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Wang M, Zhang W, Zhao J, Yang Z, Guo X, Ji H. Distinct structural strategies with similar functional responses of abundant and rare subcommunities regarding heavy metal pollution in the Beiyun river basin. CHEMOSPHERE 2022; 309:136659. [PMID: 36202374 DOI: 10.1016/j.chemosphere.2022.136659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Bacteria within a metacommunity could be partitioned into different subcommunities ecological assemblages in light of potential importance for the community function. It is unknown how abundant and rare microbial subcommunities in urban river sediments respond to heavy metal pollutants. Using high-throughput sequencing, we analyzed these response patterns in the heavliy polluted (Beijing, China). We found that this river faces substantial ecological risks, owing to high rates of Cd and Hg pollution from urban activities. Surprisingly, abundant and rare subcommunity structures showed opposite responses to heavy metals. Abundant taxa, such as Crenarchaeota and Euryarchaeota, are resistant to heavy metal pollution through the synergistic of ammonia nitrogen (NH4+-N) and total phosphorus (TP). By contrast, rare taxa, such as Verrucomicrobia, Fibrobacteres, Berkelbacteria, and Euryarchaeota, had a high synergy with NH4+-N and TP with high a resilience to heavy metal pollution. However, the functions of both abundant and rare subcommunities showed a similar response to heavy metal pollutants, especially in denitrification processes. The abundant taxa responded to heavy metal pollution through methanogenesis by CO2 reduction with H2, human pathogens nosocomia, sulfate respiration, photoheterotrophy, and dark sulfide oxidation synergy with NH4+-N and TP. The rare taxa responded to heavy metals through methanogenesis by CO2 reduction with H2, cellulolysis, sulfate respiration, intracellular parasites, nitrate reduction and plant pathogen. We observed distinct patterns between the structural and functional responses of microbial subcommunities to heavy metal pollutants. Our findings support the concept that denitrification processes are sensitive to but not inhibited by high levels of heavy metals pollution. We propose that the structures and functions of the abundant and rare microbial subcommunities could inform the management of pollutants in heavily polluted urban river ecosystems at fine geographical scales.
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Affiliation(s)
- Min Wang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Wei Zhang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Junying Zhao
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Zirou Yang
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China
| | - Xiaoyu Guo
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China.
| | - Hongbing Ji
- College of Resources Environment and Tourism, Capital Normal University, Beijing, China; School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, China.
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Wang X, Teng Y, Wang X, Xu Y, Li R, Sun Y, Hu W, Zhao L, Ren W, Luo Y. Effects of combined pollution of organic pollutants and heavy metals on biodiversity and soil multifunctionality in e-waste contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129727. [PMID: 35963091 DOI: 10.1016/j.jhazmat.2022.129727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/21/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Electronic waste (e-waste) is increasing globally, but the impact of this source of combined pollution on soil biodiversity and multiple soil functions (i.e., ecosystem multifunctionality) remains unclear. Here, we evaluated the effects of combined pollution on the biodiversity and soil multifunctionality using samples collected from upland and paddy soils chronically contaminated with e-waste. Overall biodiversity, as well as the relative abundance and biodiversity of key ecological clusters, as combined pollution concentrations increased in upland soil, while the opposite was true in paddy soil. Soil multifunctionality followed the same trend. Organic pollutants had significant negative effects on soil multifunctionality and were the main influencing factors in upland soil. Heavy metals had significant positive effects on soil multifunctionality in paddy soil. Moreover, driving soil multifunctionality was overall biodiversity in upland soil but key biodiversity in paddy soil. Importantly, a strong positive association between key organism biodiversity and soil multifunctionality was found in soil with low contamination. However, the relationship between key organism biodiversity and soil multifunctionality weakened or disappeared in highly contaminated soil, whereas overall biodiversity was significantly and positively correlated with multifunctionality. Our results emphasized that severe e-waste contamination would reduce soil biodiversity and soil multifunctionality and warrants high attention.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Hu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Uttarotai T, Mukjang N, Chaisoung N, Pathom-Aree W, Pekkoh J, Pumas C, Sattayawat P. Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal. BIOLOGY 2022; 11:biology11081226. [PMID: 36009852 PMCID: PMC9405338 DOI: 10.3390/biology11081226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022]
Abstract
