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Goff JL, Szink EG, Durrence KL, Lui LM, Nielsen TN, Kuehl JV, Hunt KA, Chandonia JM, Huang J, Thorgersen MP, Poole FL, Stahl DA, Chakraborty R, Deutschbauer AM, Arkin AP, Adams MWW. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface. ENVIRONMENTAL MICROBIOME 2024; 19:26. [PMID: 38671539 PMCID: PMC11046850 DOI: 10.1186/s40793-024-00570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Elizabeth G Szink
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Konnor L Durrence
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jiawen Huang
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Romy Chakraborty
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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2
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Hao X, Zhao Q, Zhou X, Huang Q, Liu YR. Labile carbon inputs boost microbial contribution to legacy mercury reduction and emissions from industry-polluted soils. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133122. [PMID: 38056276 DOI: 10.1016/j.jhazmat.2023.133122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Soils is a crucial reservoir influencing mercury (Hg) emissions and soil-air exchange dynamics, partially modulated by microbial reducers aiding Hg reduction. Yet, the extent to which microbial engagements contribute to soil Hg volatilization remains largely unknown. Here, we characterized Hg-reducing bacterial communities in natural and anthropogenically perturbed soil environments and quantified their contribution to soil Hg(0) volatilization. Our results revealed distinct Hg-reducing bacterial compositions alongside elevated mercuric reductase (merA) gene abundance and diversity in soils adjacent to chemical factories compared to less-impacted ecosystems. Notably, solely industry-impacted soils exhibited increased merA gene abundance along Hg gradients, indicating microbial adaption to Hg selective pressure through quantitative changes in Hg reductase and genetic diversity. Microcosm studies demonstrated that glucose inputs boosted microbial involvement and induced 2-8 fold increments in cumulative Hg(0) volatilization in industry-impacted soils. Microbially-mediated Hg reduction contributed to 41.6% of soil Hg(0) volatilization in industry-impacted soils under 25% water-holding capacity and glucose input conditions over a 21-day incubation period. Alcaligenaceae, Moraxellaceae, Nitrosomonadaceae and Shewanellaceae were identified as potential contributors to Hg(0) volatilization in the soil. Collectively, our study provides novel insights into microbially-mediated Hg reduction and soil-air exchange processes, with important implications for risk assessment and management of industrial Hg-contaminated soils.
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Affiliation(s)
- Xiuli Hao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinquan Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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3
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Saha BK, Roy V, Saha J, Chatterjee A, Pal A. Study of mercury resistance and Fourier transform infrared spectroscopy-based metabolic profiling of a potent Bacillus tropicus strain from forest soil. J Basic Microbiol 2024; 64:e2300351. [PMID: 37847888 DOI: 10.1002/jobm.202300351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/01/2023] [Accepted: 10/07/2023] [Indexed: 10/19/2023]
Abstract
Mercury (Hg) is a highly toxic heavy metal and Hg-resistant indigenous bacterial isolates may offer a green and cost-effective bioremediation strategy to counter Hg contamination. In this study, a potent Hg-resistant bacterium was isolated from the forest soil of a bird sanctuary. Identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry depicted the isolate as a strain of Bacillus tropicus, validated by morphological, biochemical, and molecular studies. The isolate demonstrated biological Hg removal efficiency and capacity of 50.67% and 19.76 mg g-1 , respectively. The plasmid borne resistance determinant, merA, encoding mercuric reductase, was detected in the bacterium endowing it with effective Hg volatilization and resistance capability. A Fourier-transform infrared spectroscopic comparative metabolic profiling revealed the involvement of various functional groups like -COOH, -CH2 , -OH, PO4 - and so on, resulting in differential spectral patterns of the bacterium both in control and Hg-exposed situations. A temporal variance in metabolic signature was also observed during the early and mid-log phase of growth in the presence of Hg. The bacterium described in this study is the first indigenous Hg-resistant strain isolated from the Uttar Dinajpur region, which could be further explored and exploited as a potent bioresource for Hg remediation.
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Affiliation(s)
- Barnan K Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Vivek Roy
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Jayanti Saha
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
- Department of Botany, Acharya Prafulla Chandra Roy Government College, Himachal Bihar, Matigara, Siliguri, West Bengal, India
| | - Abhik Chatterjee
- Design, Synthesis & Simulation Laboratory, Department of Chemistry, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
| | - Ayon Pal
- Microbiology and Computational Biology Laboratory, Department of Botany, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal, India
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Ilyas M, Purkait D, Atmakuri K. Genomic islands and their role in fitness traits of two key sepsis-causing bacterial pathogens. Brief Funct Genomics 2024; 23:55-68. [PMID: 36528816 DOI: 10.1093/bfgp/elac051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 01/21/2024] Open
Abstract
To survive and establish a niche for themselves, bacteria constantly evolve. Toward that, they not only insert point mutations and promote illegitimate recombinations within their genomes but also insert pieces of 'foreign' deoxyribonucleic acid, which are commonly referred to as 'genomic islands' (GEIs). The GEIs come in several forms, structures and types, often providing a fitness advantage to the harboring bacterium. In pathogenic bacteria, some GEIs may enhance virulence, thus altering disease burden, morbidity and mortality. Hence, delineating (i) the GEIs framework, (ii) their encoded functions, (iii) the triggers that help them move, (iv) the mechanisms they exploit to move among bacteria and (v) identification of their natural reservoirs will aid in superior tackling of several bacterial diseases, including sepsis. Given the vast array of comparative genomics data, in this short review, we provide an overview of the GEIs, their types and the compositions therein, especially highlighting GEIs harbored by two important pathogens, viz. Acinetobacter baumannii and Klebsiella pneumoniae, which prominently trigger sepsis in low- and middle-income countries. Our efforts help shed some light on the challenges these pathogens pose when equipped with GEIs. We hope that this review will provoke intense research into understanding GEIs, the cues that drive their mobility across bacteria and the ways and means to prevent their transfer, especially across pathogenic bacteria.
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Affiliation(s)
- Mohd Ilyas
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Dyuti Purkait
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Krishnamohan Atmakuri
- Bacterial Pathogenesis Lab, Infection and Immunity Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001, India
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Maslova O, Beletsky A, Mindlin S, Petrova N, Mardanov A, Petrova M. Conjugative Plasmid pPPUT-Tik1-1 from a Permafrost Pseudomonas putida Strain and Its Present-Day Counterparts Inhabiting Environments and Clinics. Int J Mol Sci 2023; 24:13518. [PMID: 37686323 PMCID: PMC10488154 DOI: 10.3390/ijms241713518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
A novel group of conjugative plasmids of Pseudomonas is characterized. The prototype plasmid pPPUT-Tik1-1 (153,663 bp), isolated from a permafrost strain of P. putida Tik1, carries a defective mercury transposon, Tn501, and a streptomycin resistance transposon, Tn5393. Ten plasmids and 34 contigs with backbone regions closely related to pPPUT-Tik1-1 have been found in GenBank. Two of these plasmids from clinical strains of P. putida and P. fulva are almost identical to the ancient plasmid. A characteristic feature of this group of plasmids is the presence of two genes encoding the initiators of replication (repA1 and repA2). None of these genes have high similarity with plasmid replication genes belonging to known incompatibility groups. It has been demonstrated that while pPPUT-Tik1-1-like plasmids have homologous backbone regions, they significantly differ by the molecular structure and the predicted functions of their accessory regions. Some of the pPPUT-Tik1-1-related plasmids carry determinants of antibiotic resistance and/or heavy metal salts. Some plasmids are characterized by the ability to degrade xenobiotics. Plasmids related to pPPUT-Tik1-1 are characterized by a narrow host range and are found in various species of the Pseudomonas genus. Interestingly, we also found shorter plasmid variants containing the same replication module, but lacking conjugation genes and containing other structural changes that strongly distinguish them from plasmids related to pPPUT-Tik1-1, indicating that the structure of the replication module cannot be used as the sole criterion for classifying plasmids. Overall, the results suggest that the plasmids of the novel group can be spread using conjugation in environmental and clinical strains of Pseudomonas and may play diverse adaptive functions due to the presence of various accessory regions.
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Affiliation(s)
- Olga Maslova
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.); (N.P.)
| | - Alexey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia; (A.B.); (A.M.)
| | - Sofia Mindlin
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.); (N.P.)
| | - Nika Petrova
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.); (N.P.)
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 117312 Moscow, Russia; (A.B.); (A.M.)
| | - Mayya Petrova
- National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.); (N.P.)
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6
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Meyer L, Guyot S, Chalot M, Capelli N. The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115185. [PMID: 37385017 DOI: 10.1016/j.ecoenv.2023.115185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/20/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023]
Abstract
Mercury (Hg) pollution is a global issue due to the high toxicity and wide dispersion of Hg around the world. Whether due to anthropogenic activities or natural processes, Hg emissions are steadily increasing, with very high levels in some regions, directly threatening human and ecosystem health. However, bacteria and fungi have evolved and adapted in response to Hg-induced stress and have developed tolerance mechanisms, notably based on the mer operon system that is involved in Hg uptake and biovolatilization via Hg reduction reactions. Other processes, such as bioaccumulation or extracellular sequestration, are involved in Hg resistance, and the study of contaminated soils has allowed the isolation of a number of microorganisms capable of these mechanisms, with strong potential for the implementation of bioremediation approaches. In addition to playing an important role in determining the fate of Hg in the biogeochemical cycle, these microorganisms can indeed be applied to reduce Hg concentrations or at least stabilize Hg for the remediation of polluted soils. Moreover, thanks to the development of biotechnological tools, bioremediation based on Hg-tolerant microorganisms can be optimized. Finally, these microorganisms are relevant candidates for biomonitoring, for example, through the engineering of biosensors, because the detection of Hg is a major issue in preserving the health of living beings.
