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Stewart DI, Vasconcelos EJR, Burke IT, Baker A. Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172507. [PMID: 38657818 DOI: 10.1016/j.scitotenv.2024.172507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.
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Affiliation(s)
- Douglas I Stewart
- School of Civil Engineering, University of Leeds, Leeds LS2 9JT, UK.
| | | | - Ian T Burke
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK.
| | - Alison Baker
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Hassan S, Bhadwal SS, Khan M, Sabreena, Nissa KU, Shah RA, Bhat HM, Bhat SA, Lone IM, Ganai BA. Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches. CHEMOSPHERE 2024; 356:141889. [PMID: 38583533 DOI: 10.1016/j.chemosphere.2024.141889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Siloni Singh Bhadwal
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Misba Khan
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Khair-Ul Nissa
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Rameez Ahmad Shah
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Haneef Mohammad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shabir Ahmad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Ishfaq Maqbool Lone
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Chen T, Wen X, Zhou J, Lu Z, Li X, Yan B. A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122667. [PMID: 37783414 DOI: 10.1016/j.envpol.2023.122667] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.
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Affiliation(s)
- Tao Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou, 510006, China.
| | - Xiaocui Wen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Jiawei Zhou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
| | - Zheng Lu
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Xueying Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing, 100875, China
| | - Bo Yan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou, 510006, China
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Das S, Najar IN, Sherpa MT, Kumar S, Sharma P, Mondal K, Tamang S, Thakur N. Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity. World J Microbiol Biotechnol 2023; 39:179. [PMID: 37133792 DOI: 10.1007/s11274-023-03631-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/04/2023]
Abstract
Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.
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Affiliation(s)
- Sayak Das
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
- Department of Life Science and Bioinformatics, Hargobind Khurana School of Life Sciences, Assam University, Silchar, Assam, 788011, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Gangtok, Sikkim, 737102, India.
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Kumar J, Sharma N, Singh SP. Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50864-50882. [PMID: 36807860 DOI: 10.1007/s11356-023-25893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India.
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Ma S, Qiao L, Liu X, Zhang S, Zhang L, Qiu Z, Yu C. Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways. ENVIRONMENTAL RESEARCH 2022; 214:113822. [PMID: 35803340 DOI: 10.1016/j.envres.2022.113822] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/04/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.
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Affiliation(s)
- Suya Ma
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Longkai Qiao
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Xiaoxia Liu
- Beijing Station of Agro-Environmental Monitoring, Test and Supervision Center of Agro-Environmental Quality, MOA, 100032 Beijing, China
| | - Shuo Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Luying Zhang
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Ziliang Qiu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083, Beijing, China.
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Nguyen TAH, Liu Y, Wu S, Huang L. Unravelling in-situ hardpan properties and functions in capping sulfidic Cu-Pb-Zn tailings and forming a duplex soil system cover. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127943. [PMID: 34894505 DOI: 10.1016/j.jhazmat.2021.127943] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/16/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Developing alternative approaches to cap and rehabilitate the large areas of tailings landscapes is critical for sustainable development of mining industry. This study revealed the potential of an in-situ hardpan-based duplex soil system as an un-conventional approach to rehabilitate sulfidic Cu-Pb-Zn tailings. Under a shallow silicious soil cover, a massive and consistent hardpan horizon had been formed in-situ at the surface layer of tailings across the trial area, which physically separated root zones (i.e., silica soil cover) from the un-weathered tailings underneath, prevented capillary enrichment of acidity and soluble solutes into the root zones, and sustained native plant growth for more than a decade. Precipitation of Si-rich ferric complexes were attributed to the stabilisation/solidification of the sulfidic tailing. The hardpan layer possesses a highly compacted texture, a low-percolating pore network, and extreme resistance to water movement in the hardpan horizon. Further, the hardpans directly interfacing with plant roots in the soil cover were geochemically stabilised and attenuated, with very low levels of soluble metal(loid)s and a circumneutral pH condition. This case study would serve as a good incentive to develop bio-chemical engineering methodology building on current knowledge for achieving sustainable rehabilitation of sulfidic and metallic tailings in future.
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Affiliation(s)
- Tuan A H Nguyen
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072 Australia.
| | - Yunjia Liu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072 Australia
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072 Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072 Australia.
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