1
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Pardhe BD, Lee MJ, Lee JH, Do H, Oh TJ. Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136. Sci Rep 2023; 13:17854. [PMID: 37857791 PMCID: PMC10587081 DOI: 10.1038/s41598-023-44968-w] [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: 08/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Abstract
Heavy metals, including mercury, are non-biodegradable and highly toxic to microorganisms even at low concentrations. Understanding the mechanisms underlying the environmental adaptability of microorganisms with Hg resistance holds promise for their use in Hg bioremediation. We characterized GbsMerA, a mercury reductase belonging to the mercury-resistant operon of Gelidibacter salicanalis PAMC21136, and found its maximum activity of 474.7 µmol/min/mg in reducing Hg+2. In the presence of Ag and Mn, the enzyme exhibited moderate activity as 236.5 µmol/min/mg and 69 µmol/min/mg, respectively. GbsMerA exhibited optimal activity at pH 7.0 and a temperature of 60 °C. Moreover, the crystal structure of GbsMerA and structural comparison with homologues indicated that GbsMerA contains residues, Tyr437´ and Asp47, which may be responsible for metal transfer at the si-face by providing a hydroxyl group (-OH) to abstract a proton from the thiol group of cysteine. The complex structure with NADPH indicated that Y174 in the re-face can change its side chain direction upon NADPH binding, indicating that Y174 may have a role as a gate for NADPH binding. Moreover, the heterologous host expressing GbsMerA (pGbsMerA) is more resistant to Hg toxicity when compared to the host lacking GbsMerA. Overall, this study provides a background for understanding the catalytic mechanism and Hg detoxification by GbsMerA and suggests the application of genetically engineered E. coli strains for environmental Hg removal.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea
| | - Min Ju Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
- Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea.
- Genome-Based BioIT Convergence Institute, Asan, 31460, Republic of Korea.
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, 31460, Republic of Korea.
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2
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Patwardhan S, Phan J, Smedile F, Vetriani C. The Genome of Varunaivibrio sulfuroxidans Strain TC8 T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea. Microorganisms 2023; 11:1366. [PMID: 37374867 DOI: 10.3390/microorganisms11061366] [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: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jonathan Phan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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3
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He Y, Zeng X, Xu F, Shao Z. Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents. Microorganisms 2022; 11:microorganisms11010100. [PMID: 36677390 PMCID: PMC9861301 DOI: 10.3390/microorganisms11010100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 105 cells/ml to 107 cells/ml;carbon dioxide fixation capacity with the δ13CVPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO42- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.
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4
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Ares Á, Sakai S, Sasaki T, Shimamura S, Mitarai S, Nunoura T. Sequestration and efflux largely account for cadmium and copper resistance in the deep-sea Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Environ Microbiol 2022; 24:6144-6163. [PMID: 36284406 PMCID: PMC10092412 DOI: 10.1111/1462-2920.16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
In deep-sea hydrothermal vent environments, metal-enriched fluids and sediments abound, making these habitats ideal to study metal resistance in prokaryotes. In this investigation, we employed transcriptomics and shotgun proteomics with scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy (STEM-EDX) to better understand mechanisms of tolerance for cadmium (Cd) and copper (Cu) at stress-inducing concentrations in Nitratiruptor sp. SB155-2 (phylum Campylobacterota). Transcriptomic profiles were remarkably different in the presence of these two metals, displaying 385 (19%) and 629 (31%) differentially transcribed genes (DTG) in the presence of Cd(II) and Cu(II), respectively, while only 7% of differentially transcribed (DT) genes were shared, with genes for non-specific metal transporters and genes involved in oxidative stress-response predominating. Transcriptomic and proteomic analyses confirmed that metal-specific DT pathways under Cu(II) stress, including those involving sulfur, cysteine, and methionine, are likely required for high-affinity efflux systems, while flagella formation and chemotaxis were over-represented under Cd(II) stress. Consistent with these differences, STEM-EDX analysis revealed that polyphosphate-like granules (pPLG), the formation of CdS particles, and the periplasmic space are crucial for Cd(II) sequestration. Overall, this study provides new insights regarding metal-specific adaptations of Campylobacterota to deep-sea hydrothermal vent environments.
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Affiliation(s)
- Ángela Ares
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Sanae Sakai
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Toshio Sasaki
- Imaging section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Shigeru Shimamura
- Super-Cutting-Edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Mitarai
- Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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Wei M, Zeng X, Han X, Shao Z, Xie Q, Dong C, Wang Y, Qiu Z. Potential autotrophic carbon-fixer and Fe(II)-oxidizer Alcanivorax sp. MM125-6 isolated from Wocan hydrothermal field. Front Microbiol 2022; 13:930601. [PMID: 36316996 PMCID: PMC9616709 DOI: 10.3389/fmicb.2022.930601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/09/2022] [Indexed: 12/02/2022] Open
Abstract
The genus Alcanivorax is common in various marine environments, including in hydrothermal fields. They were previously recognized as obligate hydrocarbonoclastic bacteria, but their potential for autotrophic carbon fixation and Fe(II)-oxidation remains largely elusive. In this study, an in situ enrichment experiment was performed using a hydrothermal massive sulfide slab deployed 300 m away from the Wocan hydrothermal vent. Furthermore, the biofilms on the surface of the slab were used as an inoculum, with hydrothermal massive sulfide powder from the same vent as an energy source, to enrich the potential iron oxidizer in the laboratory. Three dominant bacterial families, Alcanivoraceae, Pseudomonadaceae, and Rhizobiaceae, were enriched in the medium with hydrothermal massive sulfides. Subsequently, strain Alcanivorax sp. MM125-6 was isolated from the enrichment culture. It belongs to the genus Alcanivorax and is closely related to Alcanivorax profundimaris ST75FaO-1T (98.9% sequence similarity) indicated by a phylogenetic analysis based on 16S rRNA gene sequences. Autotrophic growth experiments on strain MM125-6 revealed that the cell concentrations were increased from an initial 7.5 × 105 cells/ml to 3.13 × 108 cells/ml after 10 days, and that the δ13CVPDB in the cell biomass was also increased from 234.25‰ on day 2 to gradually 345.66 ‰ on day 10. The gradient tube incubation showed that bands of iron oxides and cells formed approximately 1 and 1.5 cm, respectively, below the air-agarose medium interface. In addition, the SEM-EDS data demonstrated that it can also secrete acidic exopolysaccharides and adhere to the surface of sulfide minerals to oxidize Fe(II) with NaHCO3 as the sole carbon source, which accelerates hydrothermal massive sulfide dissolution. These results support the conclusion that strain MM125-6 is capable of autotrophic carbon fixation and Fe(II) oxidization chemoautotrophically. This study expands our understanding of the metabolic versatility of the Alcanivorax genus as well as their important role(s) in coupling hydrothermal massive sulfide weathering and iron and carbon cycles in hydrothermal fields.
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Affiliation(s)
- Mingcong Wei
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Xiqiu Han
- Ocean College, Zhejiang University, Zhoushan, China
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Xiqiu Han,
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Qian Xie
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanqi Dong
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- College of Marine Geosciences, Ocean University of China, Qingdao, China
| | - Yejian Wang
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Zhongyan Qiu
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
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6
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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7
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Du R, Gao D, Wang Y, Liu L, Cheng J, Liu J, Zhang XH, Yu M. Heterotrophic Sulfur Oxidation of Halomonas titanicae SOB56 and Its Habitat Adaptation to the Hydrothermal Environment. Front Microbiol 2022; 13:888833. [PMID: 35774465 PMCID: PMC9237845 DOI: 10.3389/fmicb.2022.888833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022] Open
Abstract
Halomonas bacteria are ubiquitous in global marine environments, however, their sulfur-oxidizing abilities and survival adaptations in hydrothermal environments are not well understood. In this study, we characterized the sulfur oxidation ability and metabolic mechanisms of Halomonas titanicae SOB56, which was isolated from the sediment of the Tangyin hydrothermal field in the Southern Okinawa Trough. Physiological characterizations showed that it is a heterotrophic sulfur-oxidizing bacterium that can oxidize thiosulfate to tetrathionate, with the Na2S2O3 degradation reaching 94.86%. Two potential thiosulfate dehydrogenase-related genes, tsdA and tsdB, were identified as encoding key catalytic enzymes, and their expression levels in strain SOB56 were significantly upregulated. Nine of fifteen examined Halomonas genomes possess TsdA- and TsdB-homologous proteins, whose amino acid sequences have two typical Cys-X2-Cys-His heme-binding regions. Moreover, the thiosulfate oxidation process in H. titanicae SOB56 might be regulated by quorum sensing, and autoinducer-2 synthesis protein LuxS was identified in its genome. Regarding the mechanisms underlying adaptation to hydrothermal environment, strain SOB56 was capable of forming biofilms and producing EPS. In addition, genes related to complete flagellum assembly system, various signal transduction histidine kinases, heavy metal transporters, anaerobic respiration, and variable osmotic stress regulation were also identified. Our results shed light on the potential functions of heterotrophic Halomonas bacteria in hydrothermal sulfur cycle and revealed possible adaptations for living at deep-sea hydrothermal fields by H. titanicae SOB56.