Simple Summary Nowadays, heavy metal polluted wastewater is one of the global challenges that leads to an insufficient supply of clean water. Taking advantage of what nature has to offer, several organisms, including microalgae, can natively bioremediate these heavy metals. However, the effectiveness of such processes does not meet expectations, especially with the increasing amount of pollution in today’s world. Therefore, with the goal of creating effective strains, synthetic biology via bioengineering is widely used as a strategy to enhance the heavy metal bio-removing capability, either by directly engineering the native ability of organisms or by transferring the ability to a more suitable host. In order to do so, a list of genes or proteins involved in the processes is crucial for stepwise engineering. Yet, a large amount of information remains to be discovered. In this work, a comprehensive library of putative proteins that are involved in heavy metal bio-removal from microalgae was constructed. Moreover, with the development of machine learning, the 3D structures of these proteins are also predicted, using machine learning-based methods, to aid the use of synthetic biology further. Abstract Synthetic biology is a principle that aims to create new biological systems with particular functions or to redesign the existing ones through bioengineering. Therefore, this principle is often utilized as a tool to put the knowledge learned to practical use in actual fields. However, there is still a great deal of information remaining to be found, and this limits the possible utilization of synthetic biology, particularly on the topic that is the focus of the present work—heavy metal bio-removal. In this work, we aim to construct a comprehensive library of putative proteins that might support heavy metal bio-removal. Hypothetical proteins were discovered from Chlorella and Scenedesmus genomes and extensively annotated. The protein structures of these putative proteins were also modeled through Alphafold2. Although a portion of this workflow has previously been demonstrated to annotate hypothetical proteins from whole genome sequences, the adaptation of such steps is yet to be done for library construction purposes. We also demonstrated further downstream steps that allow a more accurate function prediction of the hypothetical proteins by subjecting the models generated to structure-based annotation. In conclusion, a total of 72 newly discovered putative proteins were annotated with ready-to-use predicted structures available for further investigation.
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Affiliation(s)
- Toungporn Uttarotai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nilita Mukjang
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Natcha Chaisoung
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeeraporn Pekkoh
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Chayakorn Pumas
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pachara Sattayawat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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Radziemska M, Gusiatin MZ, Cydzik-Kwiatkowska A, Blazejczyk A, Kumar V, Kintl A, Brtnicky M. Effect of Biochar on Metal Distribution and Microbiome Dynamic of a Phytostabilized Metalloid-Contaminated Soil Following Freeze-Thaw Cycles. MATERIALS 2022; 15:ma15113801. [PMID: 35683097 PMCID: PMC9181493 DOI: 10.3390/ma15113801] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 02/04/2023]
Abstract
In the present paper the effectiveness of biochar-aided phytostabilization of metal/metalloid-contaminated soil under freezing-thawing conditions and using the metal tolerating test plant Lolium perenne L. is comprehensively studied. The vegetative experiment consisted of plants cultivated for over 52 days with no exposure to freezing-thawing in a glass greenhouse, followed by 64 days under freezing-thawing in a temperature-controlled apparatus and was carried out in initial soil derived from a post-industrial urban area, characterized by the higher total content of Zn, Pb, Cu, Cr, As and Hg than the limit values included in the classification provided by the Regulation of the Polish Ministry of Environment. According to the substance priority list published by the Toxic Substances and Disease Registry Agency, As, Pb, and Hg are also indicated as being among the top three most hazardous substances. The initial soil was modified by biochar obtained from willow chips. The freeze-thaw effect on the total content of metals/metalloids (metal(-loid)s) in plant materials (roots and above-ground parts) and in phytostabilized soils (non- and biochar-amended) as well as on metal(-loid) concentration distribution/redistribution between four BCR (community bureau of reference) fractions extracted from phytostabilized soils was determined. Based on metal(-loid)s redistribution in phytostabilized soils, their stability was evaluated using the reduced partition index (Ir). Special attention was paid to investigating soil microbial composition. In both cases, before and after freezing-thawing, biochar increased plant biomass, soil pH value, and metal(-loid)s accumulation in roots, and decreased metal(-loid)s accumulation in stems and total content in the soil, respectively, as compared to the corresponding non-amended series (before and after freezing-thawing, respectively). In particular, in the phytostabilized biochar-amended series after freezing-thawing, the recorded total content of Zn, Cu, Pb, and As in roots substantially increased as well as the Hg, Cu, Cr, and Zn in the soil was significantly reduced as compared to the corresponding non-amended series after freezing-thawing. Moreover, exposure to freezing-thawing itself caused redistribution of examined metal(-loid)s from mobile and/or potentially mobile into the most stable fraction, but this transformation was favored by biochar presence, especially for Cu, Pb, Cr, and Hg. While freezing-thawing greatly affected soil microbiome composition, biochar reduced the freeze-thaw adverse effect on bacterial diversity and helped preserve bacterial groups important for efficient soil nutrient conversion. In biochar-amended soil exposed to freezing-thawing, psychrotolerant and trace element-resistant genera such as Rhodococcus sp. or Williamsia sp. were most abundant.