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Affiliation(s)
- Lorraine Meyer
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France
| | - Stéphane Guyot
- Université de Bourgogne, Institut Agro, PAM UMR A 02.102, F-21000 Dijon, France
| | - Michel Chalot
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France; Université de Lorraine, F-54000 Nancy, France
| | - Nicolas Capelli
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France.
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7
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Rupa SA, Patwary MAM, Matin MM, Ghann WE, Uddin J, Kazi M. Interaction of mercury species with proteins: towards possible mechanism of mercurial toxicology. Toxicol Res (Camb) 2023; 12:355-368. [PMID: 37397928 PMCID: PMC10311172 DOI: 10.1093/toxres/tfad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 07/04/2023] Open
Abstract
The nature of the binding of mercurials (organic and inorganic) and their subsequent transformations in biological systems is a matter of great debate as several different hypotheses have been proposed and none of them has been conclusively proven to explain the characteristics of Hg binding with the proteins. Thus, the chemical nature of Hg-protein binding through the possible transportation mechanism in living tissues is critically reviewed herein. Emphasis is given to the process of transportation, and binding of Hg species with selenol-containing biomolecules that are appealing for toxicological studies as well as the advancement of environmental and biological research.
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Affiliation(s)
| | | | | | - William Emmanuel Ghann
- Center for Nanotechnology, Department of Natural Sciences, Coppin State University, Baltimore, MD 21216, USA
| | - Jamal Uddin
- Center for Nanotechnology, Department of Natural Sciences, Coppin State University, Baltimore, MD 21216, USA
| | - Mohsin Kazi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. BOX-2457, Riyadh 11451, Saudi Arabia
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Chen Y, Guo Y, Liu Y, Xiang Y, Liu G, Zhang Q, Yin Y, Cai Y, Jiang G. Advances in bacterial whole-cell biosensors for the detection of bioavailable mercury: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161709. [PMID: 36682565 DOI: 10.1016/j.scitotenv.2023.161709] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Mercury (Hg) and its organic compounds, especially monomethylmercury (MeHg), cause major damage to the ecosystem and human health. In surface water or sediments, microorganisms play a crucial role in the methylation and demethylation of Hg. Given that Hg transformation processes are intracellular reactions, accurate assessment of the bioavailability of Hg(II)/MeHg in the environment, particularly for microorganisms, is of major importance. Compared with traditional analytical methods, bacterial whole-cell biosensors (BWCBs) provide a more accurate, convenient, and cost-effective strategy to assess the environmental risks of Hg(II)/MeHg. This Review summarizes recent progress in the application of BWCBs in the detection of bioavailable Hg(II)/MeHg, providing insight on current challenges and strategies. The principle and components of BWCBs for Hg(II)/MeHg bioavailability analysis are introduced. Furthermore, the impact of water chemical factors on the bioavailability of Hg is discussed as are future perspectives of BWCBs in bioavailable Hg analysis and optimization of BWCBs.
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Affiliation(s)
- Yueqian Chen
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Yingying Guo
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanwei Liu
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuping Xiang
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Guangliang Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Qinghua Zhang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yongguang Yin
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yong Cai
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Karnachuk OV, Beletsky AV, Rakitin AL, Ikkert OP, Avakyan MR, Zyusman VS, Napilov A, Mardanov AV, Ravin NV. Antibiotic-Resistant Desulfovibrio Produces H2S from Supplements for Animal Farming. Microorganisms 2023; 11:microorganisms11040838. [PMID: 37110261 PMCID: PMC10146906 DOI: 10.3390/microorganisms11040838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Sulphate-reducing bacteria, primarily Desulfovibrio, are responsible for the active generation of H2S in swine production waste. The model species for sulphate reduction studies, Desulfovibrio vulgaris strain L2, was previously isolated from swine manure characterized by high rates of dissimilatory sulphate reduction. The source of electron acceptors in low-sulphate swine waste for the high rate of H2S formation remains uncertain. Here, we demonstrate the ability of the L2 strain to use common animal farming supplements including L-lysine-sulphate, gypsum and gypsum plasterboards as electron acceptors for H2S production. Genome sequencing of strain L2 revealed the presence of two megaplasmids and predicted resistance to various antimicrobials and mercury, which was confirmed in physiological experiments. Most of antibiotic resistance genes (ARG) are carried by two class 1 integrons located on the chromosome and on the plasmid pDsulf-L2-2. These ARGs, predicted to confer resistance to beta-lactams, aminoglycosides, lincosamides, sulphonamides, chloramphenicol and tetracycline, were probably laterally acquired from various Gammaproteobacteria and Firmicutes. Resistance to mercury is likely enabled by two mer operons also located on the chromosome and on pDsulf-L2-2 and acquired via horizontal gene transfer. The second megaplasmid, pDsulf-L2-1, encoded nitrogenase, catalase and type III secretion system suggesting close contact of the strain with intestinal cells in the swine gut. The location of ARGs on mobile elements allows us to consider D. vulgaris strain L2 as a possible vector transferring antimicrobials resistance determinants between the gut microbiote and microbial communities in environmental biotopes.
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Nivetha N, Srivarshine B, Sowmya B, Rajendiran M, Saravanan P, Rajeshkannan R, Rajasimman M, Pham THT, Shanmugam V, Dragoi EN. A comprehensive review on bio-stimulation and bio-enhancement towards remediation of heavy metals degeneration. CHEMOSPHERE 2023; 312:137099. [PMID: 36372332 DOI: 10.1016/j.chemosphere.2022.137099] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Pollution of heavy metals is one of the risky contaminations that should be managed for all intents and purposes of general well-being concerns. The bioaccumulation of these heavy metals inside our bodies and pecking orders will influence our people in the future. Bioremediation is a bio-mechanism where residing organic entities use and reuse the squanders that are reused to one more form. This could be accomplished by taking advantage of the property of explicit biomolecules or biomass that is equipped for restricting by concentrating the necessary heavy metal particles. The microorganisms can't obliterate the metal yet can change it into a less harmful substance. In this unique circumstance, this review talks about the sources, poisonousness, impacts, and bioremediation strategies of five heavy metals: lead, mercury, arsenic, chromium, and manganese. The concentrations here are the ordinary strategies for bioremediation such as biosorption methods, the use of microbes, green growth, and organisms, etc. This review demonstrates the toxicity of heavy metal contamination degradation by biotransformation through bacterioremediation and biodegradation through mycoremediation.
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Affiliation(s)
- N Nivetha
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - B Srivarshine
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - B Sowmya
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | | | - Panchamoorthy Saravanan
- Department of Petrochemical Technology, UCE - BIT Campus, Anna University, Tiruchirappalli, Tamil Nadu, India
| | - R Rajeshkannan
- Department of Chemical Engineering, Annamalai University, Tamilnadu, India
| | - M Rajasimman
- Department of Chemical Engineering, Annamalai University, Tamilnadu, India
| | - Thi Hong Trang Pham
- Institute for Global Health Innovations, Duy Tan University, Da Nang, 550000, Viet Nam; Faculty of Natural Science, Duy Tan University, Da Nang, 550000, Viet Nam
| | - VenkatKumar Shanmugam
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| | - Elena-Niculina Dragoi
- "Cristofor Simionescu" Faculty of Chemical Engineering and Environmental Protection, "Gheorghe Asachi" Technical University, Iasi, Bld Mangeron No 73, 700050, Romania
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11
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)–5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3”)-IIa, aph(3’)-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- *Correspondence: Stephanie S. R. Souza, ; orcid.org/0000-0002-4207-8231
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- Cheryl P. Andam, ; orcid.org/0000-0003-4428-0924
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12
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Sharma P, Rekhi P, Debnath M. Removal of Heavy Metal by Biosurfactant Producing Novel Halophilic
Staphylococcus sciuri subsp. rodentium
Strain SE I Isolated from Sambhar Salt Lake. ChemistrySelect 2022. [DOI: 10.1002/slct.202202970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Priyanka Sharma
- Department of Bioscience Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Pavni Rekhi
- Department of Bioscience Manipal University Jaipur Jaipur 303007 Rajasthan India
| | - Mousumi Debnath
- Department of Bioscience Manipal University Jaipur Jaipur 303007 Rajasthan India
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13
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Fang J, Jiang W, Meng S, He W, Wang G, Guo E, Yan Y. Polychaete Bioturbation Alters the Taxonomic Structure, Co-occurrence Network, and Functional Groups of Bacterial Communities in the Intertidal Flat. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02036-2. [PMID: 35604433 DOI: 10.1007/s00248-022-02036-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Polychaetes are important benthic macrofauna that lives in sediments, usually in intertidal flats with high organic content and high sulfide. It has been suggested that polychaete bioturbation could perform environmental remediation. During the process, the microbial community plays important roles. Here, we used high-throughput sequencing technology to study the bioturbation effects on the bacterial community in the polychaete (Perinereis aibuhitensis) burrows at different tidal positions in intertidal flat. The results showed that the bacterial communities were dramatically influenced by the polychaete bioturbation. The ACE, Chao, and Shannon indices of the polychaete burrows increased in summer. Dominant phyla in the polychaete burrows were Proteobacteria, Campilobacterota, Desulfobacterota, Chloroflexi, and Bacteroidota, and the dominant bacterial families were Sulfurvaceae, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, Desulfobulbaceae, and Sulfurimonadaceae. Results of linear discriminant analysis effect size (LEfSe) showed that groups that include organic matter degraders, such as Bacteroidota, Flavobacteriaceae, Rhodobacteraceae, Woeseiaceae, and groups that include sulfur oxidizers, such as Campilobacterota, Sulfurovaceae, Rhodobacteraceae, Desulfobulbaceae, and Sulfurimonadaceae, were significantly increased due to the polychaete bioturbation. The polychaete bioturbation reduced the complexity of the bacterial co-occurrence network while increased its modularity and homogeneity. The polychaete bioturbation also changed the functional groups, which significantly enhanced in functional groups of aerobic nitrite oxidation, nitration, dark thiosulfate oxidation, dark sulfur oxidation, and dark sulfite oxidation, while nitrogen respiration and nitrate respiration decreased. These results provide insight into the impact of bacterial communities under the intertidal polychaete bioturbation.
