, India.
| | - Ved Pal Singh
- Department of Botany, University of Delhi, Delhi, 110007, India
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Uhrynowski W, Radlinska M, Drewniak L. Genomic Analysis of Shewanella sp. O23S-The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction. Int J Mol Sci 2019; 20:ijms20051018. [PMID: 30813619 PMCID: PMC6429310 DOI: 10.3390/ijms20051018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 02/05/2023] Open
Abstract
Shewanella sp. O23S is a dissimilatory arsenate reducing bacterial strain involved in arsenic transformations within the abandoned gold mine in Zloty Stok (SW Poland). Previous physiological studies revealed that O23S may not only release arsenic from minerals, but also facilitate its immobilization through co-precipitation with reduced sulfur species. Given these uncommon, complementary characteristics and the application potential of the strain in arsenic-removal technologies, its genome (~5.3 Mbp), consisting of a single chromosome, two large plasmids (pSheA and pSheB) and three small plasmid-like phages (pSheC-E) was sequenced and annotated. Genes encoding putative proteins involved in heavy metal transformations, antibiotic resistance and other phenotypic traits were identified. An in-depth comparative analysis of arsenic respiration (arr) and resistance (ars) genes and their genetic context was also performed, revealing that pSheB carries the only copy of the arr genes, and a complete ars operon. The plasmid pSheB is therefore a unique natural vector of these genes, providing the host cells arsenic respiration and resistance abilities. The functionality of the identified genes was determined based on the results of the previous and additional physiological studies, including: the assessment of heavy metal and antibiotic resistance under various conditions, adhesion-biofilm formation assay and BiologTM metabolic preferences test. This combined genetic and physiological approach shed a new light on the capabilities of O23S and their molecular basis, and helped to confirm the biosafety of the strain in relation to its application in bioremediation technologies.
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Affiliation(s)
- Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Monika Radlinska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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Arsenite biotransformation and bioaccumulation by Klebsiella pneumoniae strain SSSW7 possessing arsenite oxidase (aioA) gene. Biometals 2018; 32:65-76. [PMID: 30471007 DOI: 10.1007/s10534-018-0158-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/17/2018] [Indexed: 10/27/2022]
Abstract
Arsenite oxidizing Klebsiella pneumoniae strain SSSW7 isolated from shipyard waste Goa, India showed a minimum inhibitory concentration of 21 mM in mineral salts medium. The strain possessed a small supercoiled plasmid and PCR amplification of arsenite oxidase gene (aioA) was observed on plasmid as well as chromosomal DNA. It was confirmed that arsenite oxidase enzyme was a periplasmic protein with a 47% increase in arsenite oxidase activity at 1 mM sodium arsenite. Scanning electron microscopy coupled with electron dispersive X-ray spectroscopic (SEM-EDS) analysis of 15 mM arsenite exposed cells revealed long chains of cells with no surface adsorption of arsenic. Transmission electron microscopy combined with electron dispersive X-ray spectroscopic (TEM-EDS) analysis demonstrated plasma membrane disruption, cytoplasmic condensation and periplasmic accumulation of arsenic. The bacterial strain oxidized 10 mM of highly toxic arsenite to less toxic arsenate after 24 h of incubation. Fourier transformed infrared (FTIR) spectroscopy confirmed the interaction of arsenite with functional groups present on the bacterial cell surface. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis of 5 mM arsenite exposed cells demonstrated over-expression of 87 kDa and 14 kDa proteins of two subunits aioA and aioB of heterodimer arsenite oxidase enzyme as compared to control cells. Therefore, this bacterial strain might be employed as a potential candidate for bioremediation of arsenite contaminated environmental sites.
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Ben Fekih I, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, Rensing C, Cervantes C. Distribution of Arsenic Resistance Genes in Prokaryotes. Front Microbiol 2018; 9:2473. [PMID: 30405552 PMCID: PMC6205960 DOI: 10.3389/fmicb.2018.02473] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
Arsenic is a metalloid that occurs naturally in aquatic and terrestrial environments. The high toxicity of arsenic derivatives converts this element in a serious problem of public health worldwide. There is a global arsenic geocycle in which microbes play a relevant role. Ancient exposure to arsenic derivatives, both inorganic and organic, has represented a selective pressure for microbes to evolve or acquire diverse arsenic resistance genetic systems. In addition, arsenic compounds appear to have been used as a toxin in chemical warfare for a long time selecting for an extended range of arsenic resistance determinants. Arsenic resistance strategies rely mainly on membrane transport pathways that extrude the toxic compounds from the cell cytoplasm. The ars operons, first discovered in bacterial R-factors almost 50 years ago, are the most common microbial arsenic resistance systems. Numerous ars operons, with a variety of genes and different combinations of them, populate the prokaryotic genomes, including their accessory plasmids, transposons, and genomic islands. Besides these canonical, widespread ars gene clusters, which confer resistance to the inorganic forms of arsenic, additional genes have been discovered recently, which broadens the spectrum of arsenic tolerance by detoxifying organic arsenic derivatives often used as toxins. This review summarizes the presence, distribution, organization, and redundance of arsenic resistance genes in prokaryotes.