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Affiliation(s)
- Maja Radziemska
- Institute of Environmental Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-593-5307
| | - Mariusz Z. Gusiatin
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Słoneczna St. 45G, 10-719 Olsztyn, Poland; (M.Z.G.); (A.C.-K.)
| | - Agnieszka Cydzik-Kwiatkowska
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Słoneczna St. 45G, 10-719 Olsztyn, Poland; (M.Z.G.); (A.C.-K.)
| | - Aurelia Blazejczyk
- Institute of Civil Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland;
| | - Vinod Kumar
- Department of Botany, Government Degree College, Ramban 182144, India;
| | - Antonin Kintl
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic; (A.K.); (M.B.)
- Agricultural Research, Ltd., Zahradni 400/1, 66441 Troubsko, Czech Republic
| | - Martin Brtnicky
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic; (A.K.); (M.B.)
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 61200 Brno, Czech Republic
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Chen G, Bai R, Zhang Y, Zhao B, Xiao Y. Application of metagenomics to biological wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150737. [PMID: 34606860 DOI: 10.1016/j.scitotenv.2021.150737] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/20/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Biological wastewater treatment is a process in which the microbial metabolism of complex communities transforms pollutants into low- or non-toxic products. Due to the absence of an in-depth understanding of the diversity and complexity of microbial communities, it is very likely to ignore the potential mechanisms of microbial community in wastewater treatment. Metagenomics is a technology based on molecular biology, in which massive gene sequences are obtained from environmental samples and analyzed by bioinformatics to determine the composition and function of a microbial community. Metagenomics can identify the state of microbes in their native environments more effectively than traditional molecular methods. This review summarizes the application of metagenomics to assess microbial communities in biological wastewater treatment, such as the biological removal of phosphorus and nitrogen by bacteria, the study of antibiotic resistance genes (ARGs), and the reduction of heavy metals by microbial communities, with an emphasis on the contribution of microbial diversity and metabolic diversity. Technical bottlenecks in the application of metagenomics to biological wastewater treatment are elucidated, and future research directions for metagenomics are proposed, among which the application of multi-omics will be an important research method for future biological wastewater treatment.
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Affiliation(s)
- Geng Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Rui Bai
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yiqing Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Biyi Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yong Xiao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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Effects of rare earth elements on bacteria in rhizosphere, root, phyllosphere and leaf of soil-rice ecosystem. Sci Rep 2022; 12:2089. [PMID: 35136105 PMCID: PMC8826409 DOI: 10.1038/s41598-022-06003-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 01/21/2022] [Indexed: 11/08/2022] Open
Abstract
The effects of rare earth mining on rice biomass, rare earth element (REE) content and bacterial community structure was studied through pot experiment. The research shows that the REE content in rice roots, shoots and grains was significantly positive correlated with that in soil, and the dry weight of rice roots, shoots and grains was highly correlated with soil physical and chemical properties, nutrient elements and REE contents; The exploitation of rare earth minerals inhibited a-diversity of endophytic bacteria in rhizosphere, root, phyllosphere and leaf of rice, significantly reduced the abundance index, OTU number, Chao, Ace index and also significantly reduced the diversity index-Shannon index, and also reduced uniformity index: Pielou's evenness index, which caused β-diversity of bacteria to be quite different. The exploitation of rare earth minerals reduces the diversity of bacteria, but forms dominant bacteria, such as Burkholderia, Bacillus, Buttiauxella, Acinetobacter, Bradyrhizobium, Candida koribacter, which can degrade the pollutants formed by exploitation of rare earth minerals, alleviate the compound pollution of rare earth and ammonia nitrogen, and also has the function of fixing nitrogen and resisting rare earth stress; The content of soil available phosphorus in no-mining area is lower, and the dominant bacteria of Pantoea formed in such soil, which has the function of improving soil phosphorus availability. Rare earth elements and physical and chemical properties of soil affect the community structure of bacteria in rhizosphere and phyllosphere of rice, promote the parallel movement of some bacteria in rhizosphere, root, phyllosphere and leaf of rice, promote the construction of community structure of bacteria in rhizosphere and phyllosphere of rice, give full play to the growth promoting function of Endophytes, and promote the growth of rice. The results showed that the exploitation of rare earth minerals has formed the dominant endophytic bacteria of rice and ensured the yield of rice in the mining area, however, the mining of mineral resources causes the compound pollution of rare earth and ammonia nitrogen, which makes REE content of rice in mining area significantly higher than that in non-mining area, and the excessive rare earth element may enter the human body through the food chain and affect human health, so the food security in the REE mining area deserves more attention.
