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Liang XP, Wang HJ, Zheng JR, Wang XR, Lin DM, Wu YQ, Yu RL, Hu GR, Yan Y. Comprehensive analysis of metal(loid)s and associated metal(loid) resistance genes in atmospheric particulate matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 932:173038. [PMID: 38719055 DOI: 10.1016/j.scitotenv.2024.173038] [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: 02/07/2024] [Revised: 04/15/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Despite global concerns about metal(loid)s in atmospheric particulate matter (PM), the presence of metal(loid) resistance genes (MRGs) in PM remains unknown. Therefore, we conducted a comprehensive investigation of the metal(loid)s and associated MRGs in PMs in two seasons (summer and winter) in Xiamen, China. According to the geoaccumulation index (Igeo), most metal(loid)s, except for V and Mn, exhibited enrichment in PM, suggesting potential anthropogenic sources. By employing Positive Matrix Factorization (PMF) model, utilizing a dataset encompassing both total and bioaccessible metal(loid)s, along with backward trajectory simulations, traffic emissions were determined to be the primary potential contributor of metal(loid)s in summer, whereas coal combustion was observed to have a dominant contribution in winter. The major contributor to the carcinogenic risk of metal(loid)s in both summer and winter was predominantly attributed to coal combustion, which serves as the main source of bioaccessible Cr. Bacterial communities within PMs showed lower diversity and network complexity in summer than in winter, with Pseudomonadales being the dominant order. Abundant MRGs, including the As(III) S-adenosylmethionine methyltransferase gene (arsM), Cu(I)-translocating P-type ATPase gene (copA), Zn(II)/Cd(II)/Pb(II)-translocating P-type ATPase gene (zntA), and Zn(II)-translocating P-type ATPase gene (ziaA), were detected within the PMs. Seasonal variations were observed for the metal(loid) concentration, bacterial community structure, and MRG abundance. The bacterial community composition and MRG abundance within PMs were primarily influenced by temperature, rather than metal(loid)s. This research offers novel perspectives on the occurrence of metal(loid)s and MRGs in PMs, thereby contributing to the control of air pollution.
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Affiliation(s)
- Xiu-Peng Liang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - He-Jing Wang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Jie-Ru Zheng
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Xiao-Ru Wang
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Dao-Ming Lin
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Ya-Qing Wu
- Instrumental Analysis Center of Huaqiao University, Huaqiao University, Xiamen 361021, China
| | - Rui-Lian Yu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Gong-Ren Hu
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yu Yan
- Department of Environmental Science and Engineering, Huaqiao University, Xiamen 361021, China.
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Huang Y, Hu H, Zhang T, Wang W, Liu W, Tang H. Meta-omics assisted microbial gene and strain resources mining in contaminant environment. Eng Life Sci 2024; 24:2300207. [PMID: 38708415 PMCID: PMC11065330 DOI: 10.1002/elsc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 05/07/2024] Open
Abstract
Human activities have led to the release of various environmental pollutants, triggering ecological challenges. In situ, microbial communities in these contaminated environments are usually assumed to possess the potential capacity of pollutant degradation. However, the majority of genes and microorganisms in these environments remain uncharacterized and uncultured. The advent of meta-omics provided culture-independent solutions for exploring the functional genes and microorganisms within complex microbial communities. In this review, we highlight the applications and methodologies of meta-omics in uncovering of genes and microbes from contaminated environments. These findings may assist in future bioremediation research.