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Affiliation(s)
- Rui Du
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Di Gao
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Yiting Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Lijun Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jingguang Cheng
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Min Yu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- *Correspondence: Min Yu,
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Sanz-Sáez I, Pereira-García C, Bravo AG, Trujillo L, Pla i Ferriol M, Capilla M, Sánchez P, Rodríguez Martín-Doimeadios RC, Acinas SG, Sánchez O. Prevalence of Heterotrophic Methylmercury Detoxifying Bacteria across Oceanic Regions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3452-3461. [PMID: 35245029 PMCID: PMC8928480 DOI: 10.1021/acs.est.1c05635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 05/27/2023]
Abstract
Microbial reduction of inorganic divalent mercury (Hg2+) and methylmercury (MeHg) demethylation is performed by the mer operon, specifically by merA and merB genes, respectively, but little is known about the mercury tolerance capacity of marine microorganisms and its prevalence in the ocean. Here, combining culture-dependent analyses with metagenomic and metatranscriptomic data, we show that marine bacteria that encode mer genes are widespread and active in the global ocean. We explored the distribution of these genes in 290 marine heterotrophic bacteria (Alteromonas and Marinobacter spp.) isolated from different oceanographic regions and depths, and assessed their tolerance to diverse concentrations of Hg2+ and MeHg. In particular, the Alteromonas sp. ISS312 strain presented the highest tolerance capacity and a degradation efficiency for MeHg of 98.2% in 24 h. Fragment recruitment analyses of Alteromonas sp. genomes (ISS312 strain and its associated reconstructed metagenome assembled genome MAG-0289) against microbial bathypelagic metagenomes confirm their prevalence in the deep ocean. Moreover, we retrieved 54 merA and 6 merB genes variants related to the Alteromonas sp. ISS312 strain from global metagenomes and metatranscriptomes from Tara Oceans. Our findings highlight the biological reductive MeHg degradation as a relevant pathway of the ocean Hg biogeochemical cycle.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Carla Pereira-García
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Andrea G. Bravo
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Laura Trujillo
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Martí Pla i Ferriol
- Departament
de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Miguel Capilla
- Research
Group in Environmental Engineering (GI2AM), Department of Chemical
Engineering, University of Valencia, Av. De la Universitat S/N, 46100 Burjassot, Spain
| | - Pablo Sánchez
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Rosa Carmen Rodríguez Martín-Doimeadios
- Environmental
Sciences Institute (ICAM), Department of Analytical Chemistry and
Food Technology, University of Castilla-La
Mancha, Avda. Carlos
III s/n, 45071 Toledo, Spain
| | - Silvia G. Acinas
- Departament
de Biologia Marina i Oceanografia, Institut
de Ciències del Mar, ICM-CSIC, 08003 Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament
de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Christakis CA, Barkay T, Boyd ES. Expanded Diversity and Phylogeny of mer Genes Broadens Mercury Resistance Paradigms and Reveals an Origin for MerA Among Thermophilic Archaea. Front Microbiol 2021; 12:682605. [PMID: 34248899 PMCID: PMC8261052 DOI: 10.3389/fmicb.2021.682605] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the mer operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of mer-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.
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Affiliation(s)
- Christos A. Christakis
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Eric S. Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
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10
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Microorganisms employed in the removal of contaminants from wastewater of iron and steel industries. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2021. [DOI: 10.1007/s12210-021-00982-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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11
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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12
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Patwardhan S, Smedile F, Giovannelli D, Vetriani C. Metaproteogenomic Profiling of Chemosynthetic Microbial Biofilms Reveals Metabolic Flexibility During Colonization of a Shallow-Water Gas Vent. Front Microbiol 2021; 12:638300. [PMID: 33889140 PMCID: PMC8056087 DOI: 10.3389/fmicb.2021.638300] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
Tor Caldara is a shallow-water gas vent located in the Mediterranean Sea, with active venting of CO2 and H2S. At Tor Caldara, filamentous microbial biofilms, mainly composed of Epsilon- and Gammaproteobacteria, grow on substrates exposed to the gas venting. In this study, we took a metaproteogenomic approach to identify the metabolic potential and in situ expression of central metabolic pathways at two stages of biofilm maturation. Our findings indicate that inorganic reduced sulfur species are the main electron donors and CO2 the main carbon source for the filamentous biofilms, which conserve energy by oxygen and nitrate respiration, fix dinitrogen gas and detoxify heavy metals. Three metagenome-assembled genomes (MAGs), representative of key members in the biofilm community, were also recovered. Metaproteomic data show that metabolically active chemoautotrophic sulfide-oxidizing members of the Epsilonproteobacteria dominated the young microbial biofilms, while Gammaproteobacteria become prevalent in the established community. The co-expression of different pathways for sulfide oxidation by these two classes of bacteria suggests exposure to different sulfide concentrations within the biofilms, as well as fine-tuned adaptations of the enzymatic complexes. Taken together, our findings demonstrate a shift in the taxonomic composition and associated metabolic activity of these biofilms in the course of the colonization process.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,National Research Council, Institute for Coastal Marine Environment, Messina, Italy
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Department of Biology, University of Naples "Federico II," Naples, Italy.,National Research Council, Institute for Marine Biological and Biotechnological Resources, Ancona, Italy.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
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Ma L, Wang WX. Subcellular metal distribution in two deep-sea mollusks: Insight of metal adaptation and detoxification near hydrothermal vents. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115303. [PMID: 32836047 DOI: 10.1016/j.envpol.2020.115303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/03/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
In this study, we determined the concentrations of Cu, Zn, Ni, Cd, Pb and As and their subcellular distributions within the tissues of mussels (Bathymodiolus marisindicus) and snails (Gigantopelta aegis) from two hydrothermal vent regions, i.e., Tiancheng and Longqi, at Southwest Indian Ridge. Mussels collected from the two venting regions showed comparable concentrations for Ni and Pb, but Cu, Zn, Cd and As concentrations were significantly different in mussel gills between the two vent regions. Similar ranges of metal concentrations were found in the snails as those in the mussels, but most of the metals were mainly accumulated in the viscera, except for Ni. Similar subcellular partitioning of Cu, Zn and Cd was documented in different mussel tissues, with cellular debris (50%) being the predominant fraction, followed by equivalent values in other fractions. Lead was distributed in both cellular debris and metal-rich granules (MRG) fraction, whereas Ni was predominantly distributed in MRG (90%). Arsenic was mainly partitioned in cellular debris and metallothionein-like protein. However, deep-sea snails displayed elevated subcellular partitioning of Cu in the organelles (up to 60%) and may be more susceptible to Cu stress than the mussels. Our results demonstrated the metal-specificity of detoxification strategies in these deep-sea hydrothermal vent mollusks, and the mussels may be more adaptable to high metal exposures than the snails at hydrothermal vent.