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Affiliation(s)
- Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengkang Zhang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Zhao
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hend A Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Quaiser Saquib
- Department of Zoology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Carlos Cervantes
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Mexico
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Ordoñez OF, Rasuk MC, Soria MN, Contreras M, Farías ME. Haloarchaea from the Andean Puna: Biological Role in the Energy Metabolism of Arsenic. MICROBIAL ECOLOGY 2018; 76:695-705. [PMID: 29520450 DOI: 10.1007/s00248-018-1159-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/13/2018] [Indexed: 05/25/2023]
Abstract
Biofilms, microbial mats, and microbialites dwell under highly limiting conditions (high salinity, extreme aridity, pH, and elevated arsenic concentration) in the Andean Puna. Only recent pioneering studies have described the microbial diversity of different Altiplano lakes and revealed their unexpectedly diverse microbial communities. Arsenic metabolism is proposed to be an ancient mechanism to obtain energy by microorganisms. Members of Bacteria and Archaea are able to exploit arsenic as a bioenergetic substrate in either anaerobic arsenate respiration or chemolithotrophic growth on arsenite. Only six aioAB sequences coding for arsenite oxidase and three arrA sequences coding for arsenate reductase from haloarchaea were previously deposited in the NCBI database. However, no experimental data on their expression and function has been reported. Recently, our working group revealed the prevalence of haloarchaea in a red biofilm from Diamante Lake and microbial mat from Tebenquiche Lake using a metagenomics approach. Also, a surprisingly high abundance of genes used for anaerobic arsenate respiration (arr) and arsenite oxidation (aio) was detected in the Diamante's metagenome. In order to study in depth the role of arsenic in these haloarchaeal communities, in this work, we obtained 18 haloarchaea belonging to the Halorubrum genus, tolerant to arsenic. Furthermore, the identification and expression analysis of genes involved in obtaining energy from arsenic compounds (aio and arr) showed that aio and arr partial genes were detected in 11 isolates, and their expression was verified in two selected strains. Better growth of two isolates was obtained in presence of arsenic compared to control. Moreover, one of the isolates was able to oxidize As[III]. The confirmation of the oxidation of arsenic and the transcriptional expression of these genes by RT-PCR strongly support the hypothesis that the arsenic can be used in bioenergetics processes by the microorganisms flourishing in these environments.
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Affiliation(s)
- Omar Federico Ordoñez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - María Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - Mariana Noelia Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - Manuel Contreras
- Centro de Ecología Aplicada (CEA), Suecia 3304, 56-2-2741872, Ñuñoa, Santiago, Chile
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina.
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28
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Zhou EM, Xian WD, Mefferd CC, Thomas SC, Adegboruwa AL, Williams N, Murugapiran SK, Dodsworth JA, Ganji R, Li MM, Ding YP, Liu L, Woyke T, Li WJ, Hedlund BP. Thermus sediminis sp. nov., a thiosulfate-oxidizing and arsenate-reducing organism isolated from Little Hot Creek in the Long Valley Caldera, California. Extremophiles 2018; 22:983-991. [PMID: 30219948 DOI: 10.1007/s00792-018-1055-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 09/06/2018] [Indexed: 11/26/2022]
Abstract
Thermus species are widespread in natural and artificial thermal environments. Two new yellow-pigmented strains, L198T and L423, isolated from Little Hot Creek, a geothermal spring in eastern California, were identified as novel organisms belonging to the genus Thermus. Cells are Gram-negative, rod-shaped, and non-motile. Growth was observed at temperatures from 45 to 75 °C and at salinities of 0-2.0% added NaCl. Both strains grow heterotrophically or chemolithotrophically by oxidation of thiosulfate to sulfate. L198T and L423 grow by aerobic respiration or anaerobic respiration with arsenate as the terminal electron acceptor. Values for 16S rRNA gene identity (≤ 97.01%), digital DNA-DNA hybridization (≤ 32.7%), OrthoANI (≤ 87.5%), and genome-to-genome distance (0.13) values to all Thermus genomes were less than established criteria for microbial species. The predominant respiratory quinone was menaquinone-8 and the major cellular fatty acids were iso-C15:0, iso-C17:0 and anteiso-C15:0. One unidentified phospholipid (PL1) and one unidentified glycolipid (GL1) dominated the polar lipid pattern. The new strains could be differentiated from related taxa by β-galactosidase and β-glucosidase activity and the presence of hydroxy fatty acids. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic evidence, the novel species Thermus sediminis sp. nov. is proposed, with the type strain L198T (= CGMCC 1.13590T = KCTC XXX).
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Affiliation(s)
- En-Min Zhou
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | | | - Scott C Thomas
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Arinola L Adegboruwa
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Nathan Williams
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
- Las Vegas High School PAL Program, Clark County School District, Las Vegas, NV, 89154, USA
| | | | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, San Bernardino, CA, USA
| | - Rakesh Ganji
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Yi-Ping Ding
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, 89154, USA.