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Affiliation(s)
- Yiqun Huang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Haiyang Hu
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Tingting Zhang
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Weiwei Wang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Wenzhao Liu
- China Tobacco Henan Industrial Co. Ltd.ZhengzhouPeople's Republic of China
| | - Hongzhi Tang
- State Key Laboratory of Microbial Metabolismand School of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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3
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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Mejia MP, Rojas CA, Curd E, Renshaw MA, Edalati K, Shih B, Vincent N, Lin M, Nguyen PH, Wayne R, Jessup K, Parker SS. Soil Microbial Community Composition and Tolerance to Contaminants in an Urban Brownfield Site. MICROBIAL ECOLOGY 2023; 85:998-1012. [PMID: 35802172 PMCID: PMC10156844 DOI: 10.1007/s00248-022-02061-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/21/2022] [Indexed: 05/04/2023]
Abstract
Brownfields are unused sites that contain hazardous substances due to previous commercial or industrial use. The sites are inhospitable for many organisms, but some fungi and microbes can tolerate and thrive in the nutrient-depleted and contaminated soils. However, few studies have characterized the impacts of long-term contamination on soil microbiome composition and diversity at brownfields. This study focuses on an urban brownfield-a former rail yard in Los Angeles that is contaminated with heavy metals, volatile organic compounds, and petroleum-derived pollutants. We anticipate that heavy metals and organic pollutants will shape soil microbiome diversity and that several candidate fungi and bacteria will be tolerant to the contaminants. We sequence three gene markers (16S ribosomal RNA, 18S ribosomal RNA, and the fungal internal transcribed spacer (FITS)) in 55 soil samples collected at five depths to (1) profile the composition of the soil microbiome across depths; (2) determine the extent to which hazardous chemicals predict microbiome variation; and (3) identify microbial taxonomic groups that may metabolize these contaminants. Detected contaminants in the samples included heavy metals, petroleum hydrocarbons, polycyclic aromatic hydrocarbons, and volatile organic compounds. Bacterial, eukaryotic, and fungal communities all varied with depth and with concentrations of arsenic, chromium, cobalt, and lead. 18S rRNA microbiome richness and fungal richness were positively correlated with lead and cobalt levels, respectively. Furthermore, bacterial Paenibacillus and Iamia, eukaryotic Actinochloris, and fungal Alternaria were enriched in contaminated soils compared to uncontaminated soils and represent taxa of interest for future bioremediation research. Based on our results, we recommend incorporating DNA-based multi-marker microbial community profiling at multiple sites and depths in brownfield site assessment standard methods and restoration.
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Affiliation(s)
- Maura Palacios Mejia
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Connie A Rojas
- Ecology, Evolution, and Behavior Program, Michigan State University, Lansing, MI, USA
| | - Emily Curd
- Natural Science, Landmark College, Putney, VT, USA
| | - Mark A Renshaw
- Cherokee Federal, USGS Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Kiumars Edalati
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Beverly Shih
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nitin Vincent
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meixi Lin
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peggy H Nguyen
- Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Robert Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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Tiwari P, Bae H. Trends in Harnessing Plant Endophytic Microbiome for Heavy Metal Mitigation in Plants: A Perspective. PLANTS (BASEL, SWITZERLAND) 2023; 12:1515. [PMID: 37050141 PMCID: PMC10097340 DOI: 10.3390/plants12071515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Plant microbiomes represent dynamic entities, influenced by the environmental stimuli and stresses in the surrounding conditions. Studies have suggested the benefits of commensal microbes in improving the overall fitness of plants, besides beneficial effects on plant adaptability and survival in challenging environmental conditions. The concept of 'Defense biome' has been proposed to include the plant-associated microbes that increase in response to plant stress and which need to be further explored for their role in plant fitness. Plant-associated endophytes are the emerging candidates, playing a pivotal role in plant growth, adaptability to challenging environmental conditions, and productivity, as well as showing tolerance to biotic and abiotic stresses. In this article, efforts have been made to discuss and understand the implications of stress-induced changes in plant endophytic microbiome, providing key insights into the effects of heavy metals on plant endophytic dynamics and how these beneficial microbes provide a prospective solution in the tolerance and mitigation of heavy metal in contaminated sites.