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Kalu CM, Ogola HJO, Selvarajan R, Tekere M, Ntushelo K. Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem. Curr Microbiol 2021; 79:34. [PMID: 34962589 PMCID: PMC8714630 DOI: 10.1007/s00284-021-02748-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022]
Abstract
Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.
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Affiliation(s)
- Chimdi M Kalu
- Department of Agriculture and Animal Health, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa.
| | - Henry J O Ogola
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa
- School of Agricultural and Food Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210-40601, Bondo, Kenya
| | - Ramganesh Selvarajan
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, 572000, Hainan Province, People's Republic of China
| | - Memory Tekere
- Department of Environmental Science, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, University of South Africa, Florida Science Campus, Roodepoort, 1709, South Africa
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Karthikeyan OP, Smith TJ, Dandare SU, Parwin KS, Singh H, Loh HX, Cunningham MR, Williams PN, Nichol T, Subramanian A, Ramasamy K, Kumaresan D. Metal(loid) speciation and transformation by aerobic methanotrophs. MICROBIOME 2021; 9:156. [PMID: 34229757 PMCID: PMC8262016 DOI: 10.1186/s40168-021-01112-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 05/06/2023]
Abstract
Manufacturing and resource industries are the key drivers for economic growth with a huge environmental cost (e.g. discharge of industrial effluents and post-mining substrates). Pollutants from waste streams, either organic or inorganic (e.g. heavy metals), are prone to interact with their physical environment that not only affects the ecosystem health but also the livelihood of local communities. Unlike organic pollutants, heavy metals or trace metals (e.g. chromium, mercury) are non-biodegradable, bioaccumulate through food-web interactions and are likely to have a long-term impact on ecosystem health. Microorganisms provide varied ecosystem services including climate regulation, purification of groundwater, rehabilitation of contaminated sites by detoxifying pollutants. Recent studies have highlighted the potential of methanotrophs, a group of bacteria that can use methane as a sole carbon and energy source, to transform toxic metal (loids) such as chromium, mercury and selenium. In this review, we synthesise recent advances in the role of essential metals (e.g. copper) for methanotroph activity, uptake mechanisms alongside their potential to transform toxic heavy metal (loids). Case studies are presented on chromium, selenium and mercury pollution from the tanneries, coal burning and artisanal gold mining, respectively, which are particular problems in the developing economy that we propose may be suitable for remediation by methanotrophs. Video Abstract.
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Affiliation(s)
- Obulisamy Parthiba Karthikeyan
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
- Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI USA
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX USA
| | - Thomas J. Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Shamsudeen Umar Dandare
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Kamaludeen Sara Parwin
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore, India
| | - Heetasmin Singh
- Department of Chemistry, University of Guyana, Georgetown, Guyana
| | - Hui Xin Loh
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Mark R Cunningham
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Paul Nicholas Williams
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Tim Nichol
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | | | | | - Deepak Kumaresan
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
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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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Jung GY, Rhee SK, Han YS, Kim SJ. Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland. Microorganisms 2020; 8:microorganisms8111719. [PMID: 33147874 PMCID: PMC7716213 DOI: 10.3390/microorganisms8111719] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.