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diCenzo GC, Debiec K, Krzysztoforski J, Uhrynowski W, Mengoni A, Fagorzi C, Gorecki A, Dziewit L, Bajda T, Rzepa G, Drewniak L. Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. Genes (Basel) 2018; 9:E379. [PMID: 30060533 PMCID: PMC6115938 DOI: 10.3390/genes9080379] [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: 06/14/2018] [Revised: 07/22/2018] [Accepted: 07/25/2018] [Indexed: 12/23/2022] Open
Abstract
Ensifer (Sinorhizobium) sp. M14 is an efficient arsenic-oxidizing bacterium (AOB) that displays high resistance to numerous metals and various stressors. Here, we report the draft genome sequence and genome-guided characterization of Ensifer sp. M14, and we describe a pilot-scale installation applying the M14 strain for remediation of arsenic-contaminated waters. The M14 genome contains 6874 protein coding sequences, including hundreds not found in related strains. Nearly all unique genes that are associated with metal resistance and arsenic oxidation are localized within the pSinA and pSinB megaplasmids. Comparative genomics revealed that multiple copies of high-affinity phosphate transport systems are common in AOBs, possibly as an As-resistance mechanism. Genome and antibiotic sensitivity analyses further suggested that the use of Ensifer sp. M14 in biotechnology does not pose serious biosafety risks. Therefore, a novel two-stage installation for remediation of arsenic-contaminated waters was developed. It consists of a microbiological module, where M14 oxidizes As(III) to As(V) ion, followed by an adsorption module for As(V) removal using granulated bog iron ores. During a 40-day pilot-scale test in an abandoned gold mine in Zloty Stok (Poland), water leaving the microbiological module generally contained trace amounts of As(III), and dramatic decreases in total arsenic concentrations were observed after passage through the adsorption module. These results demonstrate the usefulness of Ensifer sp. M14 in arsenic removal performed in environmental settings.
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Affiliation(s)
- George C diCenzo
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Klaudia Debiec
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Jan Krzysztoforski
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Warynskiego 1, 00-645 Warsaw, Poland.
| | - Witold Uhrynowski
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Alessio Mengoni
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Camilla Fagorzi
- Laboratory of Microbial Genetics, Department of Biology, University of Florence, via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
| | - Adrian Gorecki
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Tomasz Bajda
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Grzegorz Rzepa
- Department of Mineralogy, Petrography and Geochemistry, Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland.
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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30
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Margesin R, Albuquerque L, Zhang DC, Froufe HJC, Severino R, Roxo I, Egas C, da Costa MS. Solimicrobium silvestre gen. nov., sp. nov., isolated from alpine forest soil. Int J Syst Evol Microbiol 2018; 68:2491-2498. [PMID: 29939122 DOI: 10.1099/ijsem.0.002861] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped, motile, catalase and cytochrome c oxidase-positive bacterial strain, designated S20-91T, was isolated from alpine forest soil. Growth occurred within a temperature range of 0-25 °C. Yeast extract was required for growth. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain S20-91T was related to the genus Herminiimonas and had the highest 16S rRNA gene sequence similarity to Herminiimonas arsenicoxydans ULPAs1T (96.5 %). The strain contained ubiquinone 8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The major cellular fatty acids (>10 %) were C16 : 1ω7c (55.3 %) and C16 : 0 (25.6 %). The genomic DNA G+C content was 47.6 mol%. Combined data of genomic, phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-91T represents a novel genus and species, for which the name Solimicrobium silvestre gen. nov., sp. nov. is proposed. The type strain is S20-91T (=DSM 104733T=LMG 30010).
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Affiliation(s)
- Rosa Margesin
- 1Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Luciana Albuquerque
- 2Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - De-Chao Zhang
- 3Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, PR China
| | - Hugo J C Froufe
- 4Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Rita Severino
- 4Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Inês Roxo
- 4Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Conceição Egas
- 4Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal
| | - Milton S da Costa
- 2Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
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31
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Plewniak F, Crognale S, Rossetti S, Bertin PN. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. Front Microbiol 2018; 9:820. [PMID: 29755441 PMCID: PMC5932151 DOI: 10.3389/fmicb.2018.00820] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simona Rossetti
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
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Corsini PM, Walker KT, Santini JM. Expression of the arsenite oxidation regulatory operon in Rhizobium sp. str. NT-26 is under the control of two promoters that respond to different environmental cues. Microbiologyopen 2017; 7:e00567. [PMID: 29250936 PMCID: PMC6011840 DOI: 10.1002/mbo3.567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 10/31/2017] [Accepted: 11/03/2017] [Indexed: 12/04/2022] Open
Abstract
Rhizobium sp. str. NT‐26 is a Gram‐negative facultative chemolithoautotrophic arsenite oxidizer that has been used as a model organism to study various aspects of arsenite oxidation including the regulation of arsenite oxidation. The three regulatory genes, aioX, aioS, and aioR, are cotranscribed when NT‐26 was grown in the presence or absence of arsenite. The aioXSR operon is upregulated in stationary phase but not by the presence of arsenite in the growth medium. The two transcription start sites upstream of aioX were determined which led to the identification of two promoters, the housekeeping promoter RpoD and the growth‐phase‐dependent promoter RpoE2. Promoter–lacZ fusions confirmed their constitutive and stationary phase expressions. The involvement of the NT‐26 sigma factor RpoE2 in acting on the NT‐26 RpoE2 promoter was confirmed in vivo in Escherichia coli, which lacks a rpoE2 homolog, using a strain carrying both the promoter–lacZ fusion and the NT‐26 rpoE2 gene. An in silico approach was used to search for other RpoE2 promoters and AioR‐binding motifs and led to the identification of other genes that could be regulated by these proteins including those involved in quorum sensing, chemotaxis, and motility expanding the signaling networks important for the microbial metabolism of arsenite.