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Zhu J, Huang Q, Peng X, Zhou X, Gao S, Li Y, Luo X, Zhao Y, Rensing C, Su J, Cai P, Liu Y, Chen W, Hao X, Huang Q. MRG Chip: A High-Throughput qPCR-Based Tool for Assessment of the Heavy Metal(loid) Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10656-10667. [PMID: 35876052 DOI: 10.1021/acs.est.2c00488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial metal detoxification mechanisms have been well studied for centuries in pure culture systems. However, profiling metal resistance determinants at the community level is still a challenge due to the lack of comprehensive and reliable quantification tools. Here, a novel high-throughput quantitative polymerase chain reaction (HT-qPCR) chip, termed the metal resistance gene (MRG) chip, has been developed for the quantification of genes involved in the homeostasis of 9 metals. The MRG chip contains 77 newly designed degenerate primer sets and 9 published primer sets covering 56 metal resistance genes. Computational evaluation of the taxonomic coverage indicated that the MRG chip had a broad coverage matching 2 kingdoms, 29 phyla, 64 classes, 130 orders, 226 families, and 382 genera. Temperature gradient PCR and HT-qPCR verified that 57 °C was the optimal annealing temperature, with amplification efficiencies of over 94% primer sets achieving 80-110%, with R2 > 0.993. Both computational evaluation and the melting curve analysis of HT-qPCR validated a high specificity. The MRG chip has been successfully applied to characterize the distribution of diverse metal resistance determinants in natural and human-related environments, confirming its wide scope of application. Collectively, the MRG chip is a powerful and efficient high-throughput quantification tool for exploring the microbial metal resistome.
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Affiliation(s)
- Jiaojiao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiong Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyi Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyuan Zhou
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xuesong Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhao
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jianqiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Peng Cai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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Phurailatpam L, Dalal VK, Singh N, Mishra S. Heavy Metal Stress Alleviation Through Omics Analysis of Soil and Plant Microbiome. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2021.817932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Heavy metal (HM) contamination of soil and water resources is a global concern, which not only limits crop yield and quality, but also has serious environmental effects. Due to the non-biodegradable nature and toxicity, high concentration of HMs in food and environment is a serious threat to the entire ecosystem. Moreover, the target of supplying safe and quality food to the rising human population (expected to reach ~9–10 bn by the year 2050), necessitates effective treatment of the HM-contaminated soil. Various microbe-mediated bioremediation strategies such as biosorption, bioprecipiation, biostimulation, etc., have been found to be effective in uptake and conversion of HMs to less toxic forms. Further, in the past few years, the use of soil and plant-associated microbiome for HM stress alleviation is gaining attention among the scientific community. In general, microbes are spectacular in being dynamic and more responsive to environmental conditions in comparison to their host plants. Moreover, with the advancements in high throughput sequencing technologies, the focus is eventually shifting from just structural characterization to functional insights into the microbiome. The microbes inhabiting the HM-contaminated environments or associated with HM-tolerant plants are a source for exploring HM-tolerant microbial communities, which could be used for enhancing bioremediation efficiency and conferring HM tolerance in plants. This review discusses the application of omics techniques including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, for rapid and robust identification of HM-tolerant microbial communities, mining novel HM resistance genes, and fabricating the HM resistome.
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Bastian F, Melayah D, Hugoni M, Dempsey NM, Simonet P, Frenea-Robin M, Fraissinet-Tachet L. Eukaryotic Cell Capture by Amplified Magnetic in situ Hybridization Using Yeast as a Model. Front Microbiol 2021; 12:759478. [PMID: 34790184 PMCID: PMC8591292 DOI: 10.3389/fmicb.2021.759478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
A non-destructive approach based on magnetic in situ hybridization (MISH) and hybridization chain reaction (HCR) for the specific capture of eukaryotic cells has been developed. As a prerequisite, a HCR-MISH procedure initially used for tracking bacterial cells was here adapted for the first time to target eukaryotic cells using a universal eukaryotic probe, Euk-516R. Following labeling with superparamagnetic nanoparticles, cells from the model eukaryotic microorganism Saccharomyces cerevisiae were hybridized and isolated on a micro-magnet array. In addition, the eukaryotic cells were successfully targeted in an artificial mixture comprising bacterial cells, thus providing evidence that HCR-MISH is a promising technology to use for specific microeukaryote capture in complex microbial communities allowing their further morphological characterization. This new study opens great opportunities in ecological sciences, thus allowing the detection of specific cells in more complex cellular mixtures in the near future.