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Affiliation(s)
- Gi-Yong Jung
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Korea;
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea;
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea;
| | - Young-Soo Han
- Department of Environmental Engineering, Chungnam National University, Daejeon 34134, Korea;
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon 34132, Korea;
- Correspondence: ; Tel.: +82-42-868-3311; Fax: +82-42-868-3414
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Shi LD, Lv PL, Niu ZF, Lai CY, Zhao HP. Why does sulfate inhibit selenate reduction: Molybdenum deprivation from Mo-dependent selenate reductase. WATER RESEARCH 2020; 178:115832. [PMID: 32335368 DOI: 10.1016/j.watres.2020.115832] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/07/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Selenium pollution has become an increasingly serious global concern. Methane-fed selenate reduction has proven to be of great interest for the bioremediation of selenate-contaminated waters even with the coexistence of nitrate and dissolved oxygen. However, it is unclear if the common concurrent sulfate anion affects selenate removal. To address this question, we first introduced selenate (SeO42-) as the sole influent electron acceptor in a CH4-fed membrane biofilm reactor (CH4-MBfR); then we added different concentrations of sulfate (SO42-). The initial selenate removal efficiency (∼90%) was decreased by 50% in the presence of 15.6 μM of sulfate and completely inhibited after loading with 171.9 μM of sulfate. 16S rRNA gene sequencing showed that the selenate-reducing bacteria decreased after the addition of sulfate. Metagenomic sequencing showed that the abundance of genes encoding molybdenum (Mo)-dependent selenate reductase reduced by >50% when exposed to high concentrations of sulfate. Furthermore, the decrease in the total genes encoding all Mo-oxidoreductases was much greater than that of the genes encoding molybdate transporters, suggesting that the inhibition of selenate reduction by sulfate was most likely via the direct competition with molybdate for the transport system, leading to a lack of available Mo for Mo-dependent selenate reductases and thus reducing their activities. This result was confirmed by a batch test wherein the supplementation of molybdate mitigated the sulfate effect. Overall, this study shed light on the underlying mechanism of sulfate inhibition on selenate reduction and laid the foundation for applying the technology to practical wastewaters.
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Affiliation(s)
- Ling-Dong Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pan-Long Lv
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zi-Fan Niu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun-Yu Lai
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China; Zhejiang Prov Key Lab Water Pollut Control & Envi, Zhejiang University, Hangzhou, Zhejiang, China.
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Faheem M, Shabbir S, Zhao J, Kerr PG, Sultana N, Jia Z. Enhanced Adsorptive Bioremediation of Heavy Metals (Cd 2+, Cr 6+, Pb 2+) by Methane-Oxidizing Epipelon. Microorganisms 2020; 8:microorganisms8040505. [PMID: 32244762 PMCID: PMC7232255 DOI: 10.3390/microorganisms8040505] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
Cadmium (Cd), chromium (Cr) and lead (Pb) are heavy metals that have been classified as priority pollutants in aqueous environment while methane-oxidizing bacteria as a biofilter arguably consume up to 90% of the produced methane in the same aqueous environment before it escapes into the atmosphere. However, the underlying kinetics and active methane oxidizers are poorly understood for the hotspot of epipelon that provides a unique micro-ecosystem containing diversified guild of microorganisms including methane oxidizers for potential bioremediation of heavy metals. In the present study, the Pb2+, Cd2+and Cr6+ bioremediation potential of epipelon biofilm was assessed under both high (120,000 ppm) and near-atmospheric (6 ppm) methane concentrations. Epipelon biofilm demonstrated a high methane oxidation activity following microcosm incubation amended with a high concentration of methane, accompanied by the complete removal of 50 mg L−1 Pb2+ and 50 mg L−1 Cd2+ (14 days) and partial (20%) removal of 50 mg L−1 Cr6+ after 20 days. High methane dose stimulated a faster (144 h earlier) heavy metal removal rate compared to near-atmospheric methane concentrations. DNA-based stable isotope probing (DNA-SIP) following 13CH4 microcosm incubation revealed the growth and activity of different phylotypes of methanotrophs during the methane oxidation and heavy metal removal process. High throughput sequencing of 13C-labelled particulate methane monooxygenase gene pmoA and 16S rRNA genes revealed that the prevalent active methane oxidizers were type I affiliated methanotrophs, i.e., Methylobacter. Type II methanotrophs including Methylosinus and Methylocystis were also labeled only under high methane concentrations. These results suggest that epipelon biofilm can serve as an important micro-environment to alleviate both methane emission and the heavy metal contamination in aqueous ecosystems with constant high methane fluxes.
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Affiliation(s)
- Muhammad Faheem
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sadaf Shabbir
- College of Environment, Hohai University, Nanjing 210098, China;
| | - Jun Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
| | - Philip G. Kerr
- School of Biomedical Science, Charles Sturt University, Wagga Wagga, NSW 2678, Australia;
| | - Nasrin Sultana
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (M.F.); (J.Z.); (N.S.)
- Correspondence:
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