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Affiliation(s)
- Paula M Corsini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Kenneth T Walker
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans. Sci Rep 2017; 7:15007. [PMID: 29101383 PMCID: PMC5670224 DOI: 10.1038/s41598-017-15164-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49T (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1T (98.4%), and Herminiimonas saxobsidens NS11T (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.
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Shi K, Fan X, Qiao Z, Han Y, McDermott TR, Wang Q, Wang G. Arsenite oxidation regulator AioR regulates bacterial chemotaxis towards arsenite in Agrobacterium tumefaciens GW4. Sci Rep 2017; 7:43252. [PMID: 28256605 PMCID: PMC5335332 DOI: 10.1038/srep43252] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/23/2017] [Indexed: 11/13/2022] Open
Abstract
Some arsenite [As(III)]-oxidizing bacteria exhibit positive chemotaxis towards As(III), however, the related As(III) chemoreceptor and regulatory mechanism remain unknown. The As(III)-oxidizing bacterium Agrobacterium tumefaciens GW4 displays positive chemotaxis towards 0.5–2 mM As(III). Genomic analyses revealed a putative chemoreceptor-encoding gene, mcp, located in the arsenic gene island and having a predicted promoter binding site for the As(III) oxidation regulator AioR. Expression of mcp and other chemotaxis related genes (cheA, cheY2 and fliG) was inducible by As(III), but not in the aioR mutant. Using capillary assays and intrinsic tryptophan fluorescence spectra analysis, Mcp was confirmed to be responsible for chemotaxis towards As(III) and to bind As(III) (but not As(V) nor phosphate) as part of the sensing mechanism. A bacterial one-hybrid system technique and electrophoretic mobility shift assays showed that AioR interacts with the mcp regulatory region in vivo and in vitro, and the precise AioR binding site was confirmed using DNase I foot-printing. Taken together, these results indicate that this Mcp is responsible for the chemotactic response towards As(III) and is regulated by AioR. Additionally, disrupting the mcp gene affected bacterial As(III) oxidation and growth, inferring that Mcp may exert some sort of functional connection between As(III) oxidation and As(III) chemotaxis.
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Affiliation(s)
- Kaixiang Shi
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xia Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zixu Qiao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yushan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Qian Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.,Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Gupta P, Diwan B. Bacterial Exopolysaccharide mediated heavy metal removal: A Review on biosynthesis, mechanism and remediation strategies. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2017; 13:58-71. [PMID: 28352564 PMCID: PMC5361134 DOI: 10.1016/j.btre.2016.12.006] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/29/2016] [Accepted: 12/21/2016] [Indexed: 11/28/2022]
Abstract
Heavy metal contamination has been recognized as a major public health risk, particularly in developing countries and their toxicological manifestations are well known. Conventional remediation strategies are either expensive or they generate toxic by-products, which adversely affect the environment. Therefore, necessity for an environmentally safe strategy motivates interest towards biological techniques. One of such most profoundly driven approach in recent times is biosorption through microbial biomass and their products. Extracellular polymeric substances are such complex blend of high molecular weight microbial (prokaryotic and eukaryotic) biopolymers. They are mainly composed of proteins, polysaccharides, uronic acids, humic substances, lipids etc. One of its essential constituent is the exopolysaccharide (EPS) released out of self defense against harsh conditions of starvation, pH and temperature, hence it displays exemplary physiological, rheological and physio-chemical properties. Its net anionic makeup allows the biopolymer to effectively sequester positively charged heavy metal ions. The polysaccharide has been expounded deeply in this article with reference to its biosynthesis and emphasizes heavy metal sorption abilities of polymer in terms of mechanism of action and remediation. It reports current investigation and strategic advancements in dealing bacterial cells and their EPS in diverse forms - mixed culture EPS, single cell EPS, live, dead or immobilized EPS. A significant scrutiny is also involved highlighting the existing challenges that still lie in the path of commercialization. The article enlightens the potential of EPS to bring about bio-detoxification of heavy metal contaminated terrestrial and aquatic systems in highly sustainable, economic and eco-friendly manner.