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Affiliation(s)
- Fabiola Bastian
- DTAMB, Université Claude Bernard Lyon 1, Bât. Gregor Mendel, Villeurbanne Cedex, France
| | - Delphine Melayah
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Nora M. Dempsey
- Université Grenoble Alpes, CNRS, Grenoble INP, Institut Néel, Grenoble, France
| | - Pascal Simonet
- Université Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, INSA Lyon, CNRS, Ampère, UMR 5005, Ecully, France
| | - Marie Frenea-Robin
- Université Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, INSA Lyon, CNRS, Ampère, UMR 5005, Ecully, France
| | - Laurence Fraissinet-Tachet
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
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Thakur B, Yadav R, Mukherjee A, Melayah D, Marmeisse R, Fraissinet-Tachet L, Reddy MS. Protection from metal toxicity by Hsp40-like protein isolated from contaminated soil using functional metagenomic approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:17132-17145. [PMID: 33394429 DOI: 10.1007/s11356-020-12152-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
Pollution in the environment due to accumulation of potentially toxic metals results in deterioration of soil and water quality, thus impacting health of all living organisms including microbes. In the present investigation, a functional metagenomics approach was adopted to mine functional genes involved in metal tolerance from potentially toxic metal contaminated site. Eukaryotic cDNA library (1.0-4.0 kb) was screened for the genes providing tolerance to cadmium (Cd) toxicity through a functional complementation assay using Cd-sensitive Saccharomyces cerevisiae mutant ycf1Δ. Out of the 98 clones able to recover growth on Cd-supplemented selective medium, one clone designated as PLCc43 showed more tolerance to Cd along with some other clones. Sequence analysis revealed that cDNA PLCc43 encodes a 284 amino acid protein harbouring four characteristic zinc finger motif repeats (CXXCXGXG) and showing partial homology with heat shock protein (Hsp40) of Acanthamoeba castellanii. qPCR analysis revealed the induction of PLCc43 in the presence of Cd, which was further supported by accumulation of Cd in ycf1Δ/PLCc43 mutant. Cu-sensitive (cup1Δ), Zn-sensitive (zrc1Δ) and Co-sensitive (cot1Δ) yeast mutant strains were rescued from sensitivity when transformed with cDNA PLCc43 indicating its ability to confer tolerance to various potentially toxic metals. Oxidative stress tolerance potential of PLCc43 was also confirmed in the presence of H2O2. Present study results suggest that PLCc43 originating from a functional eukaryotic gene of soil community play an important role in detoxification of potentially toxic metals and may be used as biomarker in various contaminated sites.
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Affiliation(s)
- Bharti Thakur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Rajiv Yadav
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France
- Department of Botany, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Delphine Melayah
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Roland Marmeisse
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622, Villeurbanne, France
| | - Mondem Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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Mukherjee A, Thakur B, Pandey AK, Marmeisse R, Fraissinet-Tachet L, Reddy MS. Multi-metal tolerance of DHHC palmitoyl transferase-like protein isolated from metal contaminated soil. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:67-79. [PMID: 33159264 DOI: 10.1007/s10646-020-02301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 06/11/2023]
Abstract
The microbiota inhabiting in metal polluted environment develops strong defense mechanisms to combat pollution and sustain life. Investigating the functional genes of the eukaryotic microbiota inhabiting in these environments by using metatranscriptomics approach was the focus of this study. Size fractionated eukaryotic cDNA libraries (library A, < 0.5 kb, library B, 0.5-1.0 kb, and library C, > 1.0 kb) were constructed from RNA isolated from the metal contaminated soil. The library C was screened for Cadmium (Cd) tolerant genes by using Cd sensitive yeast mutant ycf1Δ by functional complementation assay, which yielded various clones capable of growing in Cd amended media. One of the Cd tolerant clones, PLCg39 was selected because of its ability to grow at high concentrations of Cd. Sequence analysis of PLCg39 showed homology with DHHC palmitoyl transferases, which are responsible for addition of palmitoyl groups to proteins and usually possess metal coordination domains. The cDNA PLCg39 was able to confer tolerance to Cd-sensitive (ycf1Δ), Copper-sensitive (cup1Δ) and Zn-sensitive (zrc1Δ) yeast mutants when grown at different concentrations of Cd (40-100 μM), Cu (150-1000 μM) and Zn (10-13 mM), respectively. The DHHC mutant akr1Δ transformed with PLCg39 rescued from the metal sensitivity indicating the role of DHHC palmitoyl transferase in metal tolerance. This study demonstrated that PLCg39 acts as a potential metal tolerant gene which could be used in bioremediation, biosensing and other biotechnological fields.