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Affiliation(s)
- Lan Ma
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), City University of Hong Kong, Kowloon, Hong Kong; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), City University of Hong Kong, Kowloon, Hong Kong; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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14
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Zheng R, Wu S, Sun C. MerF is a novel regulator of deep-sea Pseudomonas stutzeri flagellum biogenesis and motility. Environ Microbiol 2020; 23:110-125. [PMID: 33047460 DOI: 10.1111/1462-2920.15275] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022]
Abstract
MerF, a proposed bacterial mercury transporter, was surprisingly found to play key roles in the flagellum biogenesis and motility but not mercuric resistance of the deep-sea bacterium Pseudomonas stutzeri 273 in our previous study. However, the mechanism behind this interesting discovery has not been elucidated. Here, we firstly applied the combined transcriptomic and proteomic analysis to the P. stutzeri 273 wild type and merF deletion mutant. The results showed that expressions of extracellular flagellar components and FliS, a key factor controlling the biogenesis of extracellular flagellar filament, were significantly downregulated in the merF deletion mutant. In combination of genetic and biochemical methods, MerF was further demonstrated to regulate the expression of fliS via directly binding to its promoter, which is consistent with the discovery that MerF is essential for bacterial flagellum biogenesis and motility. Importantly, the expression of merF and fliS could be simultaneously upregulated by different heavy metals and MerF homologues exist in both bacterial and archaeal domains. To the best of our knowledge, this is the first report linking the heavy metal transporter and the flagellum biogenesis and motility in microorganisms, which provides a good model to investigate the unexplored adaptation strategies of deep-sea microbes against harsh conditions.
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Affiliation(s)
- Rikuan Zheng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shimei Wu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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15
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Wu Z, Zheng R, Liu G, Liu R, Wu S, Sun C. Calcium protects bacteria against cadmium stress via reducing nitric oxide production and increasing iron acquisition. Environ Microbiol 2020; 23:3541-3553. [PMID: 32939902 DOI: 10.1111/1462-2920.15237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/14/2020] [Indexed: 11/26/2022]
Abstract
Cadmium (Cd) is a common toxic heavy metal in the environment, and bacteria have evolved different strategies against Cd-toxicity. Here, we found that marine bacterium Bacillus sp. 98 could significantly alleviate Cd-toxicity by recruiting calcium (Ca) for reducing excessive intracellular nitric oxide (NO) and enhancing iron acquisition. To investigate the underlying mechanisms, mass spectrometry-based proteomic analysis was applied to Bacillus sp. 98 after treated with Cd supplemented with or without Ca. Compared with bacterial cells treated with Cd only, the proteomic results showed that the expression level of NO synthase was markedly down-regulated, while the expression levels of NO dioxygenase, which is responsible for converting NO to nitrate, and proteins associated with iron uptake were profoundly enhanced when Ca was supplemented. Consistently, bacterial intracellular NO amount was dramatically increased after Bacillus sp. 98 was treated with Cd, and reversed to a normal level when Ca or iron was supplemented. Notably, Ca also protected bacteria against stresses from other heavy metals including Cu, Cr, Mn, Ni and Zn, and this self-protection strategy was adopted as well in zebrafish, which encourages us to develop Ca-associated products against heavy metals toxicity in the future.
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Affiliation(s)
- Zuodong Wu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Rikuan Zheng
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Centre of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ge Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Centre of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Centre of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shimei Wu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Centre of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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16
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Wang CH, Gulmann LK, Zhang T, Farfan GA, Hansel CM, Sievert SM. Microbial colonization of metal sulfide minerals at a diffuse-flow deep-sea hydrothermal vent at 9°50'N on the East Pacific Rise. GEOBIOLOGY 2020; 18:594-605. [PMID: 32336020 DOI: 10.1111/gbi.12396] [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: 10/03/2019] [Revised: 02/24/2020] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Metal sulfide minerals, including mercury sulfides (HgS), are widespread in hydrothermal vent systems where sulfur-oxidizing microbes are prevalent. Questions remain as to the impact of mineral composition and structure on sulfur-oxidizing microbial populations at deep-sea hydrothermal vents, including the possible role of microbial activity in remobilizing elemental Hg from HgS. In the present study, metal sulfides varying in metal composition, structure, and surface area were incubated for 13 days on and near a diffuse-flow hydrothermal vent at 9°50'N on the East Pacific Rise. Upon retrieval, incubated minerals were examined by scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS), X-ray diffraction (XRD), and epifluorescence microscopy (EFM). DNA was extracted from mineral samples, and the 16S ribosomal RNA gene sequenced to characterize colonizing microbes. Sulfur-oxidizing genera common to newly exposed surfaces (Sulfurimonas, Sulfurovum, and Arcobacter) were present on all samples. Differences in their relative abundance between and within incubation sites point to constraining effects of the immediate environment and the minerals themselves. Greater variability in colonizing community composition on off-vent samples suggests that the bioavailability of mineral-derived sulfide (as influenced by surface area, crystal structure, and reactivity) exerted greater control on microbial colonization in the ambient environment than in the vent environment, where dissolved sulfide is more abundant. The availability of mineral-derived sulfide as an electron donor may thus be a key control on the activity and proliferation of deep-sea chemosynthetic communities, and this interpretation supports the potential for microbial dissolution of HgS at hydrothermal vents.
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Affiliation(s)
- Chloe H Wang
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Chemistry, Haverford College, Haverford, PA, USA
| | - Lara K Gulmann
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Tong Zhang
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, Nankai University, Tianjin, China
| | - Gabriela A Farfan
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
- Department of Mineral Sciences, Smithsonian Institution, Washington, DC, USA
| | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Stefan M Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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Genomic features and copper biosorption potential of a new Alcanivorax sp. VBW004 isolated from the shallow hydrothermal vent (Azores, Portugal). Genomics 2020; 112:3268-3273. [PMID: 32553480 DOI: 10.1016/j.ygeno.2020.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 06/06/2020] [Indexed: 11/20/2022]
Abstract
A new Alcanivorax sp. VBW004 was isolated from a shallow hydrothermal vent in Azores Island, Portugal. In this study, we determined VBW004 was resistant to copper. This strain showed maximum tolerance of copper concentrations up to 600 μg/mL. Based on 16S rRNA gene sequencing and phylogeny revealed that this strain was more closely related to Alcanivorax borkumensis SK2. We sequenced the genome of this strain that consist of 3.8 Mb size with a G + C content of 58.4 %. In addition, digital DNA-DNA hybridizations (dDDH) and the average nucleotide identities (ANI) analysis between Alcanivorax borkumensis SK2 and Alcanivorax jadensis T9 revealed that Alcanivorax sp. VBW004 belongs to new species. Functional annotation revealed that the genome acquired multiple copper resistance encoding genes that could assist VBW004 to respond to high Cu toxicity. Our results from biosorption analysis presumed that the VBW004 is an ecologically important bacterium that could be useful for copper bioremediation.
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Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems 2020; 5:5/1/e00795-19. [PMID: 31911466 PMCID: PMC6946796 DOI: 10.1128/msystems.00795-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.
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Kepel B, Ekawati Tallei T. Potential of Organic Mercury-resistant Bacteria Isolated from Mercury Contaminated Sites for Organic Mercury Remediation. Pak J Biol Sci 2019; 22:45-50. [PMID: 30796768 DOI: 10.3923/pjbs.2019.45.50] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Efforts at organic mercury detoxification can be carried out using resistant bacteria that can live in an environment contaminated with the compound. This study aimed at isolating and identifying resistant bacteria from mercury-contaminated environments and analysing their ability to detoxify organic mercury. MATERIALS AND METHODS Soil samples were obtained from 3 gold processing locations that make use of mercury in Tanoyan Village, Bolaang Mongondow district, North Sulawesi province. The identification was carried out on the mercury-resistant bacteria through morphological and molecular tests. Bacteria which were highly resistant to mercury were examined for their ability to detoxify phenyl mercury (organic mercury). RESULTS The study showed that 8 mercury-resistant bacterial colonies could be isolated from the three soil samples. The bacteria were able to grow in LB broth containing 10 mg L-1 of phenyl mercury. Four isolates (AA, BB, CC and DD) were even able to grow in 40 mg L-1 of phenyl mercury. According to the identification tests, those bacteria were Pseudomonas sp. (AA, DD), Pseudomonas aeruginosa (BB) and Proteus mirabilis (CC). Testing of organic mercury against isolates of bacteria which are highly resistant to it in order to determine their detoxification capacity revealed that all four isolates could reduce levels of the compound in media, based on the results, starting from the highest was Pseudomonas sp. 74.99%, then Pseudomonas aeruginosa 60.23% and Proteus mirabilis 47.59% after 24 h of incubation. CONCLUSION The study suggested that there are four bacteria that have potentials to remediate organic mercury contamination sites.
