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Gao S, Li S, Cao S, Zhong H, He Z. Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins. JOURNAL OF HAZARDOUS MATERIALS 2024; 480:135889. [PMID: 39362120 DOI: 10.1016/j.jhazmat.2024.135889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 09/07/2024] [Accepted: 09/17/2024] [Indexed: 10/05/2024]
Abstract
Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.
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Affiliation(s)
- Shuai Gao
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Shuangfeng Cao
- School of Life Science, Central South University, Changsha 410012, China
| | - Hui Zhong
- School of Life Science, Central South University, Changsha 410012, China.
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China; Aerospace Kaitian Environmental Technology Co., Ltd., Changsha 410100, China.
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2
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MacGregor H, Fukai I, Ash K, Arkin AP, Hazen TC. Potential applications of microbial genomics in nuclear non-proliferation. Front Microbiol 2024; 15:1410820. [PMID: 39360321 PMCID: PMC11445143 DOI: 10.3389/fmicb.2024.1410820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024] Open
Abstract
As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.
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Affiliation(s)
| | - Isis Fukai
- Bredesen Center, University of Tennessee, Knoxville, TN, United States
| | - Kurt Ash
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
| | - Adam Paul Arkin
- University of California, Berkeley, Berkeley, CA, United States
| | - Terry C. Hazen
- Bredesen Center, University of Tennessee, Knoxville, TN, United States
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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3
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Li Y, Shi X, Zeng M, Qin P, Fu M, Luo S, Tang C, Mo C, Yu F. Effect of polyethylene microplastics on antibiotic resistance genes: A comparison based on different soil types and plant types. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134581. [PMID: 38743972 DOI: 10.1016/j.jhazmat.2024.134581] [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: 02/24/2024] [Revised: 04/13/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Microplastics (MPs) and antibiotic resistance genes (ARGs) are two types of contaminants that are widely present in the soil environment. MPs can act as carriers of microbes, facilitating the colonization and spread of ARGs and thus posing potential hazards to ecosystem safety and human health. In the present study, we explored the microbial networks and ARG distribution characteristics in different soil types (heavy metal (HM)-contaminated soil and agricultural soil planted with different plants: Bidens pilosa L., Ipomoea aquatica F., and Brassica chinensis L.) after the application of MPs and evaluated environmental factors, potential microbial hosts, and ARGs. The microbial communities in the three rhizosphere soils were closely related to each other, and the modularity of the microbial networks was greater than 0.4. Moreover, the core taxa in the microbial networks, including Actinobacteriota, Proteobacteria, and Myxococcota, were important for resisting environmental stress. The ARG resistance mechanisms were dominated by antibiotic efflux in all three rhizosphere soils. Based on the annotation results, the MP treatments induced changes in the relative abundance of microbes carrying ARGs, and the G1-5 treatment significantly increased the abundance of MuxB in Verrucomicrobia, Elusimicrobia, Actinobacteria, Planctomycetes, and Acidobacteria. Path analysis showed that changes in MP particle size and dosage may indirectly affect soil enzyme activities by changing pH, which affects microbes and ARGs. We suggest that MPs may provide surfaces for ARG accumulation, leading to ARG enrichment in plants. In conclusion, our results demonstrate that MPs, as potentially persistent pollutants, can affect different types of soil environments and that the presence of ARGs may cause substantial environmental risks.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Xinwei Shi
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China
| | - Meng Zeng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Peiqing Qin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Mingyue Fu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Shiyu Luo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Chijian Tang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Cuiju Mo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, China; College of Environment and Resources, Guangxi Normal University, Guilin, China; Guangxi Key Laboratory of Environmental Processes and Remediation in Ecologically Fragile Regions, Guangxi Normal University, Guilin, China.