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Tokmina-Lukaszewska M, Shi Z, Tripet B, McDermott TR, Copié V, Bothner B, Wang G. Metabolic response of Agrobacterium tumefaciens 5A to arsenite. Environ Microbiol 2017; 19:710-721. [PMID: 27871140 DOI: 10.1111/1462-2920.13615] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/24/2016] [Accepted: 11/16/2016] [Indexed: 11/26/2022]
Abstract
Wide-spread abundance in soil and water, coupled with high toxicity have put arsenic at the top of the list of environmental contaminants. Early studies demonstrated that both concentration and the valence state of inorganic arsenic (arsenite, As(III) vs. arsenate As(V)) can be modulated by microbes. Using genetics, transcriptomic and proteomic techniques, microbe-arsenic detoxification, respiratory As(V) reduction and As(III) oxidation have since been examined. The effect of arsenic exposure on whole-cell intracellular microbial metabolism, however, has not been extensively studied. We combined LC-MS and 1 H NMR to quantify metabolic changes in Agrobacterium tumefaciens (strain 5A) upon exposure to sub-lethal concentrations of As(III). Metabolomics analysis reveals global differences in metabolite concentrations between control and As(III) exposure groups, with significant perturbations to intermediates shuttling into and cycling within the TCA cycle. These data are most consistent with the disruption of two key TCA cycle enzymes, pyruvate dehydrogenase and α-ketoglutarate dehydrogenase. Glycolysis also appeared altered following As(III) stress, with carbon accumulating as complex saccharides. These observations suggest that an important consequence of As(III) contamination in nature will be to alter microbial carbon metabolism at the microbial community level and thus has the potential to foundationally impact all biogeochemical cycles in the environment.
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Affiliation(s)
| | - Zunji Shi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Timothy R McDermott
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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Genetic analysis of arsenic metabolism in Micrococcus luteus BPB1, isolated from the Bengal basin. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1239-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kumari N, Jagadevan S. Genetic identification of arsenate reductase and arsenite oxidase in redox transformations carried out by arsenic metabolising prokaryotes - A comprehensive review. CHEMOSPHERE 2016; 163:400-412. [PMID: 27565307 DOI: 10.1016/j.chemosphere.2016.08.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Arsenic (As) contamination in water is a cause of major concern to human population worldwide, especially in Bangladesh and West Bengal, India. Arsenite (As(III)) and arsenate (As(V)) are the two common forms in which arsenic exists in soil and groundwater, the former being more mobile and toxic. A large number of arsenic metabolising microorganisms play a crucial role in microbial transformation of arsenic between its different states, thus playing a key role in remediation of arsenic contaminated water. This review focuses on advances in biochemical, molecular and genomic developments in the field of arsenic metabolising bacteria - covering recent developments in the understanding of structure of arsenate reductase and arsenite oxidase enzymes, their gene and operon structures and their mechanism of action. The genetic and molecular studies of these microbes and their proteins may lead to evolution of successful strategies for effective implementation of bioremediation programs.
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Affiliation(s)
- Nisha Kumari
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian School of Mines, Dhanbad, Jharkhand, 826004, India.
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Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A. Appl Environ Microbiol 2016; 82:3471-3480. [PMID: 27037117 DOI: 10.1128/aem.00262-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/28/2016] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED ArsR is a well-studied transcriptional repressor that regulates microbe-arsenic interactions. Most microorganisms have an arsR gene, but in cases where multiple copies exist, the respective roles or potential functional overlap have not been explored. We examined the repressors encoded by arsR1 and arsR2 (ars1 operon) and by arsR3 and arsR4 (ars2 operon) in Agrobacterium tumefaciens 5A. ArsR1 and ArsR4 are very similar in their primary sequences and diverge phylogenetically from ArsR2 and ArsR3, which are also quite similar to one another. Reporter constructs (lacZ) for arsR1, arsR2, and arsR4 were all inducible by As(III), but expression of arsR3 (monitored by reverse transcriptase PCR) was not influenced by As(III) and appeared to be linked transcriptionally to an upstream lysR-type gene. Experiments using a combination of deletion mutations and additional reporter assays illustrated that the encoded repressors (i) are not all autoregulatory as is typically known for ArsR proteins, (ii) exhibit variable control of each other's encoding genes, and (iii) exert variable control of other genes previously shown to be under the control of ArsR1. Furthermore, ArsR2, ArsR3, and ArsR4 appear to have an activator-like function for some genes otherwise repressed by ArsR1, which deviates from the well-studied repressor role of ArsR proteins. The differential regulatory activities suggest a complex regulatory network not previously observed in ArsR studies. The results indicate that fine-scale ArsR sequence deviations of the reiterated regulatory proteins apparently translate to different regulatory roles. IMPORTANCE Given the significance of the ArsR repressor in regulating various aspects of microbe-arsenic interactions, it is important to assess potential regulatory overlap and/or interference when a microorganism carries multiple copies of arsR This study explores this issue and shows that the four arsR genes in A. tumefaciens 5A, associated with two separate ars operons, encode proteins exhibiting various degrees of functional overlap with respect to autoregulation and cross-regulation, as well as control of other functional genes. In some cases, differences in regulatory activity are associated with only limited differences in protein primary structure. The experiments summarized herein also present evidence that ArsR proteins appear to have activator functions, representing novel regulatory activities for ArsR, previously known only to be a repressor.
