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Johnson J, Jain KR, Patel A, Parmar N, Joshi C, Madamwar D. Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal. World J Microbiol Biotechnol 2023; 40:52. [PMID: 38146029 DOI: 10.1007/s11274-023-03848-1] [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: 03/04/2023] [Accepted: 11/19/2023] [Indexed: 12/27/2023]
Abstract
Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.
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Affiliation(s)
- Jenny Johnson
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Kunal R Jain
- Post Graduate Department of Biosciences, Centre of Advanced Study, Sardar Patel University, Satellite Campus, Vadtal Road, Bakrol (Anand), Gujarat, 388 315, India
| | - Anand Patel
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Nidhi Parmar
- Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre, 6th Floor, M. S. Building, Sector 11, Gandhinagar, Gujarat, 382011, India
| | - Datta Madamwar
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, CHARUSAT Campus, Changa (Anand), Gujarat, 388 421, India.
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Jiang M, Zhang Y, Zheng J, Li H, Ma J, Zhang X, Wei Q, Wang X, Zhang X, Wang Z. Mechanistic insights into CO 2 pressure regulating microbial competition in a hydrogen-based membrane biofilm reactor for denitrification. CHEMOSPHERE 2022; 303:134875. [PMID: 35537631 DOI: 10.1016/j.chemosphere.2022.134875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/07/2022] [Accepted: 05/04/2022] [Indexed: 06/14/2023]
Abstract
CO2 is a proven pH regulator in hydrogen-based membrane biofilm reactor (H2-MBfR) but how its pressure regulates microbial competition in this system remains unclear. This work evaluates the CO2 pressure dependent system performance, CO2 allocation, microbial structure and activity of CO2 source H2-MBfR. The optimum system performance was reached at the CO2 pressure of 0.008 MPa, and this pressure enabled 0.18 g C/(m2·d) of dissolved inorganic carbon (DIC) allocated to denitrifying bacteria (DNB) for carbon source anabolism and denitrification-related proton compensation, while inducing a bulk liquid pH (pH 7.4) in favor of DNB activity by remaining 0.21 g C/(m2·d) of DIC as pH buffer. Increasing CO2 pressure from 0.008 to 0.016 MPa caused the markedly changed DNB composition, and the diminished DNB population was accompanied by the enrichment of sulfate-reducing bacteria (SRB). A high CO2 pressure of 0.016 MPa was estimated to induce the enhanced SRB activity and weakened DNB activity.
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Affiliation(s)
- Minmin Jiang
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Yuanyuan Zhang
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Junjian Zheng
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China.
| | - Haixiang Li
- Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China.
| | - Jinxing Ma
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China; Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xingran Zhang
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China; College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China
| | - Qiaoyan Wei
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China
| | - Xueye Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Xuehong Zhang
- College of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, 541004, China; Guangxi Key Laboratory of Environmental Pollution Control Theory and Technology, Guilin University of Technology, Guilin, 541004, China; Guangxi Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst Area, Guilin University of Technology, Guilin, 541004, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
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Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
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4
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Nguyen HT, Nguyen HL, Nguyen MH, Nguyen TKN, Dinh HT. Sulfate Reduction for Bioremediation of AMD Facilitated by an Indigenous Acidand Metal-Tolerant Sulfate-Reducer. J Microbiol Biotechnol 2020; 30:1005-1012. [PMID: 32160701 PMCID: PMC9728233 DOI: 10.4014/jmb.2001.01012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022]
Abstract
Acid mine drainage (AMD) has been a serious environmental issue that threatens soil and aquatic ecosystems. In this study, an acid-tolerant sulfate-reducing bacterium, strain S4, was isolated from the mud of an AMD storage pond in Vietnam via enrichment in anoxic mineral medium at pH 5. Comparative analyses of sequences of the 16S rRNA gene and dsrB gene involved in sulfate reduction revealed that the isolate belonged to the genus Desulfovibrio, and is most closely related to Desulfovibrio oxamicus (with 99% homology in 16S rDNA sequence and 98% homology in dsrB gene sequence). Denaturing gradient gel electrophoresis (DGGE) analyses of dsrB gene showed that strain S4 represented one of the two most abundant groups developed in the enrichment culture. Notably, strain S4 was capable of reducing sulfate in low pH environments (from 2 and above), and resistance to extremely high concentration of heavy metals (Fe 3,000 mg/l, Zn 100 mg/l, Cu 100 mg/ l). In a batch incubation experiment in synthetic AMD with pH 3.5, strain S4 showed strong effects in facilitating growth of a neutrophilic, metal sensitive Desulfovibrio sp. strain SR4H, which was not capable of growing alone in such an environment. Thus, it is postulated that under extreme conditions such as an AMD environment, acid- and metal-tolerant sulfate-reducing bacteria (SRB)- like strain S4 would facilitate the growth of other widely distributed SRB by starting to reduce sulfate at low pH, thus increasing pH and lowering the metal concentration in the environment. Owing to such unique physiological characteristics, strain S4 shows great potential for application in sustainable remediation of AMD.