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Affiliation(s)
- Jinghui Fang
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Wenwen Jiang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangdong, 510275, People's Republic of China.
| | - Shan Meng
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
- China Ocean Press, Beijing, 100081, People's Republic of China
| | - Wei He
- Laboratory for Marine Fisheries Science and Food Production Processes, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People's Republic of China
| | - Guodong Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
- Homey Group Co. Ltd, Rongcheng, 264306, People's Republic of China
| | - Enmian Guo
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Yisu Yan
- Qingdao Dagang Customs, Qingdao, 266011, People's Republic of China
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14
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Transcriptomic evidence for versatile metabolic activities of mercury cycling microorganisms in brackish microbial mats. NPJ Biofilms Microbiomes 2021; 7:83. [PMID: 34799579 PMCID: PMC8605020 DOI: 10.1038/s41522-021-00255-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 01/29/2023] Open
Abstract
Methylmercury, biomagnifying through food chains, is highly toxic for aquatic life. Its production and degradation are largely driven by microbial transformations; however, diversity and metabolic activity of mercury transformers, resulting in methylmercury concentrations in environments, remain poorly understood. Microbial mats are thick biofilms where oxic and anoxic metabolisms cooccur, providing opportunities to investigate the complexity of the microbial mercury transformations over contrasted redox conditions. Here, we conducted a genome-resolved metagenomic and metatranscriptomic analysis to identify putative activity of mercury reducers, methylators and demethylators in microbial mats strongly contaminated by mercury. Our transcriptomic results revealed the major role of rare microorganisms in mercury cycling. Mercury methylators, mainly related to Desulfobacterota, expressed a large panel of metabolic activities in sulfur, iron, nitrogen, and halogen compound transformations, extending known activities of mercury methylators under suboxic to anoxic conditions. Methylmercury detoxification processes were dissociated in the microbial mats with methylmercury cleavage being carried out by sulfide-oxidizing Thiotrichaceae and Rhodobacteraceae populations, whereas mercury reducers included members of the Verrucomicrobia, Bacteroidetes, Gammaproteobacteria, and different populations of Rhodobacteraceae. However most of the mercury reduction was potentially carried out anaerobically by sulfur- and iron-reducing Desulfuromonadaceae, revising our understanding of mercury transformers ecophysiology.
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15
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Transcription at a Distance in the Budding Yeast Saccharomyces cerevisiae. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proper transcriptional regulation depends on the collaboration of multiple layers of control simultaneously. Cells tightly balance cellular resources and integrate various signaling inputs to maintain homeostasis during growth, development and stressors, among other signals. Many eukaryotes, including the budding yeast Saccharomyces cerevisiae, exhibit a non-random distribution of functionally related genes throughout their genomes. This arrangement coordinates the transcription of genes that are found in clusters, and can occur over long distances. In this work, we review the current literature pertaining to gene regulation at a distance in budding yeast.
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16
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Huang Z, Wei Z, Tang M, Yu S, Jiao H. Biological treatments of mercury and nitrogen oxides in flue gas: biochemical foundations, technological potentials, and recent advances. ADVANCES IN APPLIED MICROBIOLOGY 2021; 116:133-168. [PMID: 34353503 DOI: 10.1016/bs.aambs.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Nitrogen oxides (NOx) and mercury (Hg) are commonly found coexistent pollutants in combustion flue gas. Ever-increasing emission of atmospheric Hg and NOx has caused considerable environmental risks. Traditional flue gas demercuration and denitration techniques have many socioeconomic, technological and environmental drawbacks. Biotechnologies can be a promising and prospective alternative strategy. This article discusses theoretical foundation (biochemistry and genomic basis) and technical potentials (Hg0 bio-oxidation coupled to denitrification) of bioremoval of Hg and NOx in flue gas and summarized recent experimental and technological advances. Finally, several specific technical perspectives have been put forward to better guide future researches.
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Affiliation(s)
- Zhenshan Huang
- School of Environmental Science and Engineering, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Zaishan Wei
- School of Environmental Science and Engineering, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China.
| | - Meiru Tang
- School of Environmental Science and Engineering, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Shan Yu
- School of Environmental Science and Engineering, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Huaiyong Jiao
- School of Environmental Science and Engineering, Sun Yat-sen University; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
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17
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Abstract
Plasmids play an important role in bacterial evolution by transferring niche-adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons, which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coexistence is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coexistence was stably maintained without positive selection for plasmid-borne gene functions and was associated with compensatory evolution to reduce fitness costs. In contrast, with positive selection, plasmid coexistence was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximize plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or nonredundancy of accessory gene functions among the coexisting plasmids.
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18
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Robas M, Jiménez PA, González D, Probanza A. Bio-Mercury Remediation Suitability Index: A Novel Proposal That Compiles the PGPR Features of Bacterial Strains and Its Potential Use in Phytoremediation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:4213. [PMID: 33923384 PMCID: PMC8071564 DOI: 10.3390/ijerph18084213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022]
Abstract
Soil pollution from heavy metals, especially mercury, is an environmental problem for human health. Biological approaches offer interesting tools, which necessarily involve the selection of organisms capable of transforming the environment via bioremediation. To evaluate the potential use of microorganisms in phytorhizoremediation, bacterial strains were isolated from rhizospheric and bulk soil under conditions of chronic natural mercury, which were identified and characterized by studying the following: (i) their plant growth promoting rhizobacteria (PGPR) activities; and (ii) their maximum bactericide concentration of mercury. Information regarding auxin production, phosphate solubilization, siderophore synthesis and 1-aminocyclopropane-1-carboxylic acid deaminase (ACCd) capacity of the isolates was compiled in order to select the strains that fit potential biotechnological use. To achieve this objective, the present work proposes the Bio-Mercury Remediation Suitability Index (BMR-SI), which reflects the integral behavior of the strains for heavy metal polluted soil bioremediation. Only those strains that rigorously fulfilled all of the established criteria were selected for further assays.
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Affiliation(s)
- Marina Robas
- Department of Pharmaceutical Science and Health, Montepríncipe Campus, CEU San Pablo University, Ctra. Boadilla del Monte Km 5.300, 28668 Boadilla del Monte, Spain; (P.A.J.); (D.G.); (A.P.)
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19
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Leclerc M, Harrison MC, Storck V, Planas D, Amyot M, Walsh DA. Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands. mSphere 2021; 6:e00021-21. [PMID: 33731467 PMCID: PMC8546676 DOI: 10.1128/msphere.00021-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023] Open
Abstract
Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10-3 day-1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day-1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.
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Affiliation(s)
- Maxime Leclerc
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
- GRIL, Département de Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | | | - Veronika Storck
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - Dolors Planas
- GRIL, Département de Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Marc Amyot
- GRIL, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montréal, Québec, Canada
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20
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
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21
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Arregui G, Hipólito P, Pallol B, Lara-Dampier V, García-Rodríguez D, Varela HP, Tavakoli Zaniani P, Balomenos D, Paape T, Coba de la Peña T, Lucas MM, Pueyo JJ. Mercury-Tolerant Ensifer medicae Strains Display High Mercuric Reductase Activity and a Protective Effect on Nitrogen Fixation in Medicago truncatula Nodules Under Mercury Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:560768. [PMID: 33519831 PMCID: PMC7840509 DOI: 10.3389/fpls.2020.560768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 12/22/2020] [Indexed: 05/27/2023]
Abstract
Mercury (Hg) is extremely toxic for all living organisms. Hg-tolerant symbiotic rhizobia have the potential to increase legume tolerance, and to our knowledge, the mechanisms underlying Hg tolerance in rhizobia have not been investigated to date. Rhizobial strains of Ensifer medicae, Rhizobium leguminosarum bv. trifolii and Bradyrhizobium canariense previously isolated from severely Hg-contaminated soils showed different levels of Hg tolerance. The ability of the strains to reduce mercury Hg2+ to Hg0, a volatile and less toxic form of mercury, was assessed using a Hg volatilization assay. In general, tolerant strains displayed high mercuric reductase activity, which appeared to be inducible in some strains when grown at a sub-lethal HgCl2 concentration. A strong correlation between Hg tolerance and mercuric reductase activity was observed for E. medicae strains, whereas this was not the case for the B. canariense strains, suggesting that additional Hg tolerance mechanisms could be playing a role in B. canariense. Transcript abundance from merA, the gene that encodes mercuric reductase, was quantified in tolerant and sensitive E. medicae and R. leguminosarum strains. Tolerant strains presented higher merA expression than sensitive ones, and an increase in transcript abundance was observed for some strains when bacteria were grown in the presence of a sub-lethal HgCl2 concentration. These results suggest a regulation of mercuric reductase in rhizobia. Expression of merA genes and mercuric reductase activity were confirmed in Medicago truncatula nodules formed by a sensitive or a tolerant E. medicae strain. Transcript accumulation in nodules formed by the tolerant strain increased when Hg stress was applied, while a significant decrease in expression occurred upon stress application in nodules formed by the Hg-sensitive strain. The effect of Hg stress on nitrogen fixation was evaluated, and in our experimental conditions, nitrogenase activity was not affected in nodules formed by the tolerant strain, while a significant decrease in activity was observed in nodules elicited by the Hg-sensitive bacteria. Our results suggest that the combination of tolerant legumes with tolerant rhizobia constitutes a potentially powerful tool in the bioremediation of Hg-contaminated soils.