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20
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Gonnella G, Adam N, Perner M. Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. BMC Genomics 2019; 20:339. [PMID: 31060509 PMCID: PMC6501319 DOI: 10.1186/s12864-019-5710-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/17/2019] [Indexed: 01/15/2023] Open
Abstract
Background Obligate sulfur oxidizing chemolithoauthotrophic strains of Hydrogenovibrio crunogenus have been isolated from multiple hydrothermal vent associated habitats. However, a hydrogenase gene cluster (encoding the hydrogen converting enzyme and its maturation/assembly machinery) detected on the first sequenced H. crunogenus strain (XCL-2) suggested that hydrogen conversion may also play a role in this organism. Yet, numerous experiments have underlined XCL-2’s inability to consume hydrogen under the tested conditions. A recent study showed that the closely related strain SP-41 contains a homolog of the XCL-2 hydrogenase (a group 1b [NiFe]-hydrogenase), but that it can indeed use hydrogen. Hence, the question remained unresolved, why SP-41 is capable of using hydrogen, while XCL-2 is not. Results Here, we present the genome sequence of the SP-41 strain and compare it to that of the XCL-2 strain. We show that the chromosome of SP-41 codes for a further hydrogenase gene cluster, including two additional hydrogenases: the first appears to be a group 1d periplasmic membrane-anchored hydrogenase, and the second a group 2b sensory hydrogenase. The region where these genes are located was likely acquired horizontally and exhibits similarity to other Hydrogenovibrio species (H. thermophilus MA2-6 and H. marinus MH-110 T) and other hydrogen oxidizing Proteobacteria (Cupriavidus necator H16 and Ghiorsea bivora TAG-1 T). The genomes of XCL-2 and SP-41 show a strong conservation in gene order. However, several short genomic regions are not contained in the genome of the other strain. These exclusive regions are often associated with signs of DNA mobility, such as genes coding for transposases. They code for transport systems and/or extend the metabolic potential of the strains. Conclusions Our results suggest that horizontal gene transfer plays an important role in shaping the genomes of these strains, as a likely mechanism for habitat adaptation, including, but not limited to the transfer of the hydrogen conversion ability. Electronic supplementary material The online version of this article (10.1186/s12864-019-5710-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giorgio Gonnella
- Universität Hamburg, MIN-Fakultät, ZBH - Center for Bioinformatics, Bundesstraße 43, Hamburg, 20146, Germany.
| | - Nicole Adam
- GEOMAR Helmholtz Center for Ocean Research Kiel, Geomicrobiology, Wischhofstr. 1-3, Kiel, 24148, Germany.,previous address: Universität Hamburg, MIN-Fakultät, Biocenter Klein Flottbek, Molecular Biology of Microbial Consortia, Ohnhorststr. 18, Hamburg, 22609, Germany
| | - Mirjam Perner
- GEOMAR Helmholtz Center for Ocean Research Kiel, Geomicrobiology, Wischhofstr. 1-3, Kiel, 24148, Germany. .,previous address: Universität Hamburg, MIN-Fakultät, Biocenter Klein Flottbek, Molecular Biology of Microbial Consortia, Ohnhorststr. 18, Hamburg, 22609, Germany.
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Superoxide Dismutase and Pseudocatalase Increase Tolerance to Hg(II) in Thermus thermophilus HB27 by Maintaining the Reduced Bacillithiol Pool. mBio 2019; 10:mBio.00183-19. [PMID: 30940703 PMCID: PMC6445937 DOI: 10.1128/mbio.00183-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermus thermophilus is a deep-branching thermophilic aerobe. It is a member of the Deinococcus-Thermus phylum that, together with the Aquificae, constitute the earliest branching aerobic bacterial lineages; therefore, this organism serves as a model for early diverged bacteria (R. K. Hartmann, J. Wolters, B. Kröger, S. Schultze, et al., Syst Appl Microbiol 11:243–249, 1989, https://doi.org/10.1016/S0723-2020(89)80020-7) whose natural heated habitat may contain mercury of geological origins (G. G. Geesey, T. Barkay, and S. King, Sci Total Environ 569-570:321–331, 2016, https://doi.org/10.1016/j.scitotenv.2016.06.080). T. thermophilus likely arose shortly after the oxidation of the biosphere 2.4 billion years ago. Studying T. thermophilus physiology provides clues about the origin and evolution of mechanisms for mercury and oxidative stress responses, the latter being critical for the survival and function of all extant aerobes. Mercury (Hg) is a widely distributed, toxic heavy metal with no known cellular role. Mercury toxicity has been linked to the production of reactive oxygen species (ROS), but Hg does not directly perform redox chemistry with oxygen. How exposure to the ionic form, Hg(II), generates ROS is unknown. Exposure of Thermus thermophilus to Hg(II) triggered ROS accumulation and increased transcription and activity of superoxide dismutase (Sod) and pseudocatalase (Pcat); however, Hg(II) inactivated Sod and Pcat. Strains lacking Sod or Pcat had increased oxidized bacillithiol (BSH) levels and were more sensitive to Hg(II) than the wild type. The ΔbshA Δsod and ΔbshA Δpcat double mutant strains were as sensitive to Hg(II) as the ΔbshA strain that lacks bacillithiol, suggesting that the increased sensitivity to Hg(II) in the Δsod and Δpcat mutant strains is due to a decrease of reduced BSH. Treatment of T. thermophilus with Hg(II) decreased aconitase activity and increased the intracellular concentration of free Fe, and these phenotypes were exacerbated in Δsod and Δpcat mutant strains. Treatment with Hg(II) also increased DNA damage. We conclude that sequestration of the redox buffering thiol BSH by Hg(II), in conjunction with direct inactivation of ROS-scavenging enzymes, impairs the ability of T. thermophilus to effectively metabolize ROS generated as a normal consequence of growth in aerobic environments.
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Geological, Mineralogical and Textural Impacts on the Distribution of Environmentally Toxic Trace Elements in Seafloor Massive Sulfide Occurrences. MINERALS 2019. [DOI: 10.3390/min9030162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With mining of seafloor massive sulfides (SMS) coming closer to reality, it is vital that we have a good understanding of the geochemistry of these occurrences and the potential toxicity impact associated with mining them. In this study, SMS samples from seven hydrothermal fields from various tectonic settings were investigated by in-situ microanalysis (electron microprobe (EMPA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS)) to highlight the distribution of potentially-toxic trace elements (Cu, Zn, Pb, Mn, Cd, As, Sb, Co, Ni, Bi, Ag and Hg) within the deposits, their minerals and textures. We demonstrate that a combination of mineralogy, trace element composition and texture characterisation of SMS from various geotectonic settings, when considered along with our current knowledge of oxidation rates and galvanic coupling, can be used to predict potential toxicity of deposit types and individual samples and highlight which may be of environmental concern. Although we cannot quantify toxicity, we observe that arc-related sulfide deposits have a high potential toxicity when compared with deposits from other tectonic settings based on their genetic association of a wide range of potentially toxic metals (As, Sb, Pb, Hg, Ag and Bi) that are incorporated into more reactive sulfosalts, galena and Fe-rich sphalerite. Thus, deposits such as these require special care when considered as mining targets. In contrast, the exclusive concern of ultra-mafic deposits is Cu, present in abundant, albeit less reactive chalcopyrite, but largely barren of other metals such as As, Pb, Sb, Cd and Hg. Whilst geological setting does dictate metal endowment, ultimately mineralogy is the largest control of trace element distribution and subsequent potential toxicity. Deposits containing abundant pyrrhotite (high-temperature deposits) and Fe-rich sphalerite (ubiquitous to all SMS deposits) as well as deposits with abundant colloform textures also pose a higher risk. This type of study can be combined with “bulk lethal toxicity” assessments and used throughout the stages of a mining project to help guide prospecting and legislation, focus exploitation and minimise environmental impact.