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Affiliation(s)
- Hai Thi Nguyen
- VNU Institute of Microbiology and Biotechnology (IMBT), Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Huong Lan Nguyen
- Hanoi University of Science and Technology (HUST), 1 Dai Co Viet Road, Hanoi, Vietnam
| | - Minh Hong Nguyen
- VNU Institute of Microbiology and Biotechnology (IMBT), Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Thao Kim Nu Nguyen
- VNU Institute of Microbiology and Biotechnology (IMBT), Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Hang Thuy Dinh
- VNU Institute of Microbiology and Biotechnology (IMBT), Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, Vietnam,Corresponding author Phone: +84-4-972-523-466 Fax: +84-24754-7407 E-mail:
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5
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Johnson DB, Sánchez-Andrea I. Dissimilatory reduction of sulfate and zero-valent sulfur at low pH and its significance for bioremediation and metal recovery. Adv Microb Physiol 2019; 75:205-231. [PMID: 31655738 DOI: 10.1016/bs.ampbs.2019.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Redox transformations of sulfur, involving dissimilatory and assimilatory oxidation and reduction reactions, occurs in water bodies and terrestrial environments worldwide, leading to dynamic cycling of this element throughout the biosphere. In cases where zero-valent (elemental) sulfur, sulfate and other oxidized forms are used as electron acceptor in (primarily) anaerobic microbial metabolisms, the end product is hydrogen sulfide (HS- or H2S, dependent on pH). While neutrophilic and alkalophilic sulfidogenic prokaryotes have been known for many decades, acid-tolerant and acidophilic strains and species have been isolated and characterized only in the past twenty or so years, even though evidence for sulfide generation on these environments was previously well documented. This review outlines the background and current status of the biodiversity and metabolisms of sulfate- and sulfur-reducing prokaryotes that are metabolically active in low pH environments, and describes the developing technologies in which they are being used to remediate acidic waste waters (which are often metal-contaminated) and to recover metal resources.
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Affiliation(s)
- D Barrie Johnson
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
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6
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Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. THE ISME JOURNAL 2019; 13:2044-2057. [PMID: 30962514 PMCID: PMC6776010 DOI: 10.1038/s41396-019-0415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022]
Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Yun Fang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Magigene Biotechnology Co. Ltd., 510000, Guangzhou, China
| | - Li-Ying Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hai-Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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7
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Qian Z, Tianwei H, Mackey HR, van Loosdrecht MCM, Guanghao C. Recent advances in dissimilatory sulfate reduction: From metabolic study to application. WATER RESEARCH 2019; 150:162-181. [PMID: 30508713 DOI: 10.1016/j.watres.2018.11.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/25/2018] [Accepted: 11/08/2018] [Indexed: 05/24/2023]
Abstract
Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.
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Affiliation(s)
- Zeng Qian
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hao Tianwei
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China; Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hamish Robert Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | | | - Chen Guanghao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, The Hong Kong University of Science and Technology, Nansha, Guangzhou, China.