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Affiliation(s)
- Gabriela Arregui
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Pablo Hipólito
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Beatriz Pallol
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Victoria Lara-Dampier
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Diego García-Rodríguez
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - Higinio P. Varela
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | | | | | - Timothy Paape
- Brookhaven National Laboratory, Upton, NY, United States
| | | | - M. Mercedes Lucas
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
| | - José J. Pueyo
- Department of Soil, Plant and Environmental Quality, Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain
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22
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Identification of a blaVIM-1-Carrying IncA/C 2 Multiresistance Plasmid in an Escherichia coli Isolate Recovered from the German Food Chain. Microorganisms 2020; 9:microorganisms9010029. [PMID: 33374123 PMCID: PMC7824508 DOI: 10.3390/microorganisms9010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022] Open
Abstract
Within the German national monitoring of zoonotic agents, antimicrobial resistance determination also targets carbapenemase-producing (CP) Escherichia coli by selective isolation from food and livestock. In this monitoring in 2019, the CP E. coli 19-AB01133 was recovered from pork shoulder. The isolate was assigned to the phylogenetic group B1 and exhibited the multi-locus sequence-type ST5869. Molecular investigations, including whole genome sequencing, of 19-AB01133 revealed that the isolate carried the resistance genes blaVIM-1, blaSHV-5 and blaCMY-13 on a self-transmissible IncA/C2 plasmid. The plasmid was closely related to the previously described VIM-1-encoding plasmid S15FP06257_p from E. coli of pork origin in Belgium. Our results indicate an occasional spread of the blaVIM-1 gene in Enterobacteriaceae of the European pig population. Moreover, the blaVIM-1 located on an IncA/C2 plasmid supports the presumption of a new, probably human source of carbapenemase-producing Enterobacteriaceae (CPE) entering the livestock and food chain sector.
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Hagee D, Abu Hardan A, Botero J, Arnone JT. Genomic clustering within functionally related gene families in Ascomycota fungi. Comput Struct Biotechnol J 2020; 18:3267-3277. [PMID: 33209211 PMCID: PMC7653285 DOI: 10.1016/j.csbj.2020.10.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/17/2022] Open
Abstract
Multiple mechanisms collaborate for proper regulation of gene expression. One layer of this regulation is through the clustering of functionally related genes at discrete loci throughout the genome. This phenomenon occurs extensively throughout Ascomycota fungi and is an organizing principle for many gene families whose proteins participate in diverse molecular functions throughout the cell. Members of this phylum include organisms that serve as model systems and those of interest medically, pharmaceutically, and for industrial and biotechnological applications. In this review, we discuss the prevalence of functional clustering through a broad range of organisms within the phylum. Position effects on transcription, genomic locations of clusters, transcriptional regulation of clusters, and selective pressures contributing to the formation and maintenance of clusters are addressed, as are common methods to identify and characterize clusters.
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Affiliation(s)
- Danielle Hagee
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Ahmad Abu Hardan
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - Juan Botero
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
| | - James T. Arnone
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA
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Kamathewatta K, Bushell R, Rafa F, Browning G, Billman-Jacobe H, Marenda M. Colonization of a hand washing sink in a veterinary hospital by an Enterobacter hormaechei strain carrying multiple resistances to high importance antimicrobials. Antimicrob Resist Infect Control 2020; 9:163. [PMID: 33087168 PMCID: PMC7580002 DOI: 10.1186/s13756-020-00828-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Background Hospital intensive care units (ICUs) are known reservoirs of multidrug resistant nosocomial bacteria. Targeted environmental monitoring of these organisms in health care facilities can strengthen infection control procedures. A routine surveillance of extended spectrum beta-lactamase (ESBL) producers in a large Australian veterinary teaching hospital detected the opportunistic pathogen Enterobacter hormaechei in a hand washing sink of the ICU. The organism persisted for several weeks, despite two disinfection attempts. Four isolates were characterized in this study. Methods Brilliance-ESBL selective plates were inoculated from environmental swabs collected throughout the hospital. Presumptive identification was done by conventional biochemistry. Genomes of multidrug resistant Enterobacter were entirely sequenced with Illumina and Nanopore platforms. Phylogenetic markers, mobile genetic elements and antimicrobial resistance genes were identified in silico. Antibiograms of isolates and transconjugants were established with Sensititre microdilution plates. Results The isolates possessed a chromosomal Tn7-associated silver/copper resistance locus and a large IncH12 conjugative plasmid encoding resistance against tellurium, arsenic, mercury and nine classes of antimicrobials. Clusters of antimicrobial resistance genes were associated with class 1 integrons and IS26, IS903 and ISCR transposable elements. The blaSHV-12, qnrB2 and mcr-9.1 genes, respectively conferring resistance to cephalosporins, quinolones and colistin, were present in a locus flanked by two IS903 copies. ESBL production and enrofloxacin resistance were confirmed phenotypically. The isolates appeared susceptible to colistin, possibly reflecting the inducible nature of mcr-9.1. Conclusions The persistence of this strain in the veterinary hospital represented a risk of further accumulation and dissemination of antimicrobial resistance, prompting a thorough disinfection of the ICU. The organism was not recovered from subsequent environmental swabs, and nosocomial Enterobacter infections were not observed in the hospital during that period. This study shows that targeted routine environmental surveillance programs to track organisms with major resistance phenotypes, coupled with disinfection procedures and follow-up microbiological cultures are useful to control these risks in sensitive areas of large veterinary hospitals.
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Affiliation(s)
- Kanishka Kamathewatta
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia
| | - Rhys Bushell
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia
| | - Fannana Rafa
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Glenn Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Marc Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, 3030, Australia.
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Durand A, Maillard F, Foulon J, Chalot M. Interactions between Hg and soil microbes: microbial diversity and mechanisms, with an emphasis on fungal processes. Appl Microbiol Biotechnol 2020; 104:9855-9876. [PMID: 33043392 DOI: 10.1007/s00253-020-10795-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/06/2020] [Accepted: 07/21/2020] [Indexed: 11/25/2022]
Abstract
Mercury (Hg) is a highly toxic metal with no known biological function, and it can be highly bioavailable in terrestrial ecosystems. Although fungi are important contributors to a number of soil processes including plant nutrient uptake and decomposition, little is known about the effect of Hg on fungi. Fungi accumulate the largest amount of Hg and are the organisms capable of the highest bioaccumulation of Hg. While referring to detailed mechanisms in bacteria, this mini-review emphasizes the progress made recently on this topic and represents the first step towards a better understanding of the mechanisms underlying Hg tolerance and accumulation in fungal species and hence on the role of fungi within the Hg cycle at Hg-contaminated sites. KEY POINTS: • The fungal communities are more resilient than bacterial communities to Hg exposure. • The exposure to Hg is a threat to microbial soil functions involved in both C and nutrient cycles. • Fungal (hyper)accumulation of Hg may be important for the Hg cycle in terrestrial environments. • Understanding Hg tolerance and accumulation by fungi may lead to new remediation biotechnologies.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Laboratoire Sols et Environnement, UMR 1120, Université de Lorraine - INRAE, 2 avenue de la Forêt de Haye BP 20 163, 54505, Vandœuvre-lès-Nancy, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, 310 Allée des Ursulines, C.P. 3300, Rimouski, QC, G5L 3A1, Canada
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 place Tharradin, BP 71427, 25211, Montbéliard, France.
- Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre-les-Nancy, France.
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Mercury oxidation coupled to autotrophic denitrifying branched sulfur oxidation and sulfur disproportionation for simultaneous removal of Hg0 and NO. Appl Microbiol Biotechnol 2020; 104:8489-8504. [DOI: 10.1007/s00253-020-10827-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 08/11/2020] [Indexed: 01/18/2023]
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Sanyal SK, Brugger J, Etschmann B, Pederson SM, Delport PWJ, Dixon R, Tearle R, Ludington A, Reith F, Shuster J. Metal resistant bacteria on gold particles: Implications of how anthropogenic contaminants could affect natural gold biogeochemical cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138698. [PMID: 32330727 DOI: 10.1016/j.scitotenv.2020.138698] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/12/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
Abstract
In Earth's near-surface environments, gold biogeochemical cycling involves gold dissolution and precipitation processes, which are partly attributed to bacteria. These biogeochemical processes as well as abrasion (via physical transport) are known to act upon gold particles, thereby resulting in particle transformation including the development of pure secondary gold and altered morphology, respectively. While previous studies have inferred gold biogeochemical cycling from gold particles obtained from natural environments, little is known about how metal contamination in an environment could impact this cycle. Therefore, this study aims to infer how potentially toxic metal contaminants could affect the structure and chemistry of gold particles and therefore the biogeochemical cycling of gold. In doing so, river sediments and gold particles from the De Kaap Valley, South Africa, were analysed using both microanalytical and molecular techniques. Of the metal contaminants detected in the sediment, mercury can chemically interact with gold particles thereby directly altering particle morphology and "erasing" textural evidence indicative of particle transformation. Other metal contaminants (including mercury) indirectly affect gold cycling by exerting a selective pressure on bacteria living on the surface of gold particles. Particles harbouring gold-tolerant bacteria with diverse metal resistant genes, such as Arthrobacter sp. and Pseudomonas sp., contained nearly two times more secondary gold relative to particles harbouring bacteria with less gold-tolerance. In conclusion, metal contaminants can have a direct or indirect effect on gold biogeochemical cycling in natural environments impacted by anthropogenic activity.