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4
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Goff JL, Szink EG, Durrence KL, Lui LM, Nielsen TN, Kuehl JV, Hunt KA, Chandonia JM, Huang J, Thorgersen MP, Poole FL, Stahl DA, Chakraborty R, Deutschbauer AM, Arkin AP, Adams MWW. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface. ENVIRONMENTAL MICROBIOME 2024; 19:26. [PMID: 38671539 PMCID: PMC11046850 DOI: 10.1186/s40793-024-00570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
- State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Elizabeth G Szink
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Konnor L Durrence
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Lauren M Lui
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jiawen Huang
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michael P Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Romy Chakraborty
- Earth and Environmental Science Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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5
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Rafie SAA, Blentlinger LR, Putt AD, Williams DE, Joyner DC, Campa MF, Schubert MJ, Hoyt KP, Horn SP, Franklin JA, Hazen TC. Impact of prescribed fire on soil microbial communities in a Southern Appalachian Forest clear-cut. Front Microbiol 2024; 15:1322151. [PMID: 38741734 PMCID: PMC11090169 DOI: 10.3389/fmicb.2024.1322151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Escalating wildfire frequency and severity, exacerbated by shifting climate patterns, pose significant ecological and economic challenges. Prescribed burns, a common forest management tool, aim to mitigate wildfire risks and protect biodiversity. Nevertheless, understanding the impact of prescribed burns on soil and microbial communities in temperate mixed forests, considering temporal dynamics and slash fuel types, remains crucial. Our study, conducted at the University of Tennessee Forest Resources AgResearch and Education Center in Oak Ridge, TN, employed controlled burns across various treatments, and the findings indicate that low-intensity prescribed burns have none or minimal short-term effects on soil parameters but may alter soil nutrient concentrations, as evidenced by significant changes in porewater acetate, formate, and nitrate concentrations. These burns also induce shifts in microbial community structure and diversity, with Proteobacteria and Acidobacteria increasing significantly post-fire, possibly aiding soil recovery. In contrast, Verrucomicrobia showed a notable decrease over time, and other specific microbial taxa correlated with soil pH, porewater nitrate, ammonium, and phosphate concentrations. Our research contributes to understanding the intricate relationships between prescribed fire, soil dynamics, and microbial responses in temperate mixed forests in the Southern Appalachian Region, which is valuable for informed land management practices in the face of evolving environmental challenges.
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Affiliation(s)
- S. A. A. Rafie
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - L. R. Blentlinger
- Department of Geography, University of Tennessee, Knoxville, TN, United States
| | - A. D. Putt
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
| | - D. E. Williams
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - D. C. Joyner
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - M. F. Campa
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Bredesen Center—Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - M. J. Schubert
- Forest Resources AgResearch and Education Center, Knoxville, TN, United States
| | - K. P. Hoyt
- Forest Resources AgResearch and Education Center, Knoxville, TN, United States
| | - S. P. Horn
- Department of Geography, University of Tennessee, Knoxville, TN, United States
| | - J. A. Franklin
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States
| | - T. C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, United States
- Institute for a Secure and Sustainable Environment, University of Tennessee, Knoxville, TN, United States
- Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, United States
- Bredesen Center—Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
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6
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Sajjad W, Ilahi N, Haq A, Shang Z, Nabi G, Rafiq M, Bahadur A, Banerjee A, Kang S. Bacteria populating freshly appeared supraglacial lake possess metals and antibiotic-resistant genes. ENVIRONMENTAL RESEARCH 2024; 247:118288. [PMID: 38262510 DOI: 10.1016/j.envres.2024.118288] [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: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 01/25/2024]