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8
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Bukhtiyarova PA, Antsiferov DV, Brasseur G, Avakyan MR, Frank YA, Ikkert OP, Pimenov NV, Tuovinen OH, Karnachuk OV. Isolation, characterization, and genome insights into an anaerobic sulfidogenic Tissierella bacterium from Cu-bearing coins. Anaerobe 2019; 56:66-77. [PMID: 30776428 DOI: 10.1016/j.anaerobe.2019.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/27/2019] [Accepted: 02/14/2019] [Indexed: 01/19/2023]
Abstract
Recent reports on antimicrobial effects of metallic Cu prompted this study of anaerobic microbial communities on copper surfaces. Widely circulating copper-containing coinage was used as a potential source for microorganisms that had had human contact and were tolerant to copper. This study reports on the isolation, characterization, and genome of an anaerobic sulfidogenic Tissierella sp. P1from copper-containing brass coinage. Dissimilatory (bi)sulfite reductase dsrAB present in strain P1 genome and the visible absorbance around 630 nm in the cells suggested the presence of a desulfoviridin-type protein. However, the sulfate reduction rate measurements with 35SO42- did not confirm the dissimilatory sulfate reduction by the strain. The P1 genome lacks APS reductase, sulfate adenylyltransferase, DsrC, and DsrMK necessary for dissimilatory sulfate reduction. The isolate produced up to 0.79 mM H2S during growth, possibly due to cysteine synthase (CysK) and/or cysteine desulfhydrase (CdsH) activities, encoded in the genome. The strain can tolerate up to 2.4 mM Cu2+(150 mg/l) in liquid medium, shows affinity to metallic copper, and can survive on copper-containing coins up to three days under ambient air and dry conditions. The genome sequence of strain P1 contained cutC, encoding a copper resistance protein, which distinguishes it from all other Tissierella strains with published genomes.
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Affiliation(s)
- Polina A Bukhtiyarova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Dmitry V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, Mediterranean Institute of Microbiology, Marseille, France
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Yulia A Frank
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Olga P Ikkert
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia
| | - Nikolay V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olli H Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, 43210, USA
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, Tomsk, Russia.
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9
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Rüffel V, Maar M, Dammbrück MN, Hauröder B, Neu TR, Meier J. Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation. Environ Microbiol 2018; 20:3717-3731. [PMID: 30105784 DOI: 10.1111/1462-2920.14374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 01/22/2023]
Abstract
Sulfate reducing prokaryotes are promising candidates for the remediation of acidic metal-rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S-rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6-6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X-ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free-living cells. These findings point out the importance of cell-mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.
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Affiliation(s)
- Viola Rüffel
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Mona Maar
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Markus N Dammbrück
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Bärbel Hauröder
- Department of Pathology, Electron Microscopy, Bundeswehr Central Hospital Coblenz, 56070, Koblenz, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre of Environmental Research - UFZ, 39114, Magdeburg, Germany
| | - Jutta Meier
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
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10
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Selection for novel, acid-tolerant Desulfovibrio spp. from a closed Transbaikal mine site in a temporal pH-gradient bioreactor. Antonie van Leeuwenhoek 2017; 110:1669-1679. [DOI: 10.1007/s10482-017-0917-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
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11
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Mardanov AV, Beletskii AV, Ivasenko DA, Pimenov NV, Karnachuk OV, Ravin NV. Sulfate-reducing bacteria in the microbial community of acidic drainage from a gold deposit tailing storage. Microbiology (Reading) 2017. [DOI: 10.1134/s002626171702014x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Zhang M, Huang F, Wang G, Liu X, Wen J, Zhang X, Huang Y, Xia Y. Geographic distribution of cadmium and its interaction with the microbial community in the Longjiang River: risk evaluation after a shocking pollution accident. Sci Rep 2017; 7:227. [PMID: 28331217 PMCID: PMC5427973 DOI: 10.1038/s41598-017-00280-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/17/2017] [Indexed: 12/14/2022] Open
Abstract
A shocking Longjiang River cadmium pollution accident occurred in 2012, the effects of which on microbial communities remain unclear. Alkaline precipitation technology was applied for remediation, but concerns rose about the stability of this technology. To understand the geographic distribution of cadmium and its correlation with microbes, in this study, 39 water samples and 39 sludge samples from this river and 2 soil samples from the nearby farmland were collected for chemical and microbial analyses. The Cd concentrations of all water samples were lower than 0.005 mg/L and reached the quality standards for Chinese surface water. A ranking of sludge samples based on Cd contents showed sewage outfall > dosing sites > farmland, all of which were higher than the quality standard for soil. Alkaline precipitation technology was effective for Cd precipitation. Cd was unstable; it was constantly dissolving and being released from the sludge. The Cd content of each phase was mainly influenced by the total Cd content. Over 40,000 effective sequences were detected in each sample, and a total of 59,833 OTUs and 1,273 genera were found using Illumina MiSeq sequencing. Two phyla and 39 genera were notably positively correlated with the Cd distribution, while the cases of 10 phyla and 6 genera were the opposite.