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Affiliation(s)
- Santonu Kumar Sanyal
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
| | - Joël Brugger
- Monash University, Clayton, Victoria 3800, Australia
| | | | - Stephen M Pederson
- Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Roger Dixon
- University of Pretoria, Pretoria 0001, South Africa
| | - Rick Tearle
- Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Davies Research Centre, School of Animal & Veterinary Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alastair Ludington
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Bioinformatics Hub, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Frank Reith
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia
| | - Jeremiah Shuster
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; CSIRO Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia 5064, Australia.
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Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs. Appl Environ Microbiol 2020; 86:AEM.00176-20. [PMID: 32414793 DOI: 10.1128/aem.00176-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/07/2020] [Indexed: 12/18/2022] Open
Abstract
Geothermal systems emit substantial amounts of aqueous, gaseous, and methylated mercury, but little is known about microbial influences on mercury speciation. Here, we report results from genome-resolved metagenomics and mercury speciation analysis of acidic warm springs in the Ngawha Geothermal Field (<55°C, pH <4.5), Northland Region, Aotearoa New Zealand. Our aim was to identify the microorganisms genetically equipped for mercury methylation, demethylation, or Hg(II) reduction to volatile Hg(0) in these springs. Dissolved total and methylated mercury concentrations in two adjacent springs with different mercury speciation ranked among the highest reported from natural sources (250 to 16,000 ng liter-1 and 0.5 to 13.9 ng liter-1, respectively). Total solid mercury concentrations in spring sediments ranged from 1,274 to 7,000 μg g-1 In the context of such ultrahigh mercury levels, the geothermal microbiome was unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic-resistant bacteria, and thermophilic and acidophilic archaea. By integrating microbiome structure and metagenomic potential with geochemical constraints, we constructed a conceptual model for biogeochemical mercury cycling in geothermal springs. The model includes abiotic and biotic controls on mercury speciation and illustrates how geothermal mercury cycling may couple to microbial community dynamics and sulfur and iron biogeochemistry.IMPORTANCE Little is currently known about biogeochemical mercury cycling in geothermal systems. The manuscript presents a new conceptual model, supported by genome-resolved metagenomic analysis and detailed geochemical measurements. The model illustrates environmental factors that influence mercury cycling in acidic springs, including transitions between solid (mineral) and aqueous phases of mercury, as well as the interconnections among mercury, sulfur, and iron cycles. This work provides a framework for studying natural geothermal mercury emissions globally. Specifically, our findings have implications for mercury speciation in wastewaters from geothermal power plants and the potential environmental impacts of microbially and abiotically formed mercury species, particularly where they are mobilized in spring waters that mix with surface or groundwaters. Furthermore, in the context of thermophilic origins for microbial mercury volatilization, this report yields new insights into how such processes may have evolved alongside microbial mercury methylation/demethylation and the environmental constraints imposed by the geochemistry and mineralogy of geothermal systems.
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Bertel-Sevilla A, Cervantes-Ceballos L, Tirado-Ballestas I, Maldonado-Rojas W, Alzate-Restrepo J, Olivero-Verbel J. Biodegradation of biodiesel-oil by Cellulosimicrobium sp. Isolated from Colombian Caribbean soils. ENVIRONMENTAL TECHNOLOGY 2020; 41:2337-2349. [PMID: 30596345 DOI: 10.1080/09593330.2018.1564798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Biodiesel is considered to be a natural substitute for fossil fuel. The comparatively low toxicity of biodiesel and its susceptibility to microbial biodegradation could reduce its environmental impact. Currently, biodiesel is sold previously mixed with petroleum-based hydrocarbons. The aim of this work was to measure the biodegradation potential of commercially available biodiesel, using bacterial strains (BBCOL-001, BBCOL-002, and BBCOL-003) isolated from a tropical forest soils in the Colombian Caribbean. According to nucleotide sequencing of the gene encoding for 16S rRNA, the strains belong to members of the genus Cellulosimicrobium. GC-MS analysis showed that biodiesel-oil alkanes were degraded by an average of 81.5% with optical density reaching 0.2-0.3 in minimal salt media at 37°C for 5 days. Individual diesel-oil alkanes were degraded by the strains at rates between 64.9% to 100%. The increase in bacterial biomass confirmed the use of the substrates by the microorganisms, suggesting these hydrocarbons are a carbon source. Changes in the biochemical behaviour of the strains suggested their capacity to adapt to environmental conditions might be an important resource for bioremediation.
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Affiliation(s)
- Angela Bertel-Sevilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Leonor Cervantes-Ceballos
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Irina Tirado-Ballestas
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Wilson Maldonado-Rojas
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Juan Alzate-Restrepo
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellin, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
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Salam LB. Unravelling the antibiotic and heavy metal resistome of a chronically polluted soil. 3 Biotech 2020; 10:238. [PMID: 32405442 PMCID: PMC7205953 DOI: 10.1007/s13205-020-02219-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022] Open
Abstract
The antibiotic and heavy metal resistome of a chronically polluted soil (3S) obtained from an automobile workshop in Ilorin, Kwara State, Nigeria was deciphered via functional annotation of putative ORFs (open reading frames). Functional annotation of antibiotic and heavy metal resistance genes in 3S metagenome was conducted using the Comprehensive Antibiotic Resistance Database (CARD), Antibiotic Resistance Gene-annotation (ARG-ANNOT) and Antibacterial Biocide and Metal Resistance Gene Database (BacMet). Annotation revealed detection of resistance genes for 15 antibiotic classes with the preponderance of beta lactamases, mobilized colistin resistance determinant (mcr), glycopepetide and tetracycline resistance genes, the OqxBgb and OqxA RND-type multidrug efflux pumps, among others. The dominance of resistance genes for antibiotics effective against members of the Enterobacteriaceae indicate possible contamination with faecal materials. Annotation of heavy metal resistance genes revealed diverse resistance genes responsible for the uptake, transport, detoxification, efflux and regulation of copper, zinc, cadmium, nickel, chromium, cobalt, mercury, arsenic, iron, molybdenum and several others. Majority of the antibiotic and heavy metal resistance genes detected in this study are borne on mobile genetic elements, which facilitate their spread and dissemination in the polluted soil. The presence of the heavy metal resistance genes is strongly believed to play a major role in the proliferation of antibiotic resistance genes. This study has established that soil is a huge repertoire of antibiotic and heavy metal resistome and due to the intricate link between human, animals and the soil environment, it may be a major contributor to the proliferation of multidrug-resistant clinical pathogens.
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Affiliation(s)
- Lateef Babatunde Salam
- Microbiology Unit, Department of Biological Sciences, Summit University, Offa, Kwara Nigeria
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Garcia-Graells C, Berbers B, Verhaegen B, Vanneste K, Marchal K, Roosens NHC, Botteldoorn N, De Keersmaecker SCJ. First detection of a plasmid located carbapenem resistant bla VIM-1 gene in E. coli isolated from meat products at retail in Belgium in 2015. Int J Food Microbiol 2020; 324:108624. [PMID: 32302878 DOI: 10.1016/j.ijfoodmicro.2020.108624] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/25/2020] [Accepted: 03/29/2020] [Indexed: 11/24/2022]
Abstract
Carbapenemase-producing Enterobacteriaceae (CPE) confer resistance to antibiotics that are of critical importance to human medicine. There have only been a few reported cases of CPEs in the European food chain. We report the first detection of a carbapenemase-producing Escherichia coli (ST 5869) in the Belgian food chain. Our aim was to characterize the origin of the carbapenem resistance in the E. coli isolate. The isolate was detected during the screening of 178 minced pork samples and was shown to contain the carbapenemase gene blaVIM-1 by PCR and Sanger sequencing. Whole genome short and long read sequencing (MiSeq and MinION) was performed to characterize the isolate. With a hybrid assembly we reconstructed a 190,205 bp IncA/C2 plasmid containing blaVIM-1 (S15FP06257_p), in addition to other critically important resistance genes. This plasmid showed only low similarity to plasmids containing blaVIM-1 previously reported in Germany. Moreover, no sequences existed in the NCBI nucleotide database that completely covered S15FP06257_p. Analysis of the blaVIM-1 gene cassette demonstrated that it likely originated from an integron of a Klebsiella plasmid reported previously in a clinical isolate in Europe, suggesting that the meat could have been contaminated by human handling in one of the steps of the food chain. This study shows the relevance of fully reconstructing plasmids to characterize their genetic content and to allow source attribution. This is especially important in view of the potential risk of antimicrobial resistance gene transmission through mobile elements as was reported here for the of public health concern blaVIM-1.