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40
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Nocelli N, Bogino PC, Banchio E, Giordano W. Roles of Extracellular Polysaccharides and Biofilm Formation in Heavy Metal Resistance of Rhizobia. MATERIALS 2016; 9:ma9060418. [PMID: 28773540 PMCID: PMC5456807 DOI: 10.3390/ma9060418] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/09/2016] [Accepted: 05/17/2016] [Indexed: 12/04/2022]
Abstract
Bacterial surface components and extracellular compounds, particularly flagella, lipopolysaccharides (LPSs), and exopolysaccharides (EPSs), in combination with environmental signals and quorum-sensing signals, play crucial roles in bacterial autoaggregation, biofilm development, survival, and host colonization. The nitrogen-fixing species Sinorhizobium meliloti (S. meliloti) produces two symbiosis-promoting EPSs: succinoglycan (or EPS I) and galactoglucan (or EPS II). Studies of the S.meliloti/alfalfa symbiosis model system have revealed numerous biological functions of EPSs, including host specificity, participation in early stages of host plant infection, signaling molecule during plant development, and (most importantly) protection from environmental stresses. We evaluated functions of EPSs in bacterial resistance to heavy metals and metalloids, which are known to affect various biological processes. Heavy metal resistance, biofilm production, and co-culture were tested in the context of previous studies by our group. A range of mercury (Hg II) and arsenic (As III) concentrations were applied to S. meliloti wild type strain and to mutant strains defective in EPS I and EPS II. The EPS production mutants were generally most sensitive to the metals. Our findings suggest that EPSs are necessary for the protection of bacteria from either Hg (II) or As (III) stress. Previous studies have described a pump in S. meliloti that causes efflux of arsenic from cells to surrounding culture medium, thereby protecting them from this type of chemical stress. The presence of heavy metals or metalloids in culture medium had no apparent effect on formation of biofilm, in contrast to previous reports that biofilm formation helps protect various microorganism species from adverse environmental conditions. In co-culture experiments, EPS-producing heavy metal resistant strains exerted a protective effect on AEPS-non-producing, heavy metal-sensitive strains; a phenomenon termed “rescuing” of the non-resistant strain.
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Affiliation(s)
- Natalia Nocelli
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba X5804BYA, Argentina.
| | - Pablo C Bogino
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba X5804BYA, Argentina.
| | - Erika Banchio
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba X5804BYA, Argentina.
| | - Walter Giordano
- Departamento de Biología Molecular, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba X5804BYA, Argentina.
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Lee HM, Liao CT, Chiang YC, Chang YY, Yeh YT, Du SC, Hsiao YM. Characterization of genes encoding proteins containing HD-related output domain in Xanthomonas campestris pv. campestris. Antonie van Leeuwenhoek 2016; 109:509-22. [PMID: 26821378 DOI: 10.1007/s10482-016-0656-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/19/2016] [Indexed: 11/30/2022]
Abstract
The Gram-negative plant pathogen Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers. The production of Xcc virulence factors is regulated by Clp and RpfF. HD-related output domain (HDOD) is a protein domain of unknown biochemical function. The genome of Xcc encodes three proteins (GsmR, HdpA, and HdpB) with an HDOD. The GsmR has been reported to play a role in the general stress response and cell motility and its expression is positively regulated by Clp. Here, the function and transcription of hdpA and hdpB were characterized. Mutation of hdpA resulted in enhanced bacterial attachment. In addition, the expression of hdpA was positively regulated by RpfF but not by Clp, subject to catabolite repression and affected by several stress conditions. However, mutational analysis and reporter assay showed that hdpB had no effect on the production of a range of virulence factors and its expression was independent of Clp and RpfF. The results shown here not only extend the previous work on RpfF regulation to show that it influences the expression of hdpA in Xcc, but also expand knowledge of the function of the HDOD containing proteins in bacteria.
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Affiliation(s)
- Hsien-Ming Lee
- Institute of Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Ying-Chuan Chiang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Yu-Yin Chang
- Institute of Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Yu-Tzu Yeh
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Shin-Chiao Du
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan.
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Andres J, Bertin PN. The microbial genomics of arsenic. FEMS Microbiol Rev 2016; 40:299-322. [DOI: 10.1093/femsre/fuv050] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 12/17/2022] Open
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Casas-Flores S, Gómez-Rodríguez EY, García-Meza JV. Community of thermoacidophilic and arsenic resistant microorganisms isolated from a deep profile of mine heaps. AMB Express 2015; 5:132. [PMID: 26283066 PMCID: PMC4539307 DOI: 10.1186/s13568-015-0132-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 07/17/2015] [Indexed: 11/23/2022] Open
Abstract
Soluble arsenic (As) in acidic feed solution may inhibit the copper (Cu) bioleaching process within mine heaps. To clarify the effect of soluble arsenic on the live biomass and bioxidative activity in heaps, toxicological assays were performed using a synthetic feed solution given by a mine company. The microorganisms had previously been isolated from two heap samples at up to 66 m depth, and cultured using specific media for chemolithotrophic acidophiles (pH 1–2) and moderate thermophiles (48°C), for arsenic tolerance assay. The four media with the highest biomass were selected to assay As-resistance; one culture (Q63h) was chosen to assay biooxidative activity, using a heap sample that contained chalcopyrite and covellite. We found that 0.5 g/L of As does not affect living biomass or biooxidative activity on Cu sulfides, but it dissolves Cu, while As precipitates as arsenic acid (H3AsO4·½H2O). The arsenic tolerant community, as identified by 16S rDNA gene sequence analysis, was composed of three main metabolic groups: chemolithotrophs (Leptospirillum, Sulfobacillus); chemolithoheterotrophs and organoheterotrophs as Acidovorax temperans, Pseudomonas alcaligenes, P. mendocina and Sphingomonas spp. Leptospirillum spp. and S.thermosulfidooxidans were the dominant taxa in the Q63–66 cultures from the deepest sample of the oldest, highest-temperature heap. The results indicated arsenic resistance in the microbial community, therefore specific primers were used to amplify ars (arsenic resistance system), aio (arsenite oxidase), or arr (arsenate respiratory reduction) genes from total sample DNA. Presence of arsB genes in S. thermosulfidooxidans in the Q63–66 cultures permits H3AsO4-As(V) detoxification and strengthens the community’s response to As.