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Affiliation(s)
- Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Bharti Thakur
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute, Sector-81, Knowledge city, Mohali, 140306, Punjab, India
| | - Roland Marmeisse
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Ecologie Microbienne, UMR CNRS, UMR INRA, Université Claude Bernard Lyon 1 Université de Lyon, F-69622, Villeurbanne, France
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, 147004, Punjab, India.
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Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines. Biosci Rep 2020; 40:226508. [PMID: 32970113 PMCID: PMC7538681 DOI: 10.1042/bsr20202956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/23/2022] Open
Abstract
Sinorhizobium meliloti is a nitrogen-fixing bacterium forming symbiotic nodules with the legume Medicago truncatula. S. meliloti possesses two BolA-like proteins (BolA and YrbA), the function of which is unknown. In organisms where BolA proteins and monothiol glutaredoxins (Grxs) are present, they contribute to the regulation of iron homeostasis by bridging a [2Fe–2S] cluster into heterodimers. A role in the maturation of iron–sulfur (Fe–S) proteins is also attributed to both proteins. In the present study, we have performed a structure–function analysis of SmYrbA showing that it coordinates diverse divalent metal ions (Fe2+, Co2+, Ni2+, Cu2+ and Zn2+) using His32 and His67 residues, that are also used for Fe–S cluster binding in BolA–Grx heterodimers. It also possesses the capacity to form heterodimers with the sole monothiol glutaredoxin (SmGrx2) present in this species. Using cellular approaches analyzing the metal tolerance of S. meliloti mutant strains inactivated in the yrbA and/or bolA genes, we provide evidence for a connection of YrbA with the regulation of iron homeostasis. The mild defects in M. truncatula nodulation reported for the yrbA bolA mutant as compared with the stronger defects in nodule development previously observed for a grx2 mutant suggest functions independent of SmGrx2. These results help in clarifying the physiological role of BolA-type proteins in bacteria.
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12
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Pei Y, Mamtimin T, Ji J, Khan A, Kakade A, Zhou T, Yu Z, Zain H, Yang W, Ling Z, Zhang W, Zhang Y, Li X. The guanidine thiocyanate-high EDTA method for total microbial RNA extraction from severely heavy metal-contaminated soils. Microb Biotechnol 2020; 14:465-478. [PMID: 32578381 PMCID: PMC7936289 DOI: 10.1111/1751-7915.13615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/19/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular analyses relying on RNA, as a direct way to unravel active microbes and their functional genes, have received increasing attention from environmental researchers recently. However, extracting sufficient and high‐quality total microbial RNA from seriously heavy metal‐contaminated soils is still a challenge. In this study, the guanidine thiocyanate‐high EDTA (GTHE) method was established and optimized for recovering high quantity and quality of RNA from long‐term heavy metal‐contaminated soils. Due to the low microbial biomass in the soils, we combined multiple strong denaturants and intense mechanical lysis to break cells for increasing RNA yields. To minimize RNAase and heavy metals interference on RNA integrity, the concentrations of guanidine thiocyanate and EDTA were increased from 0.5 to 0.625 ml g−1 soil and 10 to 100 mM, respectively. This optimized GTHE method was applied to seven severely contaminated soils, and the RNA recovery efficiencies were 2.80 ~ 59.41 μg g−1 soil. The total microbial RNA of non‐Cr(VI) (NT) and Cr(VI)‐treated (CT) samples was utilized for molecular analyses. The result of qRT‐PCR demonstrated that the expressions of two tested genes, chrA and yieF, were respectively upregulated 4.12‐ and 62.43‐fold after Cr(VI) treatment. The total microbial RNA extracted from NT and CT samples, respectively, reached to 26.70 μg and 30.75 μg, which were much higher than the required amount (5 μg) for metatranscriptomic library construction. Besides, ratios of mRNA read were more than 86%, which indicated the high‐quality libraries constructed for metatranscriptomic analysis. In summary, the GTHE method is useful to study microbes of contaminated habitats.