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Affiliation(s)
| | - Bas Berbers
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium; Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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Mariano C, Mello IS, Barros BM, da Silva GF, Terezo AJ, Soares MA. Mercury alters the rhizobacterial community in Brazilian wetlands and it can be bioremediated by the plant-bacteria association. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:13550-13564. [PMID: 32030584 DOI: 10.1007/s11356-020-07913-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
This study examined how soil mercury contamination affected the structure and functionality of rhizobacteria communities from Aeschynomene fluminensis and Polygonum acuminatum and how rhizobacteria mediate metal bioremediation. The strains were isolated using culture-dependent methods, identified through 16S rDNA gene sequencing, and characterized with respect to their functional traits related to plant growth promotion and resistance to metals and antibiotics. The bioremediation capacity of the rhizobacteria was determined in greenhouse using corn plants. The isolated bacteria belonged to the phyla Actinobacteria, Deinococcus-Thermus, Firmicutes, and Proteobacteria, with great abundance of the species Microbacterium trichothecenolyticum. The rhizobacteria abundance, richness, and diversity were greater in mercury-contaminated soils. Bacteria isolated from contaminated environments had higher minimum inhibitory concentration values, presented plasmids and the merA gene, and were multi-resistant to metals and antibiotics. Enterobacter sp._C35 and M. trichothecenolyticum_C34 significantly improved (Dunnett's test, p < 0.05) corn plant growth in mercury-contaminated soil. These bacteria helped to reduce up to 87% of the mercury content in the soil, and increased the mercury bioaccumulation factor by up to 94%. Mercury bioremediation mitigated toxicity of the contaminated substrate. Enterobacter sp._C35, Bacillus megaterium_C28, and Bacillus mycoides_C1 stimulated corn plant growth and could be added to biofertilizers produced in research and related industries.
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Affiliation(s)
- Caylla Mariano
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Ivani Souza Mello
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Breno Martins Barros
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | | | - Ailton Jose Terezo
- Central Analytical of Fuels, Department of Chemistry, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Marcos Antônio Soares
- Laboratory of Biotechnology and Microbial Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, Mato Grosso, Brazil.
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Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates. mSystems 2019; 4:4/6/e00588-19. [PMID: 31848306 PMCID: PMC6918032 DOI: 10.1128/msystems.00588-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.
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Fong JC, De Guzman BE, Lamborg CH, Sison-Mangus MP. The Mercury-Tolerant Microbiota of the Zooplankton Daphnia Aids in Host Survival and Maintains Fecundity under Mercury Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14688-14699. [PMID: 31747751 DOI: 10.1021/acs.est.9b05305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many aquatic organisms can thrive in polluted environments by having the genetic capability to withstand suboptimal conditions. However, the contributions of microbiomes under these stressful environments are poorly understood. We investigated whether a mercury-tolerant microbiota can extend its phenotype to its host by ameliorating host survival and fecundity under mercury-stress. We isolated microbiota members from various clones of Daphnia magna, screened for the mercury-biotransforming merA gene, and determined their mercury tolerance levels. We then introduced the mercury-tolerant microbiota, Pseudomonas-10, to axenic D. magna and quantified its merA gene expression, mercury reduction capability, and measured its impact on host survival and fecundity. The expression of the merA gene was up-regulated in Pseudomonas-10, both in isolation and in host-association with mercury exposure. Pseudomonas-10 is also capable of significantly reducing mercury concentration in the medium. Notably, mercury-exposed daphnids containing only Pseudomonas-10 exhibited higher survival and fecundity than mercury-exposed daphnids supplemented with parental microbiome. Our study showed that zooplankton, such as Daphnia, naturally harbor microbiome members that are eco-responsive and tolerant to mercury exposure and can aid in host survival and maintain host fecundity in a mercury-contaminated environment. This study further demonstrates that under stressful environmental conditions, the fitness of the host can depend on the genotype and the phenotype of its microbiome.
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Affiliation(s)
- Jiunn C Fong
- Department of Ocean Sciences and Institute for Marine Sciences , University of California Santa Cruz , Santa Cruz , California 95064 , United States
| | - Brandon E De Guzman
- Department of Ocean Sciences and Institute for Marine Sciences , University of California Santa Cruz , Santa Cruz , California 95064 , United States
| | - Carl H Lamborg
- Department of Ocean Sciences and Institute for Marine Sciences , University of California Santa Cruz , Santa Cruz , California 95064 , United States
| | - Marilou P Sison-Mangus
- Department of Ocean Sciences and Institute for Marine Sciences , University of California Santa Cruz , Santa Cruz , California 95064 , United States
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Swift evolutionary response of microbes to a rise in anthropogenic mercury in the Northern Hemisphere. ISME JOURNAL 2019; 14:788-800. [PMID: 31831837 PMCID: PMC7031220 DOI: 10.1038/s41396-019-0563-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/17/2019] [Indexed: 01/22/2023]
Abstract
Anthropogenic mercury remobilization has considerably increased since the Industrial Revolution in the late 1700s. The Minamata Convention on Mercury is a United Nations treaty (2017) aiming at curbing mercury emissions. Unfortunately, evaluating the effectiveness of such a global treaty is hampered by our inability to determine the lag in aquatic ecosystem responses to a change in atmospheric mercury deposition. Whereas past metal concentrations are obtained from core samples, there are currently no means of tracking historical metal bioavailability or toxicity. Here, we recovered DNA from nine dated sediment cores collected in Canada and Finland, and reconstructed the past demographics of microbes carrying genes coding for the mercuric reductase (MerA)—an enzyme involved in Hg detoxification—using Bayesian relaxed molecular clocks. We found that the evolutionary dynamics of merA exhibited a dramatic increase in effective population size starting from 1783.8 ± 3.9 CE, which coincides with both the Industrial Revolution, and with independent measurements of atmospheric Hg concentrations. We show that even low levels of anthropogenic mercury affected the evolutionary trajectory of microbes in the Northern Hemisphere, and that microbial DNA encoding for detoxification determinants stored in environmental archives can be used to track historical pollutant toxicity.
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Identification of A Novel Arsenic Resistance Transposon Nested in A Mercury Resistance Transposon of Bacillus sp. MB24. Microorganisms 2019; 7:microorganisms7110566. [PMID: 31744069 PMCID: PMC6920998 DOI: 10.3390/microorganisms7110566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 12/03/2022] Open
Abstract
A novel TnMERI1-like transposon designated as TnMARS1 was identified from mercury resistant Bacilli isolated from Minamata Bay sediment. Two adjacent ars operon-like gene clusters, ars1 and ars2, flanked by a pair of 78-bp inverted repeat sequences, which resulted in a 13.8-kbp transposon-like fragment, were found to be sandwiched between two transposable genes of the TnMERI1-like transposon of a mercury resistant bacterium, Bacillus sp. MB24. The presence of a single transcription start site in each cluster determined by 5′-RACE suggested that both are operons. Quantitative real time RT-PCR showed that the transcription of the arsR genes contained in each operon was induced by arsenite, while arsR2 responded to arsenite more sensitively and strikingly than arsR1 did. Further, arsenic resistance complementary experiments showed that the ars2 operon conferred arsenate and arsenite resistance to an arsB-knocked out Bacillus host, while the ars1 operon only raised arsenite resistance slightly. This transposon nested in TnMARS1 was designated as TnARS1. Multi-gene cluster blast against bacteria and Bacilli whole genome sequence databases suggested that TnMARS1 is the first case of a TnMERI1-like transposon combined with an arsenic resistance transposon. The findings of this study suggested that TnMERI1-like transposons could recruit other mobile elements into its genetic structure, and subsequently cause horizontal dissemination of both mercury and arsenic resistances among Bacilli in Minamata Bay.
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Din G, Hasan F, Conway M, Denney B, Ripp S, Shah A. Engineering a bioluminescent bioreporter from an environmentally sourced mercury‐resistantEnterobacter cloacaestrain for the detection of bioavailable mercury. J Appl Microbiol 2019; 127:1125-1134. [DOI: 10.1111/jam.14399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/08/2019] [Accepted: 07/09/2019] [Indexed: 12/17/2022]
Affiliation(s)
- G. Din
- Department of Microbiology, Faculty of Biological Sciences Quaid‐i‐Azam University Islamabad Pakistan
- Center for Environmental Biotechnology University of Tennessee Knoxville TN USA
| | - F. Hasan
- Department of Microbiology, Faculty of Biological Sciences Quaid‐i‐Azam University Islamabad Pakistan
| | - M. Conway
- Center for Environmental Biotechnology University of Tennessee Knoxville TN USA
| | - B. Denney
- Center for Environmental Biotechnology University of Tennessee Knoxville TN USA
| | - S. Ripp
- Center for Environmental Biotechnology University of Tennessee Knoxville TN USA
| | - A.A. Shah
- Department of Microbiology, Faculty of Biological Sciences Quaid‐i‐Azam University Islamabad Pakistan
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Assessing genetic diversity and similarity of 435 KPC-carrying plasmids. Sci Rep 2019; 9:11223. [PMID: 31375735 PMCID: PMC6677891 DOI: 10.1038/s41598-019-47758-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023] Open
Abstract
The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over the last decade in the health care setting. blaKPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.
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Nanda M, Kumar V, Sharma DK. Multimetal tolerance mechanisms in bacteria: The resistance strategies acquired by bacteria that can be exploited to 'clean-up' heavy metal contaminants from water. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 212:1-10. [PMID: 31022608 DOI: 10.1016/j.aquatox.2019.04.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 05/27/2023]
Abstract
Heavy metal pollution is one of the major environmental concerns worldwide. Toxic heavy metals when untreated get accumulated in environment and can pose severe threats to living organisms. It is well known that metals play a major role either directly or indirectly in different metabolic processes of bacteria. This allows bacterial cells to grow even in the presence of some toxic heavy metals. Microbial biotechnology has thus emerged as an effective and eco friendly solution in recent years for bioremediation of heavy metals. Therefore, this review is focused on summarising bacterial adaptation mechanisms for various heavy metals. It also shares some applications of have metal tolerant bacteria in bioremediation. Bacteria have evolved a number of processes for heavy metal tolerance viz., transportation across cell membrane, accumulation on cell wall, intra as well as extracellular entrapment, formation of complexes and redox reactions which form the basis of different bioremediation strategies. The genetic determinants for most of these resistances are located on plasmids however some may be chromosomal as well. Bacterial cells can uptake heavy by both ATP dependent and ATP independent processes. Bacterial cell wall also plays a very important role in accumulating heavy metals by bacterial cells. Gram-positive bacteria accumulate much higher concentrations of heavy metals on their cell walls than that of metals gram -ve bacteria. The role of bacterial metallothioneins (MTs) in heavy metal has also been reported. Thus, heavy metal tolerant bacteria are important for bioremediation of heavy metal pollutants from areas containing high concentrations of particular heavy metals.