Abstract
Antibiotic resistance (AR) has been extensively studied in natural habitats and clinical applications. AR is mainly reported with the use and misuse of antibiotics; however, little is known about its presence in antibiotic-free remote supraglacial lake environments. This study evaluated bacterial strains isolated from supraglacial lake debris and meltwater in Dook Pal Glacier, northern Pakistan, for antibiotic-resistant genes (ARGs) and metal-tolerant genes (MTGs) using conventional PCR. Several distinct ARGs were reported in the bacterial strains isolated from lake debris (92.5%) and meltwater (100%). In lake debris, 57.5% of isolates harbored the blaTEM gene, whereas 58.3% of isolates in meltwater possessed blaTEM and qnrA each. Among the ARGs, qnrA was dominant in debris isolates (19%), whereas in meltwater isolates, qnrA (15.2%) and blaTEM (15.2%) were dominant. ARGs were widely distributed among the bacterial isolates and different bacteria shared similar types of ARGs. Relatively greater number of ARGs were reported in Gram-negative bacterial strains. In addition, 92.5% of bacterial isolates from lake debris and 83.3% of isolates from meltwater harbored MTGs. Gene copA was dominant in meltwater isolates (50%), whereas czcA was greater in debris bacterial isolates (45%). Among the MTGs, czcA (18.75%) was dominant in debris strains, whereas copA (26.0%) was greater in meltwater isolates. This presents the co-occurrence and co-selection of MTGs and ARGs in a freshly appeared supraglacial lake. The same ARGs and MTGs were present in different bacteria, exhibiting horizontal gene transfer (HGT). Both positive and negative correlations were determined between ARGs and MTGs. The research provides insights into the existence of MTGs and ARGs in bacterial strains isolated from remote supraglacial lake environments, signifying the need for a more detailed study of bacteria harboring ARGs and MTGs in supraglacial lakes.
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Affiliation(s)
- Wasim Sajjad
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Nikhat Ilahi
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Abdul Haq
- Peshawar Laboratories Complex, Pakistan Council of Scientific and Industrial Research, Peshawar, 25120, Pakistan
| | - Zhanhuan Shang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Ghulam Nabi
- Institute of Nature Conservation, Polish Academy of Sciences, Krakow, Poland
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Ali Bahadur
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Abhishek Banerjee
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Shichang Kang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
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7
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He J, Zhang B, Yan W, Lai Y, Tang Y, Han Y, Liu J. Deciphering Vanadium Speciation in Smelting Ash and Adaptive Responses of Soil Microorganisms. ACS NANO 2024; 18:2464-2474. [PMID: 38197778 DOI: 10.1021/acsnano.3c11204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Abundant smelting ash is discharged during pyrometallurgical vanadium (V) production. However, its associated V speciation and resultant ecological impact have remained elusive. In this study, V speciation in smelting ash and its influence on the metabolism of soil microorganisms were investigated. Smelting ashes from V smelters contained abundant V (19.6-115.9 mg/g). V(V) was the dominant species for soluble V, while solid V primarily existed in bioavailable forms. Previously unrevealed V nanoparticles (V-NPs) were prevalently detected, with a peak concentration of 1.3 × 1013 particles/g, a minimal size of 136.0 ± 0.6 nm, and primary constituents comprising FeVO4, VO2, and V2O5. Incubation experiments implied that smelting ash reshaped the soil microbial community. Metagenomic binning, gene transcription, and component quantification revealed that Microbacterium sp. and Tabrizicola sp. secreted extracellular polymeric substances through epsB and yhxB gene regulation for V-NPs aggregation to alleviate toxicity under aerobic operations. The V K-edge X-ray absorption near-edge structure (XANES) spectra suggested that VO2 NPs were oxidized to V2O5 NPs. In the anaerobic case, Comamonas sp. and Achromobacter sp. reduced V(V) to V(IV) for detoxification regulated by the napA gene. This study provides a deep understanding of the V speciation in smelting ash and microbial responses, inspiring promising bioremediation strategies to reduce its negative environmental impacts.