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Affiliation(s)
- Yaxin Pei
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Tursunay Mamtimin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Jing Ji
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Aman Khan
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Apurva Kakade
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Tuoyu Zhou
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Hajira Zain
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Wenzhi Yang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Zhenmin Ling
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China
| | - Xiangkai Li
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, Gansu, 730000, China.,Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu Province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou, Gansu, 730000, China
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Balzano S, Sardo A, Blasio M, Chahine TB, Dell’Anno F, Sansone C, Brunet C. Microalgal Metallothioneins and Phytochelatins and Their Potential Use in Bioremediation. Front Microbiol 2020; 11:517. [PMID: 32431671 PMCID: PMC7216689 DOI: 10.3389/fmicb.2020.00517] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/10/2020] [Indexed: 01/02/2023] Open
Abstract
The persistence of heavy metals (HMs) in the environment causes adverse effects to all living organisms; HMs accumulate along the food chain affecting different levels of biological organizations, from cells to tissues. HMs enter cells through transporter proteins and can bind to enzymes and nucleic acids interfering with their functioning. Strategies used by microalgae to minimize HM toxicity include the biosynthesis of metal-binding peptides that chelate metal cations inhibiting their activity. Metal-binding peptides include genetically encoded metallothioneins (MTs) and enzymatically produced phytochelatins (PCs). A number of techniques, including genetic engineering, focus on increasing the biosynthesis of MTs and PCs in microalgae. The present review reports the current knowledge on microalgal MTs and PCs and describes the state of art of their use for HM bioremediation and other putative biotechnological applications, also emphasizing on techniques aimed at increasing the cellular concentrations of MTs and PCs. In spite of the broad metabolic and chemical diversity of microalgae that are currently receiving increasing attention by biotechnological research, knowledge on MTs and PCs from these organisms is still limited to date.
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Affiliation(s)
- Sergio Balzano
- Stazione Zoologica Anton Dohrn Napoli (SZN), Naples, Italy
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Angela Sardo
- Stazione Zoologica Anton Dohrn Napoli (SZN), Naples, Italy
| | - Martina Blasio
- Stazione Zoologica Anton Dohrn Napoli (SZN), Naples, Italy
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Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance. Appl Environ Microbiol 2020; 86:AEM.02907-19. [PMID: 32111593 DOI: 10.1128/aem.02907-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/15/2020] [Indexed: 12/18/2022] Open
Abstract
Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.
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15
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Mukherjee A, Reddy MS. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech 2020; 10:71. [PMID: 32030340 DOI: 10.1007/s13205-020-2057-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 01/06/2020] [Indexed: 02/02/2023] Open
Abstract
Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.
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Affiliation(s)
- Arkadeep Mukherjee
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004 India
| | - M Sudhakara Reddy
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab 147004 India
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16
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Yu X, Ding Z, Ji Y, Zhao J, Liu X, Tian J, Wu N, Fan Y. An operon consisting of a P-type ATPase gene and a transcriptional regulator gene responsible for cadmium resistances in Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. BMC Microbiol 2020; 20:18. [PMID: 31964334 PMCID: PMC6975044 DOI: 10.1186/s12866-020-1705-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cadmium (Cd) is a severely toxic heavy metal to most microorganisms. Many bacteria have developed Cd2+ resistance. RESULTS In this study, we isolated two different Cd2+ resistance Bacillus sp. strains, Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25, which could be grown in the presence of Cd2+ at concentration up to 0.3 mM and 0.8 mM, respectively. According to the genomic sequencing, transcriptome analysis under cadmium stress, and other related experiments, a gene cluster in plasmid p25 was found to be a major contributor to Cd2+ resistance in B. marisflavi 151-25. The cluster in p25 contained orf4802 and orf4803 which encodes an ATPase transporter and a transcriptional regulator protein, respectively. Although 151-6 has much lower Cd2+ resistance than 151-25, they contained similar gene cluster, but in different locations. A gene cluster on the chromosome containing orf4111, orf4112 and orf4113, which encodes an ATPase transporter, a cadmium efflux system accessory protein and a cadmium resistance protein, respectively, was found to play a major role on the Cd2+ resistance for B. vietamensis 151-6. CONCLUSIONS This work described cadmium resistance mechanisms in newly isolated Bacillus vietamensis 151-6 and Bacillus marisflavi 151-25. Based on homologies to the cad system (CadA-CadC) in Staphylococcus aureus and analysis of transcriptome under Cd2+ induction, we inferred that the mechanisms of cadmium resistance in B. marisflavi 151-25 was as same as the cad system in S. aureus. Although Bacillus vietamensis 151-6 also had the similar gene cluster to B. marisflavi 151-25 and S. aureus, its transcriptional regulatory mechanism of cadmium resistance was not same. This study explored the cadmium resistance mechanism for B. vietamensis 151-6 and B. marisflavi 151-25 and has expanded our understanding of the biological effects of cadmium.