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Affiliation(s)
- Manisha Nanda
- Department of Biotechnology, Dolphin (PG) Institute of Biomedical and Natural Sciences, Dehradun, 248007, India.
| | - Vinod Kumar
- Department of Chemistry, Uttaranchal University, Dehradun, 248007, India.
| | - D K Sharma
- Department of Zoology and Biotechnology, H.N.B. Garhwal Central University, SRT Campus, Badshahi Thaul, Tehri, Uttarakhand, India
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Ruan Y, Wu C, Guo X, Xu Z, Xing C, Cao H, Zhang C, Hu G, Liu P. High Doses of Copper and Mercury Changed Cecal Microbiota in Female Mice. Biol Trace Elem Res 2019; 189:134-144. [PMID: 30105432 DOI: 10.1007/s12011-018-1456-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022]
Abstract
The aim of the present study was to investigate the effects of high doses of copper (Cu) and mercury (Hg) on the cecal microbiota in female mice. Forty-eight Kunming mice were randomly divided into the control group (CCk group), the Cu group (CCu group), the Hg group (CHg group), and the Cu + Hg group (CCH group). At the 90th day, cecal tissues were prepared for histopathological analysis and cecal contents for analysis by 16S rRNA sequencing method. Cecal tissues from treatment groups had histopathological lesions including increased thickness of inner muscularis and outer muscularis, widened submucosa, decreased goblet cells, mild to moderate necrosis of enterocytes, blunting of intestinal villi, and severe atrophy of central lacteal. Furthermore, compared to the CCk group, the abundance of bacteria genera Rikenella, Jeotgailcoccus, and Staphylococcus were significantly decreased, whereas the bacteria genus Corynebacterium was significantly increased in the CCu group. The abundance of bacteria genera of Sporosarcina, Jeotgailcoccus, and Staphylococcus were significantly decreased in the CHg group and CCH group. The bacteria genus Anaeroplasma was significantly increased in the CCH group. The results indicated that high doses of Cu and Hg caused histopathological lesions and changed the diversity of microbiota in the cecum of female mice, which provide a theoretical basis for more accurate assessment of the risk in intestinal diseases caused by Cu and Hg.
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Affiliation(s)
- Yezhao Ruan
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Cong Wu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Xiaoquan Guo
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Zheng Xu
- Department of Statistics and Quantitative Life Sciences Initiative, The University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Chenghong Xing
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Huabin Cao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Caiying Zhang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Guoliang Hu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China.
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health Economic and Technological Development District, College of Animal Science and Technology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang, 330045, Jiangxi, People's Republic of China.
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Lee CS, Fisher NS. Microbial generation of elemental mercury from dissolved methylmercury in seawater. LIMNOLOGY AND OCEANOGRAPHY 2019; 64:679-693. [PMID: 31105337 PMCID: PMC6519744 DOI: 10.1002/lno.11068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Elemental mercury (Hg0) formation from other mercury species in seawater results from photoreduction and microbial activity, leading to possible evasion from seawater to overlying air. Microbial conversion of monomethylmercury (MeHg) to Hg0 in seawater remains unquantified. A rapid radioassay method was developed using gamma-emitting 203Hg as a tracer to evaluate Hg0 production from Hg(II) and MeHg in the low pM range. Bacterioplankton assemblages in Atlantic surface seawater and Long Island Sound water were found to rapidly produce Hg0, with production rate constants being directly related to bacterial biomass and independent of dissolved Hg(II) and MeHg concentrations. About 32% of Hg(II) and 19% of MeHg were converted to Hg0 in 4 d in Atlantic surface seawater containing low bacterial biomass, and in Long Island Sound water with higher bacterial biomass, 54% of Hg(II) and 8% of MeHg were transformed to Hg0. Decreasing temperatures from 24°C to 4°C reduced Hg0 production rates cell-1 from Hg(II) 3.3 times as much as from a MeHg source. Because Hg0 production rates were linearly related to microbial biomass and temperature, and microbial mercuric reductase was detected in our field samples, we inferred that microbial metabolic activities and enzymatic reactions primarily govern Hg0 formation in subsurface waters where light penetration is diminished.
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Li J, Hu R, Guo Y, Chen S, Xie X, Qin JG, Ma Z, Zhu C, Pei S. Bioturbation of peanut worms Sipunculus nudus on the composition of prokaryotic communities in a tidal flat as revealed by 16S rRNA gene sequences. Microbiologyopen 2019; 8:e00802. [PMID: 30734523 PMCID: PMC6692553 DOI: 10.1002/mbo3.802] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 11/21/2022] Open
Abstract
To understand the impacts of peanut worms Sipunculus nudus on the prokaryotic community composition in a tidal flat, an onsite investigation was conducted in Suixi in the Beibu Gulf (109.82E, 21.35N) in the burrow sediments, non‐burrow sediments and the sediments without peanut worm disturbance (control). The16S rRNA gene Illumina MiSeq sequencing was used to investigate the microbial communities and their response to bioturbation by S. nudus in a sandy tidal flat. A total of 18 bacteria phyla were detected, and Proteobacteria and Cyanobacteria constituted the majority of the prokaryotic community in the samples. The distribution of the relative abundances of genera showed that approximately 6.99%–17% of the reads in the samples were classified into 25 known genera. Sulfate‐reducing bacteria (Desulfococcus and Desulfosarcina) were the most abundant taxa, followed by Thermodesulfovibrionaceae LCP‐6, indicating that sulfate reduction is the main process in the sandy tidal flat. The abundances of Desulfococcus, LCP‐6 and Cyanobacterium in the non‐burrow sediment were greater than in the burrow sediment, suggesting that the anoxic condition is more suitable for Desulfococcus and LCP‐6 when the activity of S. nudus is absent. The biomass of Cyanobacterium was decreased by the feeding bioturbation of S. nudus. Meanwhile, the relative abundance of the Bacteroidetes Luteimonas in the burrow sediments was significantly greater than in the non‐burrow sediment, and there was a strong relationship between S. nudus bioturbation and increased in oxygen contents and oxidation‐reduction potentials in the burrow sediment. The abundances of Desulfococcus and LCP‐6 were greater in the middle layer (20–30 cm) than in the top layer in the non‐burrow sediment. However, the middle and bottom layers (20–30, 30–40 cm) had higher abundances of these genera than did the upper layers (0–10, 10–20 cm) in the burrow sediments. The abundances of the Fusobacteria Propionigenium and the Spirochaetes Spirochaeta were greater in the middle and bottom layers (20–30 cm, 30–40 cm) than in the top layers (0–10, 10–20 cm) in the burrow sediment, but this phenomenon was not found in the non‐burrow sediment. This study demonstrates that bioturbation by S. nudus plays an important role in reshaping the bacterial community composition in intertidal regions.
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Affiliation(s)
- Junwei Li
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Ruiping Hu
- Guangzhou Haiwei Aquatic Science and Technology Co., Ltd, Guangzhou, PR China
| | - Yongjian Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Suwen Chen
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Xiaoyong Xie
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Jian G Qin
- College of Sciences and Engineering, Flinders University, Adelaide, SA, Australia
| | - Zhenhua Ma
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Changbo Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization of Ministry of Agriculture of China, Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China
| | - Surui Pei
- Annoroad Gene Technology Co., Ltd., Beijing, PR China
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Shi LD, Chen YS, Du JJ, Hu YQ, Shapleigh JP, Zhao HP. Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. Front Microbiol 2019; 9:3297. [PMID: 30687279 PMCID: PMC6333641 DOI: 10.3389/fmicb.2018.03297] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/18/2018] [Indexed: 02/01/2023] Open
Abstract
Heavy metal pollution has become an increasingly serious problem worldwide. Co-contamination with toxic mercury (Hg) and arsenic (As) presents a particularly difficult bioremediation trouble. By oxidizing the greenhouse gas methane, methanotrophs have been demonstrated to have high denitrification activity in eutrophic waters, indicating their possible potential for use in bioremediation of Hg(II) and As(V) in polluted water. Using metagenomics, a novel Methylocystis species (HL18), which was one of the most prevalent bacteria (9.9% of the relative abundance) in a CH4-based bio-reactor, is described here. The metagenomic-assembled genome (MAG) HL18 had gene products whose average amino acid identity against other known Methylocystis species varied from 69 to 85%, higher than the genus threshold but lower than the species boundary. Genomic analysis indicated that HL18 possessed all the genes necessary for the reduction of Hg(II) and As(V). Phylogenetic investigation of mercuric reductase (MerA) found that the HL18 protein was most closely affiliated with proteins from two Hg(II)-reducing bacteria, Bradyrhizobium sp. strain CCH5-F6 and Paracoccus halophilus. The genomic organization and phylogeny of the genes in the As(V)-reducing operon (arsRCCB) had significant identity with those from a As(V)-reducing bacterium belonging to the Rhodopseudomonas genus, indicating their reduction capability of As(V). Further analysis found that at least eight genera of methanotrophs possess both Hg(II) and As(V) reductases, illustrating the generally overlooked metabolic potential of methanotrophs. These results suggest that methanotrophs have greater bioremediation potential in heavy metal contaminated water than has been appreciated and could play an important role in the mitigation of heavy metal toxicity of contaminated wastewater.