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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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Homologous Recombination in Core Genomes Facilitates Marine Bacterial Adaptation. Appl Environ Microbiol 2018; 84:AEM.02545-17. [PMID: 29572211 DOI: 10.1128/aem.02545-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/20/2018] [Indexed: 01/01/2023] Open
Abstract
Acquisition of ecologically relevant genes is common among ocean bacteria, but whether it has a major impact on genome evolution in marine environments remains unknown. Here, we analyzed the core genomes of 16 phylogenetically diverse and ecologically relevant bacterioplankton lineages, each consisting of up to five genomes varying at the strain level. Statistical approaches identified from each lineage up to ∼50 loci showing anomalously high divergence at synonymous sites, which is best explained by recombination with distantly related organisms. The enriched gene categories in these outlier loci match well with the characteristics previously identified as the key phenotypes of these lineages. Examples are antibiotic synthesis and detoxification in Phaeobacter inhibens, exopolysaccharide production in Alteromonas macleodii, hydrocarbon degradation in Marinobacter hydrocarbonoclasticus, and cold adaptation in Pseudoalteromonas haloplanktis Intriguingly, the outlier loci feature polysaccharide catabolism in Cellulophaga baltica but not in Cellulophaga lytica, consistent with their primary habitat preferences in macroalgae and beach sands, respectively. Likewise, analysis of Prochlorococcus showed that photosynthesis-related genes listed in the outlier loci are found only in the high-light-adapted ecotype and not in the low-light adapted ecotype. These observations strongly suggest that recombination with distant relatives is a key mechanism driving the ecological diversification among marine bacterial lineages.IMPORTANCE Acquisition of new metabolic genes has been known as an important mechanism driving bacterial evolution and adaptation in the ocean, but acquisition of novel alleles of existing genes and its potential ecological role have not been examined. Guided by population genetic theories, our genomic analysis showed that divergent allele acquisition is prevalent in phylogenetically diverse marine bacterial lineages and that the affected loci often encode metabolic functions that underlie the known ecological roles of the lineages under study.
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Zheng R, Wu S, Ma N, Sun C. Genetic and Physiological Adaptations of Marine Bacterium Pseudomonas stutzeri 273 to Mercury Stress. Front Microbiol 2018; 9:682. [PMID: 29675016 PMCID: PMC5895735 DOI: 10.3389/fmicb.2018.00682] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/22/2018] [Indexed: 12/18/2022] Open
Abstract
Mercury-mediated toxicity remains one of the greatest barriers against microbial survival, even though bacterial resistance to mercury compounds can occur. However, the genetic and physiological adaptations of bacteria to mercury stress still remains unclear. Here, we show that the marine bacterium Pseudomonas stutzeri 273 is resistant to 50 μM Hg2+ and removes up to 94% Hg2+ from culture. Using gene homologous recombination and complementation, we show that genes encoding Hg2+-transport proteins MerT, MerP, the mercuric reductase MerA and the regulatory protein MerD are essential for bacterial mercuric resistance when challenged with Hg2+. Further, mercury stress inhibits flagellar development, motility, chemotaxis and biofilm formation of P. stutzeri 273, which are verified by transcriptomic and physiological analyses. Surprisingly, we discover that MerF, a previously reported Hg2+-transporter, determines flagellar development, motility and biofilm formation in P. stutzeri 273 by genetic and physiological analyses. Our results strongly indicate that MerF plays an integral role in P. stutzeri 273 to develop physiological responses to mercury stress. Notably, MerF homologs are also prevalent in different human pathogens. Using this unique target may provide novel strategies to control these pathogenic bacteria, given the role of MerF in flagella and biofilm formation. In summary, our data provide an original report on MerF in bacterial physiological development and suggest that the mer in marine bacteria has evolved through progressive, sequential recruitment of novel functions over time.
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Affiliation(s)
- Rikuan Zheng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shimei Wu
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Ning Ma
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Leal-Acosta ML, Shumilin E, Mirlean N, Baturina EL, Sánchez-Rodríguez I, Delgadillo-Hinojosa F, Borges-Souza J. Intertidal geothermal hot springs as a source of trace elements to the coastal zone: A case study from Bahía Concepción, Gulf of California. MARINE POLLUTION BULLETIN 2018; 128:51-64. [PMID: 29571403 DOI: 10.1016/j.marpolbul.2018.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 06/08/2023]
Abstract
We investigated the influence of the intertidal geothermal hot spring (GHS) on the biogeochemistry of trace elements in Santispac Bight, Bahía Concepción (Gulf of California). The geothermal fluids were enriched in As and Hg mainly in ionic form. The suspended particulate matter of the GHS had elevated enrichment factor (EF) >1 of As, Bi, Cd, Co, Cu, Mn, Mo, Sb, Sn, Sr, Ti, U and Zn. The sediment core from GHS1 had high concentration of As, Hg, Corg, S, V, Mo, and U and the extremely high EF of these elements at 8cm of the core. The maximum bioaccumulation of As and Hg was in seaweeds Sargassum sinicola collected near the GHS2. The results confirm the input of trace elements to the coastal zone in Bahía Concepción from geothermal fluids and the evident modification of the chemical composition of the adjacent marine environment.
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Affiliation(s)
- María Luisa Leal-Acosta
- Instituto de Industrias, Universidad del Mar, Campus Puerto Ángel, Distrito de San Pedro Pochutla, Puerto Ángel CP 70902, Oaxaca, Mexico.
| | - Evgueni Shumilin
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. IPN s/n, Colonia Playa Palo de Santa Rita, Apdo. postal 592, La Paz, Baja California Sur 23096, Mexico
| | - Nicolai Mirlean
- Oceanography Geological Laboratory, Oceanography Institute, Federal University of Rio Grande, CP 474, Rio Grande, Brazil
| | - Elena Lounejeva Baturina
- ARC Centre of Excellence in Ore Deposits (CODES), School of Physical Sciences, University of Tasmania, Private Bag 79, Hobart, Tasmania 7001, Australia
| | - Ignacio Sánchez-Rodríguez
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. IPN s/n, Colonia Playa Palo de Santa Rita, Apdo. postal 592, La Paz, Baja California Sur 23096, Mexico
| | - Francisco Delgadillo-Hinojosa
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Km 103, Carretera Tijuana-Ensenada, CP 22869 Ensenada, Baja California, Mexico
| | - José Borges-Souza
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Av. IPN s/n, Colonia Playa Palo de Santa Rita, Apdo. postal 592, La Paz, Baja California Sur 23096, Mexico
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Ranawat P, Rawat S. Metal-tolerant thermophiles: metals as electron donors and acceptors, toxicity, tolerance and industrial applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:4105-4133. [PMID: 29238927 DOI: 10.1007/s11356-017-0869-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously. Metals are essential for biological systems, as they participate in biochemistries that cannot be achieved only by organic molecules. However, the excess concentration of metals can disrupt natural biogeochemical processes and can impose toxicity. Thermophiles counteract metal toxicity via their unique cell wall, metabolic factors and enzymes that carry out metal-based redox transformations, metal sequestration by metallothioneins and metallochaperones as well as metal efflux. Thermophilic metal resistance is heterogeneous at both genetic and physiology levels and may be chromosomally, plasmid or transposon encoded with one or more genes being involved. These effective response mechanisms either individually or synergistically make proliferation of thermophiles in metal-rich habitats possibly. This article presents the state of the art and future perspectives of responses of thermophiles to metals at genetic as well as physiological levels.