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Affiliation(s)
- Jinxi He
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China
| | - Baogang Zhang
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China
| | - Wenyue Yan
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China
| | - Yujian Lai
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Tang
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China
| | - Yawei Han
- MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China
| | - Jingfu Liu
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
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8
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Goff JL, Lui LM, Nielsen TN, Poole FL, Smith HJ, Walker KF, Hazen TC, Fields MW, Arkin AP, Adams MWW. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. ISME COMMUNICATIONS 2024; 4:ycae064. [PMID: 38800128 PMCID: PMC11128244 DOI: 10.1093/ismeco/ycae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/11/2024] [Indexed: 05/29/2024]
Abstract
Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.
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Affiliation(s)
- Jennifer L Goff
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Farris L Poole
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Heidi J Smith
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Kathleen F Walker
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37916, United States
- Genome Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, United States
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
- Department of Bioengineering, University of California, Berkeley, CA 94720, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
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9
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Akinduro A, Onyekwelu CI, Oyelumade T, Ajibade OA, Odetoyin B, Olaniyi OO. Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes. J Antibiot (Tokyo) 2023; 76:548-562. [PMID: 37308603 DOI: 10.1038/s41429-023-00633-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 06/14/2023]
Abstract
This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.
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Affiliation(s)
- Adebayonle Akinduro
- Department of Microbiology, Federal University of Technology, Akure, Nigeria
| | | | - Tomisin Oyelumade
- Department of Microbiology, Federal University of Technology, Akure, Nigeria
- Department of Biomedical Sciences, University of East London, London, UK
| | | | - Babatunde Odetoyin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University, Ile-Ife, Nigeria
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10
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Wang X, Wang X, Wu F, Zhang J, Ai S, Liu Z. Microbial community composition and degradation potential of petroleum-contaminated sites under heavy metal stress. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131814. [PMID: 37307728 DOI: 10.1016/j.jhazmat.2023.131814] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/21/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Total petroleum hydrocarbons (n-alkanes), semi-volatile organic compounds, and heavy metals pose major ecological risks at petrochemical-contaminated sites. The efficiency of natural remediation in situ is often unsatisfactory, particularly under heavy metal pollution stress. This study aimed to verify the hypothesis that after long-term contamination and restoration, microbial communities in situ exhibit significantly different biodegradation efficiencies under different concentrations of heavy metals. Moreover, they determine the appropriate microbial community to restore the contaminated soil. Therefore, we investigated the heavy metals in petroleum-contaminated soils and observed that heavy metals effects on distinct ecological clusters varied significantly. Finally, alterations in the native microbial community degradation ability were demonstrated through the occurrence of petroleum pollutant degradation function genes in different communities at the tested sites. Furthermore, structural equation modeling (SEM) was used to explain the influence of all factors on the degradation function of petroleum pollution. These results suggest that heavy metal contamination from petroleum-contaminated sites reduces the efficiency of natural remediation. In addition, it infers that MOD1 microorganisms have greater degradation potential under heavy metal stress. Utilizing appropriate microorganisms in situ may effectively help resist the stress of heavy metals and continuously degrade petroleum pollutants.
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Affiliation(s)
- Xusheng Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China
| | - Xiaonan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China.
| | - Fan Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Jiawen Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China
| | - Shunhao Ai
- The College of Life Science, Nanchang University, Nanchang 330047, PR China
| | - Zhengtao Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, PR China; State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China.
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11
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Behera S, Das S. Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations. Microbiol Res 2023; 273:127399. [PMID: 37150049 DOI: 10.1016/j.micres.2023.127399] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/22/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants.
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Affiliation(s)
- Shivananda Behera
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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12
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [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: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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13
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Goff JL, Chen Y, Thorgersen MP, Hoang LT, Poole FL, Szink EG, Siuzdak G, Petzold CJ, Adams MWW. Mixed heavy metal stress induces global iron starvation response. THE ISME JOURNAL 2023; 17:382-392. [PMID: 36572723 PMCID: PMC9938188 DOI: 10.1038/s41396-022-01351-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/28/2022]
Abstract
Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.