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Affiliation(s)
- MingJiang Zhang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - FuKe Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - GuangYuan Wang
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XingYu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China.
| | - JianKang Wen
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
| | - XiaoSheng Zhang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - YaoSi Huang
- Institute of HeChi Scientific-Technical Information, No. 385 West Ring Road of HeChi City, GuangXi Zhuang Autonomous Region, 547000, China
| | - Yu Xia
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, No. 2 Xinjiekouwai Street, Beijing, 100088, China
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13
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Kovaliova A, Kadnikov VV, Antsiferov DV, Beletsky AV, Danilova EV, Avakyan MR, Mardanov AV, Karnachuk OV. Genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. GENOMICS DATA 2017; 11:125-127. [PMID: 28217441 PMCID: PMC5300300 DOI: 10.1016/j.gdata.2017.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/25/2017] [Indexed: 11/29/2022]
Abstract
Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9 Mb and encodes multiple K+-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clusters together with the acid-tolerant Desulfovibrio sp. TomC and Desulfovibrio magneticus. The draft genome sequence and annotation have been deposited at GenBank under the accession number MLBG00000000.
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Affiliation(s)
- Anastasiia Kovaliova
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dmitrii V Antsiferov
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Ehrzena V Danilova
- Institute of General and Experimental Biology, Siberian Branch Russian Academy of Sciences, 670047 Ulan-Ude, Buryatia, Russia
| | - Marat R Avakyan
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
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14
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Le Pape P, Battaglia-Brunet F, Parmentier M, Joulian C, Gassaud C, Fernandez-Rojo L, Guigner JM, Ikogou M, Stetten L, Olivi L, Casiot C, Morin G. Complete removal of arsenic and zinc from a heavily contaminated acid mine drainage via an indigenous SRB consortium. JOURNAL OF HAZARDOUS MATERIALS 2017; 321:764-772. [PMID: 27720469 DOI: 10.1016/j.jhazmat.2016.09.060] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/01/2016] [Accepted: 09/26/2016] [Indexed: 05/27/2023]
Abstract
Acid mine drainages (AMD) are major sources of pollution to the environment. Passive bio-remediation technologies involving sulfate-reducing bacteria (SRB) are promising for treating arsenic contaminated waters. However, mechanisms of biogenic As-sulfide formation need to be better understood to decontaminate AMDs in acidic conditions. Here, we show that a high-As AMD effluent can be decontaminated by an indigenous SRB consortium. AMD water from the Carnoulès mine (Gard, France) was incubated with the consortium under anoxic conditions and As, Zn and Fe concentrations, pH and microbial activity were monitored during 94days. Precipitated solids were analyzed using electron microscopy (SEM/TEM-EDXS), and Extended X-Ray Absorption Fine Structure (EXAFS) spectroscopy at the As K-edge. Total removal of arsenic and zinc from solution (1.06 and 0.23mmol/L, respectively) was observed in two of the triplicates. While Zn precipitated as ZnS nanoparticles, As precipitated as amorphous orpiment (am-AsIII2S3) (33-73%), and realgar (AsIIS) (0-34%), the latter phase exhibiting a particular nanowire morphology. A minor fraction of As is also found as thiol-bound AsIII (14-23%). We propose that the formation of the AsIIS nanowires results from AsIII2S3 reduction by biogenic H2S, enhancing the efficiency of As removal. The present description of As immobilization may help to set the basis for bioremediation strategies using SRB.