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Affiliation(s)
- Preeti Ranawat
- Department of Botany and Microbiology, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal), Uttarakhand, India
| | - Seema Rawat
- School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.
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Low-Molecular-Weight Thiols and Thioredoxins Are Important Players in Hg(II) Resistance in Thermus thermophilus HB27. Appl Environ Microbiol 2018; 84:AEM.01931-17. [PMID: 29150497 DOI: 10.1128/aem.01931-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
Mercury (Hg), one of the most toxic and widely distributed heavy metals, has a high affinity for thiol groups. Thiol groups reduce and sequester Hg. Therefore, low-molecular-weight (LMW) and protein thiols may be important cell components used in Hg resistance. To date, the role of low-molecular-weight thiols in Hg detoxification remains understudied. The mercury resistance (mer) operon of Thermus thermophilus suggests an evolutionary link between Hg(II) resistance and low-molecular-weight thiol metabolism. The mer operon encodes an enzyme involved in methionine biosynthesis, Oah. Challenge with Hg(II) resulted in increased expression of genes involved in the biosynthesis of multiple low-molecular-weight thiols (cysteine, homocysteine, and bacillithiol), as well as the thioredoxin system. Phenotypic analysis of gene replacement mutants indicated that Oah contributes to Hg resistance under sulfur-limiting conditions, and strains lacking bacillithiol and/or thioredoxins are more sensitive to Hg(II) than the wild type. Growth in the presence of either a thiol-oxidizing agent or a thiol-alkylating agent increased sensitivity to Hg(II). Furthermore, exposure to 3 μM Hg(II) consumed all intracellular reduced bacillithiol and cysteine. Database searches indicate that oah2 is present in all Thermus sp. mer operons. The presence of a thiol-related gene was also detected in some alphaproteobacterial mer operons, in which a glutathione reductase gene was present, supporting the role of thiols in Hg(II) detoxification. These results have led to a working model in which LMW thiols act as Hg(II)-buffering agents while Hg is reduced by MerA.IMPORTANCE The survival of microorganisms in the presence of toxic metals is central to life's sustainability. The affinity of thiol groups for toxic heavy metals drives microbe-metal interactions and modulates metal toxicity. Mercury detoxification (mer) genes likely originated early in microbial evolution in geothermal environments. Little is known about how mer systems interact with cellular thiol systems. Thermus spp. possess a simple mer operon in which a low-molecular-weight thiol biosynthesis gene is present, along with merR and merA In this study, we present experimental evidence for the role of thiol systems in mercury resistance. Our data suggest that, in T. thermophilus, thiolated compounds may function side by side with mer genes to detoxify mercury. Thus, thiol systems function in consort with mer-mediated resistance to mercury, suggesting exciting new questions for future research.
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Pop Ristova P, Pichler T, Friedrich MW, Bühring SI. Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles). Front Microbiol 2017; 8:2400. [PMID: 29255454 PMCID: PMC5722836 DOI: 10.3389/fmicb.2017.02400] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022] Open
Abstract
Shallow-water hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range of chemical compounds. Yet, little is known about their diversity or factors shaping their structure or how they compare to coastal sediments not impacted by hydrothermalism. To this end, we have used automated ribosomal intergenic spacer analysis (ARISA) and high-throughput Illumina sequencing combined with porewater geochemical analysis to investigate microbial communities along geochemical gradients in two shallow-water hydrothermal systems off the island of Dominica (Lesser Antilles). At both sites, venting of hydrothermal fluids substantially altered the porewater geochemistry by enriching it with silica, iron and dissolved inorganic carbon, resulting in island-like habitats with distinct biogeochemistry. The magnitude of fluid flow and difference in sediment grain size, which impedes mixing of the fluids with seawater, were correlated with the observed differences in the porewater geochemistry between the two sites. Concomitantly, individual sites harbored microbial communities with a significantly different community structure. These differences could be statistically linked to variations in the porewater geochemistry and the hydrothermal fluids. The two shallow-water hydrothermal systems of Dominica harbored bacterial communities with high taxonomical and metabolic diversity, predominated by heterotrophic microorganisms associated with the Gammaproteobacterial genera Pseudomonas and Pseudoalteromonas, indicating the importance of heterotrophic processes. Overall, this study shows that shallow-water hydrothermal systems contribute substantially to the biogeochemical heterogeneity and bacterial diversity of coastal sediments.
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Affiliation(s)
- Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Thomas Pichler
- Geochemistry and Hydrogeology, University of Bremen, Bremen, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Solveig I. Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Centre for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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30
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Bafana A, Khan F, Suguna K. Structural and functional characterization of mercuric reductase from Lysinibacillus sphaericus strain G1. Biometals 2017; 30:809-819. [PMID: 28894951 DOI: 10.1007/s10534-017-0050-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/04/2017] [Indexed: 11/25/2022]
Abstract
In response to the widespread presence of inorganic Hg in the environment, bacteria have evolved resistance systems with mercuric reductase (MerA) as the key enzyme. MerA enzymes have still not been well characterized from gram positive bacteria. Current study reports physico-chemical, kinetic and structural characterization of MerA from a multiple heavy metal resistant strain of Lysinibacillus sphaericus, and discusses its implications in bioremediation application. The enzyme was homodimeric with subunit molecular weight of about 60 kDa. The Km and Vmax were found to be 32 µM of HgCl2 and 18 units/mg respectively. The enzyme activity was enhanced by β-mercaptoethanol and NaCl up to concentrations of 500 µM and 100 mM respectively, followed by inhibition at higher concentrations. The enzyme showed maximum activity in the pH range of 7-7.5 and temperature range of 25-50 °C, with melting temperature of 67 °C. Cu2+ exhibited pronounced inhibition of the enzyme with mixed inhibition pattern. The enzyme contained FAD as the prosthetic group and used NADPH as the preferred electron donor, but it showed slight activity with NADH as well. Structural characterization was carried out by circular dichroism spectrophotometry and X-ray crystallography. X-ray confirmed the homodimeric structure of enzyme and gave an insight on the residues involved in catalytic binding. In conclusion, the investigated enzyme showed higher catalytic efficiency, temperature stability and salt tolerance as compared to MerA enzymes from other mesophiles. Therefore, it is proposed to be a promising candidate for Hg2+ bioremediation.
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Affiliation(s)
- Amit Bafana
- Environmental Impact and Sustainability Division, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India.
| | - Farha Khan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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Geesey GG, Barkay T, King S. Microbes in mercury-enriched geothermal springs in western North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:321-331. [PMID: 27344121 DOI: 10.1016/j.scitotenv.2016.06.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.
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Affiliation(s)
- Gill G Geesey
- Department of Microbiology and Immunology, Thermal Biology Institute, Montana State University, Bozeman, MT 59717-3520, USA.
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901-8525, USA.
| | - Sue King
- 2908 3rd Avenue North, Great Falls, MT 59401, USA.
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Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, Pinhassi J. Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO 2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Front Microbiol 2016; 7:1670. [PMID: 27818655 PMCID: PMC5073097 DOI: 10.3389/fmicb.2016.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/05/2023] Open
Abstract
To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
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Affiliation(s)
- Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
- Department of Marine Sciences, University of OtagoDunedin, New Zealand
- National Institute of Water and Atmospheric Research (NIWA)/University of Otago Research Centre for OceanographyDunedin, New Zealand
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Joakim Palovaara
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Itziar Lekunberri
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Institut Català de Recerca de l'AiguaGirona, Spain
| | - Thomas Reinthaler
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
| | - Gerhard J. Herndl
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
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Marques CR. Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:165-180. [PMID: 27161138 DOI: 10.1016/j.scitotenv.2016.04.119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/17/2016] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner.