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Lassalle F, Muller D, Nesme X. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Res Microbiol 2015; 166:729-41. [DOI: 10.1016/j.resmic.2015.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/28/2015] [Accepted: 06/30/2015] [Indexed: 11/30/2022]
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45
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Zhao C, Zhang Y, Chan Z, Chen S, Yang S. Insights into arsenic multi-operons expression and resistance mechanisms in Rhodopseudomonas palustris CGA009. Front Microbiol 2015; 6:986. [PMID: 26441915 PMCID: PMC4585019 DOI: 10.3389/fmicb.2015.00986] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/04/2015] [Indexed: 11/21/2022] Open
Abstract
Arsenic (As) is widespread in the environment and causes numerous health problems. Rhodopseudomonas palustris has been regarded as a good model organism for studying arsenic detoxification since it was first demonstrated to methylate environmental arsenic by conversion to soluble or gaseous methylated species. However, the detailed arsenic resistance mechanisms remain unknown though there are at least three arsenic-resistance operons (ars1, ars2, and ars3) in R. palustris. In this study, we investigated how arsenic multi-operons contributed to arsenic detoxification in R. palustris. The expression of ars2 or ars3 operons increased with increasing environmental arsenite (As(III)) concentrations (up to 1.0 mM) while transcript of ars1 operon was not detected in the middle log-phase (55 h). ars2 operon was actively expressed even at the low concentration of As(III) (0.01 μM), whereas the ars3 operon was expressed at 1.0 μM of As(III), indicating that there was a differential regulation mechanism for the three arsenic operons. Furthermore, ars2 and ars3 operons were maximally transcribed in the early log-phase where ars2 operon was 5.4-fold higher than that of ars3 operon. A low level of ars1 transcript was only detected at 43 h (early log-phase). Arsenic speciation analysis demonstrated that R. palustris could reduce As(V) to As(III). Collectively, strain CGA009 detoxified arsenic by using arsenic reduction and methylating arsenic mechanism, while the latter might occur with the presence of higher concentrations of arsenic.
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Affiliation(s)
- Chungui Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University Xiamen, China
| | - Yi Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University Xiamen, China
| | - Zhuhua Chan
- Department of Bioengineering and Biotechnology, Huaqiao University Xiamen, China ; State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, State Oceanic Administration Xiamen, China
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University Xiamen, China
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Hu M, Li F, Liu C, Wu W. The diversity and abundance of As(III) oxidizers on root iron plaque is critical for arsenic bioavailability to rice. Sci Rep 2015; 5:13611. [PMID: 26324258 PMCID: PMC4555042 DOI: 10.1038/srep13611] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/30/2015] [Indexed: 01/31/2023] Open
Abstract
Iron plaque is a strong adsorbent on rice roots, acting as a barrier to prevent metal uptake by rice. However, the role of root iron plaque microbes in governing metal redox cycling and metal bioavailability is unknown. In this study, the microbial community structure on the iron plaque of rice roots from an arsenic-contaminated paddy soil was explored using high-throughput next-generation sequencing. The microbial composition and diversity of the root iron plaque were significantly different from those of the bulk and rhizosphere soils. Using the aoxB gene as an identifying marker, we determined that the arsenite-oxidizing microbiota on the iron plaque was dominated by Acidovorax and Hydrogenophaga-affiliated bacteria. More importantly, the abundance of arsenite-oxidizing bacteria (AsOB) on the root iron plaque was significantly negatively correlated with the arsenic concentration in the rice root, straw and grain, indicating that the microbes on the iron plaque, particularly the AsOB, were actively catalyzing arsenic transformation and greatly influencing metal uptake by rice. This exploratory research represents a preliminary examination of the microbial community structure of the root iron plaque formed under arsenic pollution and emphasizes the importance of the root iron plaque environment in arsenic biogeochemical cycling compared with the soil-rhizosphere biotope.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Fangbai Li
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Chuanping Liu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
| | - Weijian Wu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China
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Arsène-Ploetze F, Bertin PN, Carapito C. Proteomic tools to decipher microbial community structure and functioning. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:13599-13612. [PMID: 25475614 PMCID: PMC4560766 DOI: 10.1007/s11356-014-3898-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing information on key players that carry out main metabolic functions and addressing the adaptation capacities of living organisms in situ. In this review, a wide range of proteomic approaches applied to investigate the structure and functioning of microbial communities as well as recent examples of such studies are presented.