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Affiliation(s)
- Xiaoxia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zundan Ding
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yangyang Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
| | - Jintong Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. THE ISME JOURNAL 2017; 11:1949-1963. [PMID: 28574490 PMCID: PMC5563950 DOI: 10.1038/ismej.2017.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
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Affiliation(s)
- Esther Singer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Michael Wagner
- University of Vienna, Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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18
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Wegner CE, Liesack W. Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags. Front Microbiol 2017; 8:1023. [PMID: 28642744 PMCID: PMC5462947 DOI: 10.3389/fmicb.2017.01023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.
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Affiliation(s)
- Carl-Eric Wegner
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Werner Liesack
- Department of Biogeochemistry, Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen. Appl Environ Microbiol 2016; 81:1375-86. [PMID: 25501482 DOI: 10.1128/aem.03682-14] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for 1% and 0.1% of the total non-rRNAs, respectively. The majority (98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.
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Bragalini C, Ribière C, Parisot N, Vallon L, Prudent E, Peyretaillade E, Girlanda M, Peyret P, Marmeisse R, Luis P. Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples. DNA Res 2014; 21:685-94. [PMID: 25281543 PMCID: PMC4263301 DOI: 10.1093/dnares/dsu030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.
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Affiliation(s)
- Claudia Bragalini
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Céline Ribière
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Nicolas Parisot
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Laurent Vallon
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Elsa Prudent
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Eric Peyretaillade
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Mariangela Girlanda
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125, Italy
| | - Pierre Peyret
- EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France
| | - Roland Marmeisse
- Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
| | - Patricia Luis
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France
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Yadav RK, Barbi F, Ziller A, Luis P, Marmeisse R, Reddy MS, Fraissinet-Tachet L. Construction of sized eukaryotic cDNA libraries using low input of total environmental metatranscriptomic RNA. BMC Biotechnol 2014; 14:80. [PMID: 25183040 PMCID: PMC4170940 DOI: 10.1186/1472-6750-14-80] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/21/2014] [Indexed: 11/25/2022] Open
Abstract
Background Construction of high quality cDNA libraries from the usually low amounts of eukaryotic mRNA extracted from environmental samples is essential in functional metatranscriptomics for the selection of functional, full-length genes encoding proteins of interest. Many of the inserts in libraries constructed by standard methods are represented by truncated cDNAs due to premature stoppage of reverse transcriptase activity and preferential cloning of short cDNAs. Results We report here a simple and cost effective technique for preparation of sized eukaryotic cDNA libraries from as low as three microgram of total soil RNA dominated by ribosomal and bacterial RNA. cDNAs synthesized by a template switching approach were size-fractionated by two dimensional agarose gel electrophoresis prior to PCR amplification and cloning. Effective size selection was demonstrated by PCR amplification of conserved gene families specific of each size class. Libraries of more than one million independent inserts whose sizes ranged between one and four kb were thus produced. Up to 80% of the insert sequences were homologous to eukaryotic gene sequences present in public databases. Conclusions A simple and cost effective technique has been developed to construct sized eukaryotic cDNA libraries from environmental samples. This technique will facilitate expression cloning of environmental eukaryotic genes and contribute to a better understanding of basic biological and/or ecological processes carried out by eukaryotic microbial communities.
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Affiliation(s)
- Rajiv Kumar Yadav
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Lyon 1, Université de Lyon, Villeurbanne, France.
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