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Affiliation(s)
- Catarina R Marques
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Russell JA, León-Zayas R, Wrighton K, Biddle JF. Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria. Front Microbiol 2016; 7:678. [PMID: 27242705 PMCID: PMC4861733 DOI: 10.3389/fmicb.2016.00678] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/26/2016] [Indexed: 12/04/2022] Open
Abstract
Studies of subsurface microorganisms have yielded few environmentally relevant isolates for laboratory studies. In order to address this lack of cultivated microorganisms, we initiated several enrichments on sediment and underlying basalt samples from North Pond, a sediment basin ringed by basalt outcrops underlying an oligotrophic water-column west of the Mid-Atlantic Ridge at 22°N. In contrast to anoxic enrichments, growth was observed in aerobic, heterotrophic enrichments from sediment of IODP Hole U1382B at 4 and 68 m below seafloor (mbsf). These sediment depths, respectively, correspond to the fringes of oxygen penetration from overlying seawater in the top of the sediment column and upward migration of oxygen from oxic seawater from the basalt aquifer below the sediment. Here we report the enrichment, isolation, initial characterization and genomes of three isolated aerobic heterotrophs from North Pond sediments; an Arthrobacter species from 4 mbsf, and Paracoccus and Pseudomonas species from 68 mbsf. These cultivated bacteria are represented in the amplicon 16S rRNA gene libraries created from whole sediments, albeit at low (up to 2%) relative abundance. We provide genomic evidence from our isolates demonstrating that the Arthrobacter and Pseudomonas isolates have the potential to respire nitrate and oxygen, though dissimilatory nitrate reduction could not be confirmed in laboratory cultures. The cultures from this study represent members of abundant phyla, as determined by amplicon sequencing of environmental DNA extracts, and allow for further studies into geochemical factors impacting life in the deep subsurface.
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Affiliation(s)
- Joseph A Russell
- College of Earth, Ocean and Environment, University of Delaware Lewes, DE, USA
| | - Rosa León-Zayas
- College of Earth, Ocean and Environment, University of Delaware Lewes, DE, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University Columbus, OH, USA
| | - Jennifer F Biddle
- College of Earth, Ocean and Environment, University of Delaware Lewes, DE, USA
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Figueiredo NL, Canário J, O'Driscoll NJ, Duarte A, Carvalho C. Aerobic Mercury-resistant bacteria alter Mercury speciation and retention in the Tagus Estuary (Portugal). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 124:60-67. [PMID: 26461264 DOI: 10.1016/j.ecoenv.2015.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 06/05/2023]
Abstract
Aerobic mercury-resistant bacteria were isolated from the sediments of two highly mercury-polluted areas of the Tagus Estuary (Barreiro and Cala do Norte) and one natural reserve area (Alcochete) in order to test their capacity to transform mercury. Bacterial species were identified using 16S rRNA amplification and sequencing techniques and the results indicate the prevalence of Bacillus sp. Resistance patterns to mercurial compounds were established by the determination of minimal inhibitory concentrations. Representative Hg-resistant bacteria were further tested for transformation pathways (reduction, volatilization and methylation) in cultures containing mercury chloride. Bacterial Hg-methylation was carried out by Vibrio fluvialis, Bacillus megaterium and Serratia marcescens that transformed 2-8% of total mercury into methylmercury in 48h. In addition, most of the HgR bacterial isolates showed Hg(2+)-reduction andHg(0)-volatilization resulting 6-50% mercury loss from the culture media. In summary, the results obtained under controlled laboratory conditions indicate that aerobic Hg-resistant bacteria from the Tagus Estuary significantly affect both the methylation and reduction of mercury and may have a dual face by providing a pathway for pollution dispersion while forming methylmercury, which is highly toxic for living organisms.
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Affiliation(s)
- Neusa L Figueiredo
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - João Canário
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Nelson J O'Driscoll
- Department of Earth & Environmental Sciences, Acadia University, K.C. Irving Environmental Science Center, 32 University Avenue, Wolfville, Nova Scotia, Canada
| | - Aida Duarte
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - Cristina Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal.
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Mercury (II) removal by resistant bacterial isolates and mercuric (II) reductase activity in a new strain of Pseudomonas sp. B50A. N Biotechnol 2016; 33:216-23. [DOI: 10.1016/j.nbt.2015.05.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 05/17/2015] [Accepted: 05/26/2015] [Indexed: 11/22/2022]
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Artz JH, White SN, Zadvornyy OA, Fugate CJ, Hicks D, Gauss GH, Posewitz MC, Boyd ES, Peters JW. Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula. Front Bioeng Biotechnol 2015. [PMID: 26217660 PMCID: PMC4500099 DOI: 10.3389/fbioe.2015.00097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme.
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Affiliation(s)
- Jacob H Artz
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Spencer N White
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Oleg A Zadvornyy
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Corey J Fugate
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Danny Hicks
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - George H Gauss
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines , Golden, CO , USA
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University , Bozeman, MT , USA ; Thermal Biology Institute, Montana State University , Bozeman, MT , USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, MT , USA
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Bonificio WD, Clarke DR. Bacterial recovery and recycling of tellurium from tellurium-containing compounds by Pseudoalteromonas sp. EPR3. J Appl Microbiol 2014; 117:1293-304. [PMID: 25175548 DOI: 10.1111/jam.12629] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/20/2014] [Accepted: 08/26/2014] [Indexed: 11/25/2022]
Abstract
AIMS Tellurium-based devices, such as photovoltaic (PV) modules and thermoelectric generators, are expected to play an increasing role in renewable energy technologies. Tellurium, however, is one of the scarcest elements in the earth's crust, and current production and recycling methods are inefficient and use toxic chemicals. This study demonstrates an alternative, bacterially mediated tellurium recovery process. METHODS AND RESULTS We show that the hydrothermal vent microbe Pseudoalteromonas sp. strain EPR3 can convert tellurium from a wide variety of compounds, industrial sources and devices into metallic tellurium and a gaseous tellurium species. These compounds include metallic tellurium (Te(0)), tellurite (TeO3(2-)), copper autoclave slime, tellurium dioxide (TeO2), tellurium-based PV material (cadmium telluride, CdTe) and tellurium-based thermoelectric material (bismuth telluride, Bi2Te3). Experimentally, this was achieved by incubating these tellurium sources with the EPR3 in both solid and liquid media. CONCLUSIONS Despite the fact that many of these tellurium compounds are considered insoluble in aqueous solution, they can nonetheless be transformed by EPR3, suggesting the existence of a steady state soluble tellurium concentration during tellurium transformation. SIGNIFICANCE AND IMPACT OF THE STUDY These experiments provide insights into the processes of tellurium precipitation and volatilization by bacteria, and their implications on tellurium production and recycling.
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Affiliation(s)
- W D Bonificio
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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Santos-Gandelman JF, Giambiagi-deMarval M, Muricy G, Barkay T, Laport MS. Mercury and methylmercury detoxification potential by sponge-associated bacteria. Antonie van Leeuwenhoek 2014; 106:585-90. [DOI: 10.1007/s10482-014-0224-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/25/2014] [Indexed: 10/25/2022]
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Potential Application in Mercury Bioremediation of a Marine Sponge-Isolated Bacillus cereus strain Pj1. Curr Microbiol 2014; 69:374-80. [DOI: 10.1007/s00284-014-0597-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/11/2014] [Indexed: 11/24/2022]
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Pérez-Valdespino A, Celestino-Mancera M, Villegas-Rodríguez VL, Curiel-Quesada E. Characterization of mercury-resistant clinical Aeromonas species. Braz J Microbiol 2014; 44:1279-83. [PMID: 24688523 PMCID: PMC3958199 DOI: 10.1590/s1517-83822013000400036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 04/04/2013] [Indexed: 01/14/2023] Open
Abstract
Mercury-resistant Aeromonas strains isolated from diarrhea were studied. Resistance occurs via mercuric ion reduction but merA and merR genes were only detected in some strains using PCR and dot hybridization. Results indicate a high variability in mer operons in Aeromonas. To our knowledge, this is the first report of mercury-resistant clinical Aeromonas strains.
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Affiliation(s)
- Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Martin Celestino-Mancera
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
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Survival of the fittest: overcoming oxidative stress at the extremes of Acid, heat and metal. Life (Basel) 2012; 2:229-42. [PMID: 25371104 PMCID: PMC4187130 DOI: 10.3390/life2030229] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/14/2012] [Accepted: 08/17/2012] [Indexed: 11/29/2022] Open
Abstract
The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea.