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Affiliation(s)
- Ling-Dong Shi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yu-Shi Chen
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jia-Jie Du
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yi-Qing Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.,Zhejiang Province Key Laboratory for Water Pollution Control and Environment, Zhejiang University, Hangzhou, China.,MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
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Tyakht AV, Manolov AI, Kanygina AV, Ischenko DS, Kovarsky BA, Popenko AS, Pavlenko AV, Elizarova AV, Rakitina DV, Baikova JP, Ladygina VG, Kostryukova ES, Karpova IY, Semashko TA, Larin AK, Grigoryeva TV, Sinyagina MN, Malanin SY, Shcherbakov PL, Kharitonova AY, Khalif IL, Shapina MV, Maev IV, Andreev DN, Belousova EA, Buzunova YM, Alexeev DG, Govorun VM. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn's disease discovered using metagenomic and genomic analyses. BMC Genomics 2018; 19:968. [PMID: 30587114 PMCID: PMC6307143 DOI: 10.1186/s12864-018-5306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated. Methods We performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability. Results The abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes. Conclusions The genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-5306-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Tyakht
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia. .,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700. .,ITMO University, 49 Kronverkskiy pr, Saint-Petersburg, Russian Federation, 197101.
| | - Alexander I Manolov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexandra V Kanygina
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Dmitry S Ischenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Boris A Kovarsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna S Popenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Alexander V Pavlenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Anna V Elizarova
- Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Daria V Rakitina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Julia P Baikova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Valentina G Ladygina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Elena S Kostryukova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Irina Y Karpova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana A Semashko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Andrei K Larin
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia
| | - Tatyana V Grigoryeva
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Mariya N Sinyagina
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Sergei Y Malanin
- Kazan Federal University, 18 Kremlyovskaya St., Kazan, Russian Federation, 420008
| | - Petr L Shcherbakov
- Moscow Clinical Scientific Center, 86 Shosse Entuziastov St., Moscow, Russian Federation, 111123
| | - Anastasiya Y Kharitonova
- Clinical and Research Institute of Emergency Children's Surgery and Trauma, 22 Bolshaya Polyanka St., Moscow, Russian Federation, 119180
| | - Igor L Khalif
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Marina V Shapina
- State Scientific Center of Coloproctology, 2 Salam Adil St., Moscow, Russian Federation, 123423
| | - Igor V Maev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Dmitriy N Andreev
- Moscow State University of Medicine and Dentistry, Build. 6, 20 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Elena A Belousova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Yulia M Buzunova
- Moscow Regional Research and Clinical Institute, 61/2 Shchepkina str, Moscow, Russian Federation, 129110
| | - Dmitry G Alexeev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700
| | - Vadim M Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, Russian Federation, 141700.,M.M. Shemyakin - Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, Russian Federation, 117997
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Naguib MM, El-Gendy AO, Khairalla AS. Microbial Diversity of Mer Operon Genes and Their Potential Rules in Mercury Bioremediation and Resistance. ACTA ACUST UNITED AC 2018. [DOI: 10.2174/1874070701812010056] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:Mercury is a toxic metal that is present in small amounts in the environment, but its level is rising steadily, due to different human activities, such as industrialization. It can reach humans through the food chain, amalgam fillings, and other sources, causing different neurological disorders, memory loss, vision impairment, and may even lead to death; making its detoxification an urgent task.Methods:Various physical and chemical mercury remediation techniques are available, which generally aim at: (i) reducing its mobility or solubility; (ii) causing its vaporization or condensation; (iii) its separation from contaminated soils. Biological remediation techniques, commonly known as bioremediation, are also another possible alternative, which is considered as cheaper than the conventional means and can be accomplished using either (i) organisms harboring themeroperon genes (merB,merA,merR,merP,merT,merD,merF,merC,merE,merHandmerG), or (ii) plants expressing metal-binding proteins. Recently, differentmerdeterminants have been genetically engineered into several organisms, including bacteria and plants, to aid in detoxification of both ionic and organic forms of mercury.Results:Bacteria that are resistant to mercury compounds have at least a mercuric reductase enzyme (MerA) that reduces Hg+2to volatile Hg0, a membrane-bound protein (MerT) for Hg+2uptake and an additional enzyme, MerB, that degrades organomercurials by protonolysis. Presence of bothmerA andmerB genes confer broad-spectrum mercury resistance. However,merA alone confers narrow spectrum inorganic mercury resistance.Conclusion:To conclude, this review discusses the importance of mercury-resistance genes in mercury bioremediation. Functional analysis ofmeroperon genes and the recent advances in genetic engineering techniques could provide the most environmental friendly, safe, effective and fantastic solution to overcome mercuric toxicity.
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Lee DW, Lee H, Lee AH, Kwon BO, Khim JS, Yim UH, Kim BS, Kim JJ. Microbial community composition and PAHs removal potential of indigenous bacteria in oil contaminated sediment of Taean coast, Korea. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 234:503-512. [PMID: 29216488 DOI: 10.1016/j.envpol.2017.11.097] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 05/15/2023]
Abstract
The tidal flats near Sinduri beach in Taean, Korea, have been severely contaminated by heavy crude oils due to the Korea's worst oil spill accident, say the Hebei Spirit Oil Spill, in 2007. Crude oil compounds, including polycyclic aromatic hydrocarbons (PAHs), pose significant environmental damages due to their wide distribution, persistence, high toxicity, mutagenicity, and carcinogenicity. Microbial community of Sinduri beach sediments samples was analyzed by metagenomic data with 16S rRNA gene amplicons. Three phyla (Proteobacteria, Firmicutes, and Bacteroidetes) accounted for approximately ≥93.0% of the total phyla based on metagenomic analysis. Proteobacteria was the dominant phylum in Sinduri beach sediments. Cultivable bacteria were isolated from PAH-enriched cultures, and bacterial diversity was investigated through performing culture characterization followed by molecular biology methods. Sixty-seven isolates were obtained, comprising representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, and Bacteroidetes. PAH catabolism genes, such as naphthalene dioxygenase (NDO) and aromatic ring hydroxylating dioxygenase (ARHDO), were used as genetic markers to assess biodegradation of PAHs in the cultivable bacteria. The ability to degrade PAHs was demonstrated by monitoring the removal of PAHs using a gas chromatography mass spectrometer. Overall, various PAH-degrading bacteria were widely present in Sinduri beach sediments and generally reflected the restored microbial community. Among them, Cobetia marina, Rhodococcus soli, and Pseudoalteromonas agarivorans were found to be significant in degradation of PAHs. This large collection of PAH-degrading strains represents a valuable resource for studies investigating mechanisms of PAH degradation and bioremediation in oil contaminated coastal environment, elsewhere.
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Affiliation(s)
- Dong Wan Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea; BK21 Plus Eco-Leader Education Center, Korea University, Seoul, 02841, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Aslan Hwanhwi Lee
- Department of Civil and Geological Engineering, University of Saskatchewan, 57 Campus Drive, Saskatoon, SK, S7N 5A9, Canada
| | - Bong-Oh Kwon
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science & Research Institute of Oceanography, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Un Hyuk Yim
- Oil and POPs Research Group, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | - Beom Seok Kim
- Division of Biotechnology, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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Mercury bioremediation by mercury resistance transposon-mediated in situ molecular breeding. Appl Microbiol Biotechnol 2018; 102:3037-3048. [DOI: 10.1007/s00253-018-8847-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
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Bio-prospectus of cadmium bioadsorption by lactic acid bacteria to mitigate health and environmental impacts. Appl Microbiol Biotechnol 2018; 102:1599-1615. [PMID: 29352397 DOI: 10.1007/s00253-018-8743-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 12/15/2022]
Abstract
Foodstuffs and water are the key sources of cadmium biomagnifiaction. The available strategies to mitigate this problem are unproductive and expensive for practical large-scale use. Biological decontamination of metals through environmental microbes has been known since long time, whereas lactic acid bacteria (LAB) have not been extensively studied for this purpose. The LAB are known for maintaining homeostasis and suppression of pathogens in humans and animals. They also play a vital role in bioremediation of certain heavy metals. Recently in-vivo research findings strongly complement the in-vitro results in relation to decreased total body cadmium burden in animal model. This review summarizes the currently available information on impact of toxic metal (Cd) on human and animal health as well as cadmium sequestration through microbes placed broadly, whereas preeminent attention grabbed on LAB-cadmium interaction to explore their possible role in bioremediation of cadmium from foods and environment to safeguard human as well as environment health.
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Guo G, Yumvihoze E, Poulain AJ, Man Chan H. Monomethylmercury degradation by the human gut microbiota is stimulated by protein amendments. J Toxicol Sci 2018; 43:717-725. [DOI: 10.2131/jts.43.717] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Galen Guo
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Canada K1N 9B4
| | - Emmanuel Yumvihoze
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Canada K1N 9B4
| | - Alexandre J. Poulain
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Canada K1N 9B4
| | - Hing Man Chan
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Canada K1N 9B4
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Dash HR, Sahu M, Mallick B, Das S. Functional efficiency of MerA protein among diverse mercury resistant bacteria for efficient use in bioremediation of inorganic mercury. Biochimie 2017; 142:207-215. [DOI: 10.1016/j.biochi.2017.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
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