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Affiliation(s)
- Pierre Le Pape
- Sorbonne Universités - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR IRD 206, UPMC Université Paris VI, 4 place Jussieu, 75252 Paris cedex 05, France.
| | | | - Marc Parmentier
- French Geological Survey (BRGM), 3 av. Claude Guillemin, 45060, BP 36009, Orléans Cedex 2, France
| | - Catherine Joulian
- French Geological Survey (BRGM), 3 av. Claude Guillemin, 45060, BP 36009, Orléans Cedex 2, France
| | - Cindy Gassaud
- French Geological Survey (BRGM), 3 av. Claude Guillemin, 45060, BP 36009, Orléans Cedex 2, France
| | - Lidia Fernandez-Rojo
- HydroSciences Montpellier, UMR 5569 CNRS-IRD-UM, CC57, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Jean-Michel Guigner
- Sorbonne Universités - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR IRD 206, UPMC Université Paris VI, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Maya Ikogou
- Sorbonne Universités - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR IRD 206, UPMC Université Paris VI, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Lucie Stetten
- Sorbonne Universités - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR IRD 206, UPMC Université Paris VI, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Luca Olivi
- Sincrotrone Trieste ELETTRA, I-34012 Trieste, Italy
| | - Corinne Casiot
- HydroSciences Montpellier, UMR 5569 CNRS-IRD-UM, CC57, 163 rue Auguste Broussonet, 34090 Montpellier, France
| | - Guillaume Morin
- Sorbonne Universités - Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), UMR IRD 206, UPMC Université Paris VI, 4 place Jussieu, 75252 Paris cedex 05, France
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15
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Bryukhanov AL, Korneeva VA, Dinarieva TY, Karnachuk OV, Netrusov AI, Pimenov NV. Components of antioxidant systems in the cells of aerotolerant sulfate-reducing bacteria of the genus Desulfovibrio (strains A2 and TomC) isolated from metal mining waste. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716060047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Zhou C, Ontiveros-Valencia A, Wang Z, Maldonado J, Zhao HP, Krajmalnik-Brown R, Rittmann BE. Palladium Recovery in a H2-Based Membrane Biofilm Reactor: Formation of Pd(0) Nanoparticles through Enzymatic and Autocatalytic Reductions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2546-2555. [PMID: 26883809 DOI: 10.1021/acs.est.5b05318] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recovering palladium (Pd) from waste streams opens up the possibility of augmenting the supply of this important catalyst. We evaluated Pd reduction and recovery as a novel application of a H2-based membrane biofilm reactor (MBfR). At steady states, over 99% of the input soluble Pd(II) was reduced through concomitant enzymatic and autocatalytic processes at acidic or near neutral pHs. Nanoparticulate Pd(0), at an average crystallite size of 10 nm, was recovered with minimal leaching and heterogeneously associated with microbial cells and extracellular polymeric substances in the biofilm. The dominant phylotypes potentially responsible for Pd(II) reduction at circumneutral pH were denitrifying β-proteobacteria mainly consisting of the family Rhodocyclaceae. Though greatly shifted by acidic pH, the biofilm microbial community largely bounced back when the pH was returned to 7 within 2 weeks. These discoveries infer that the biofilm was capable of rapid adaptive evolution to stressed environmental change, and facilitated Pd recovery in versatile ways. This study demonstrates the promise of effective microbially driven Pd recovery in a single MBfR system that could be applied for the treatment of the waste streams, and it documents the role of biofilms in this reduction and recovery process.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Aura Ontiveros-Valencia
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Zhaocheng Wang
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
- Department of Water Engineering and Science, College of Civil Engineering, Hunan University , Changsha, China
| | - Juan Maldonado
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - He-Ping Zhao
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University , Hangzhou, China
| | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
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