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Mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic Aquificae. Appl Environ Microbiol 2012; 78:6568-75. [PMID: 22773655 DOI: 10.1128/aem.01060-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mercury (Hg) resistance (mer) by the reduction of mercuric to elemental Hg is broadly distributed among the Bacteria and Archaea and plays an important role in Hg detoxification and biogeochemical cycling. MerA is the protein subunit of the homodimeric mercuric reductase (MR) enzyme, the central function of the mer system. MerA sequences in the phylum Aquificae form the deepest-branching lineage in Bayesian phylogenetic reconstructions of all known MerA homologs. We therefore hypothesized that the merA homologs in two thermophilic Aquificae, Hydrogenobaculum sp. strain Y04AAS1 (AAS1) and Hydrogenivirga sp. strain 128-5-R1-1 (R1-1), specified Hg resistance. Results supported this hypothesis, because strains AAS1 and R1-1 (i) were resistant to >10 μM Hg(II), (ii) transformed Hg(II) to Hg(0) during cellular growth, and (iii) possessed Hg-dependent NAD(P)H oxidation activities in crude cell extracts that were optimal at temperatures corresponding with the strains' optimal growth temperatures, 55°C for AAS1 and 70°C for R1-1. While these characteristics all conformed with the mer system paradigm, expression of the Aquificae mer operons was not induced by exposure to Hg(II) as indicated by unity ratios of merA transcripts, normalized to gyrA transcripts for hydrogen-grown AAS1 cultures, and by similar MR specific activities in thiosulfate-grown cultures with and without Hg(II). The Hg(II)-independent expression of mer in the deepest-branching lineage of MerA from bacteria whose natural habitats are Hg-rich geothermal environments suggests that regulated expression of mer was a later innovation likely in environments where microorganisms were intermittently exposed to toxic concentrations of Hg.
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Wang Y, Wiatrowski HA, John R, Lin CC, Young LY, Kerkhof LJ, Yee N, Barkay T. Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments. Biodegradation 2012; 24:33-46. [PMID: 22678127 DOI: 10.1007/s10532-012-9555-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022]
Abstract
The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.
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Affiliation(s)
- Yanping Wang
- Department of Biochemistry and Microbiology, Rutgers University, 223C Lipman Hall, 76 Lipman Dr., New Brunswick, NJ 08901, USA.
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KHODIJAH CHAERUN SITI, HASNI SAKINAH, SANWANI EDY, RAMDANI MOEIS MAELITA. Mercury (Hg)-Resistant Bacteria in Hg-Polluted Gold Mine Sites of Bandung, West Java Province, Indonesia. MICROBIOLOGY INDONESIA 2012. [DOI: 10.5454/mi.6.2.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Isolation and characterization of environmental bacteria capable of extracellular biosorption of mercury. Appl Environ Microbiol 2011; 78:1097-106. [PMID: 22156431 DOI: 10.1128/aem.06522-11] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accumulation of toxic metals in the environment represents a public health and wildlife concern. Bacteria resistant to toxic metals constitute an attractive biomass for the development of systems to decontaminate soils, sediments, or waters. In particular, biosorption of metals within the bacterial cell wall or secreted extracellular polymeric substances (EPS) is an emerging process for the bioremediation of contaminated water. Here the isolation of bacteria from soil, effluents, and river sediments contaminated with toxic metals permitted the selection of seven bacterial isolates tolerant to mercury and associated with a mucoid phenotype indicative of the production of EPS. Inductively coupled plasma-optical emission spectroscopy and transmission electron microscopy in conjunction with X-ray energy dispersive spectrometry revealed that bacteria incubated in the presence of HgCl2 sequestered mercury extracellularly as spherical or amorphous deposits. Killed bacterial biomass incubated in the presence of HgCl2 also generated spherical extracellular mercury deposits, with a sequestration capacity (40 to 120 mg mercury per g [dry weight] of biomass) superior to that of live bacteria (1 to 2 mg mercury per g [dry weight] of biomass). The seven strains were shown to produce EPS, which were characterized by Fourier transform-infrared (FT-IR) spectroscopy and chemical analysis of neutral-carbohydrate, uronic acid, and protein contents. The results highlight the high potential of Hg-tolerant bacteria for applications in the bioremediation of mercury through biosorption onto the biomass surface or secreted EPS.
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Liu YR, He JZ, Zhang LM, Zheng YM. Effects of long-term fertilization on the diversity of bacterial mercuric reductase gene in a Chinese upland soil. J Basic Microbiol 2011; 52:35-42. [DOI: 10.1002/jobm.201100211] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 07/21/2011] [Indexed: 11/12/2022]
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Wang Y, Boyd E, Crane S, Lu-Irving P, Krabbenhoft D, King S, Dighton J, Geesey G, Barkay T. Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A. MICROBIAL ECOLOGY 2011; 62:739-752. [PMID: 21713435 DOI: 10.1007/s00248-011-9890-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/04/2011] [Indexed: 05/31/2023]
Abstract
The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.
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Affiliation(s)
- Yanping Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
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Mathema VB, Thakuri BC, Sillanpää M. Bacterial mer operon-mediated detoxification of mercurial compounds: a short review. Arch Microbiol 2011; 193:837-44. [PMID: 21912976 DOI: 10.1007/s00203-011-0751-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 11/30/2022]
Abstract
Mercury pollution has emerged as a major problem in industrialized zones and presents a serious threat to environment and health of local communities. Effectiveness and wide distribution of mer operon by horizontal and vertical gene transfer in its various forms among large community of microbe reflect importance and compatibility of this mechanism in nature. This review specifically describes mer operon and its generic molecular mechanism with reference to the central role played by merA gene and its related gene products. The combinatorial action of merA and merB together maintains broad spectrum mercury detoxification system for substantial detoxification of mercurial compounds. Feasibility of mer operon to coexist with antibiotic resistance gene (ampr, kanr, tetr) clusters enables extensive adaptation of bacterial species to adverse environment. Flexibility of the mer genes to exist as intricate part of chromosome, plasmids, transposons, and integrons enables high distribution of these genes in wider microbial gene pool. Unique ability of this system to manipulate oligodynamic property of mercurial compounds for volatilization of mercuric ions (Hg2+) makes it possible for a wide range of microbes to tolerate mercury-mediated toxicity.
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Affiliation(s)
- Vivek Bhakta Mathema
- Department of Biotechnology, Kathmandu University, P.O. BOX: 7570 KTM, Dhulikhel, Nepal.
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Barkay T, Kritee K, Boyd E, Geesey G. A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase. Environ Microbiol 2011; 12:2904-17. [PMID: 20545753 DOI: 10.1111/j.1462-2920.2010.02260.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mercuric reductase (MerA) is central to the mercury (Hg) resistance (mer) system, catalyzing the reduction of ionic Hg to volatile Hg(0). A total of 213 merA homologues were identified in sequence databases, the majority of which belonged to microbial lineages that occupy oxic environments. merA was absent among phototrophs and in lineages that inhabit anoxic environments. Phylogenetic reconstructions of MerA indicate that (i) merA originated in a thermophilic bacterium following the divergence of the Archaea and Bacteria with a subsequent acquisition in Archaea via horizontal gene transfer (HGT), (ii) HGT of merA was rare across phylum boundaries and (iii) MerA from marine bacteria formed distinct and strongly supported lineages. Collectively, these observations suggest that a combination of redox, light and salinity conditions constrain MerA to microbial lineages that occupy environments where the most oxidized and toxic form of Hg, Hg(II), predominates. Further, the taxon-specific distribution of MerA with and without a 70 amino acid N-terminal extension may reflect intracellular levels of thiols. In conclusion, MerA likely evolved following the widespread oxygenation of the biosphere in a thermal environment and its subsequent evolution has been modulated by the interactions of Hg with the intra- and extracellular environment of the organism.
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Affiliation(s)
- Tamar Barkay
- Department of Biochemistry and Microbiology, Rutgers University, Lipman Hall, New Brunswick, NJ 08901, USA.
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