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Affiliation(s)
- Florence Arsène-Ploetze
- Génétique moléculaire, Génomique et Microbiologie, Université de Strasbourg, UMR7156 CNRS, Strasbourg, France,
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48
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Guo H, Liu Z, Ding S, Hao C, Xiu W, Hou W. Arsenate reduction and mobilization in the presence of indigenous aerobic bacteria obtained from high arsenic aquifers of the Hetao basin, Inner Mongolia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 203:50-59. [PMID: 25863882 DOI: 10.1016/j.envpol.2015.03.034] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
Intact aquifer sediments were collected to obtain As-resistant bacteria from the Hetao basin. Two strains of aerobic As-resistant bacteria (Pseudomonas sp. M17-1 and Bacillus sp. M17-15) were isolated from the aquifer sediments. Those strains exhibited high resistances to both As(III) and As(V). Results showed that both strains had arr and ars genes, and led to reduction of dissolved As(V), goethite-adsorbed As(V), scorodite As(V) and sediment As(V), in the presence of organic carbon as the carbon source. After reduction of solid As(V), As release was observed from the solids to solutions. Strain M17-15 had a higher ability than strain M17-1 in reducing As(V) and promoting the release of As. These results suggested that the strains would mediate As(V) reduction to As(III), and thereafter release As(III), due to the higher mobility of As(III) in most aquifer systems. The processes would play an important role in genesis of high As groundwater.
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Affiliation(s)
- Huaming Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China.
| | - Zeyun Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China; Shanxi Conservancy Technical Institute, Yuncheng 044004, PR China
| | - Susu Ding
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Chunbo Hao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Wei Xiu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, PR China
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, PR China
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Corsini A, Colombo M, Muyzer G, Cavalca L. Characterization of the arsenite oxidizer Aliihoeflea sp. strain 2WW and its potential application in the removal of arsenic from groundwater in combination with Pf-ferritin. Antonie van Leeuwenhoek 2015; 108:673-84. [PMID: 26149126 DOI: 10.1007/s10482-015-0523-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
A heterotrophic arsenite-oxidizing bacterium, strain 2WW, was isolated from a biofilter treating arsenic-rich groundwater. Comparative analysis of 16S rRNA gene sequences showed that it was closely related (98.7 %) to the alphaproteobacterium Aliihoeflea aesturari strain N8(T). However, it was physiologically different by its ability to grow at relatively low substrate concentrations, low temperatures and by its ability to oxidize arsenite. Here we describe the physiological features of strain 2WW and compare these to its most closely related relative, A. aestuari strain N8(T). In addition, we tested its efficiency to remove arsenic from groundwater in combination with Pf-ferritin. Strain 2WW oxidized arsenite to arsenate between pH 5.0 and 8.0, and from 4 to 30 °C. When the strain was used in combination with a Pf-ferritin-based material for arsenic removal from natural groundwater, the removal efficiency was significantly higher (73 %) than for Pf-ferritin alone (64 %). These results showed that arsenite oxidation by strain 2WW combined with Pf-ferritin-based material has a potential in arsenic removal from contaminated groundwater.
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Affiliation(s)
- Anna Corsini
- DeFENS - Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy
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Sousa T, Branco R, Piedade AP, Morais PV. Hyper Accumulation of Arsenic in Mutants of Ochrobactrum tritici Silenced for Arsenite Efflux Pumps. PLoS One 2015; 10:e0131317. [PMID: 26132104 PMCID: PMC4489015 DOI: 10.1371/journal.pone.0131317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 06/01/2015] [Indexed: 11/19/2022] Open
Abstract
Ochrobactrum tritici SCII24T is a highly As-resistant bacterium, with two previously described arsenic resistance operons, ars1 and ars2. Among a large number of genes, these operons contain the arsB and Acr3 genes that encode the arsenite efflux pumps responsible for arsenic resistance. Exploring the genome of O. tritici SCII24T, an additional putative operon (ars3) was identified and revealed the presence of the Acr3_2 gene that encodes for an arsenite efflux protein but which came to prove to not be required for full As resistance. The genes encoding for arsenite efflux pumps, identified in this strain, were inactivated to develop microbial accumulators of arsenic as new tools for bioremediation. Six different mutants were produced, studied and three were more useful as biotools. O. tritici wild type and the Acr3-mutants showed the highest resistance to As(III), being able to grow up to 50 mM of arsenite. On the other hand, arsB-mutants were not able to grow at concentrations higher than 1 mM As(III), and were the most As(III) sensitive mutants. In the presence of 1 mM As(III), the strain with arsB and Acr3_1 mutated showed the highest intracellular arsenic concentration (up to 17 ng(As)/mg protein), while in assays with 5 mM As(III), the single arsB-mutant was able to accumulate the highest concentration of arsenic (up to 10 ng(As)/mg protein). Therefore, arsB is the main gene responsible for arsenite resistance in O. tritici. However, both genes arsB and Acr3_1 play a crucial role in the resistance mechanism, depending on the arsenite concentration in the medium. In conclusion, at moderate arsenite concentrations, the double arsB- and Acr3_1-mutant exhibited a great ability to accumulate arsenite and can be seen as a promising bioremediation tool for environmental arsenic detoxification.
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Affiliation(s)
| | | | - Ana Paula Piedade
- CEMUC-Department of Mechanical Engineering, University of Coimbra, 3030–788 Coimbra, Portugal
| | - Paula V. Morais
- IMAR-CMA, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- * E-mail:
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