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Affiliation(s)
- Jennifer L. Goff
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Yan Chen
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael P. Thorgersen
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Linh T. Hoang
- grid.214007.00000000122199231Scripps Center for Metabolomics, Scripps Research, La Jolla, CA USA
| | - Farris L. Poole
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Elizabeth G. Szink
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
| | - Gary Siuzdak
- grid.214007.00000000122199231Scripps Center for Metabolomics, Scripps Research, La Jolla, CA USA
| | - Christopher J. Petzold
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Michael W. W. Adams
- grid.213876.90000 0004 1936 738XDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, GA USA
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14
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Jroundi F, Povedano-Priego C, Pinel-Cabello M, Descostes M, Grizard P, Purevsan B, Merroun ML. Evidence of microbial activity in a uranium roll-front deposit: Unlocking their potential role as bioenhancers of the ore genesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 861:160636. [PMID: 36464038 DOI: 10.1016/j.scitotenv.2022.160636] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Uranium (U) roll-front deposits constitute a valuable source for an economical extraction by in situ recovery (ISR) mining. Such technology may induce changes in the subsurface microbiota, raising questions about the way their activities could build a functional ecosystem in such extreme environments (i.e.: oligotrophy and high SO4 concentration and salinity). Additionally, more information is needed to dissipate the doubts about the microbial role in the genesis of such U orebodies. A U roll-front deposit hosted in an aquifer driven system (in Zoovch Ovoo, Mongolia), intended for mining by acid ISR, was previously explored and showed to be governed by a complex bacterial diversity, linked to the redox zonation and the geochemical conditions. Here for the first time, transcriptional activities of microorganisms living in such U ore deposits are determined and their metabolic capabilities allocated in the three redox-inherited compartments, naturally defined by the roll-front system. Several genes encoding for crucial metabolic pathways demonstrated a strong biological role controlling the subsurface cycling of many elements including nitrate, sulfate, metals and radionuclides (e.g.: uranium), through oxidation-reduction reactions. Interestingly, the discovered transcriptional behaviour gives important insights into the good microbial adaptation to the geochemical conditions and their active contribution to the stabilization of the U ore deposits. Overall, evidences on the importance of these microbial metabolic activities in the aquifer system are discussed that may clarify the doubts on the microbial role in the genesis of low-temperature U roll-front deposits, along the Zoovch Ovoo mine.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain.
| | - Cristina Povedano-Priego
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - María Pinel-Cabello
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
| | - Michael Descostes
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France; Centre de Géosciences, MINES ParisTech, PSL University, 35 rue St Honoré, 77300 Fontainebleau, France
| | - Pierre Grizard
- ORANO Mining, 125 Avenue de Paris, 92330 Châtillon, France
| | - Bayaarma Purevsan
- Badrakh Energy LLC, Jamyan Gun Avenue - 9, Sukhbaatar district, 1st khoroo, UB-14240, Mongolia
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva s/n, 18071 Granada, Spain
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15
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Shi W, Tang S, Zhang S. Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin. Microorganisms 2023; 11:microorganisms11020497. [PMID: 36838462 PMCID: PMC9963281 DOI: 10.3390/microorganisms11020497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ13CDIC and TDS and lower SO42-, Fe3+ and NO3- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3- and SO42-, causing a decrease in the content of these two ions in the stagnant areas.
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Affiliation(s)
- Wei Shi
- MOE Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Beijing 100083, China
- MOLR Key Lab of Shale Gas Resources Survey and Strategic Evaluation, Beijing 100083, China
- School of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
| | - Shuheng Tang
- MOE Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Beijing 100083, China
- MOLR Key Lab of Shale Gas Resources Survey and Strategic Evaluation, Beijing 100083, China
- School of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
- Correspondence:
| | - Songhang Zhang
- MOE Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, Beijing 100083, China
- MOLR Key Lab of Shale Gas Resources Survey and Strategic Evaluation, Beijing 100083, China
- School of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China
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16
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Zhou J, Song W, Tu Q. To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities. Brief Bioinform 2023; 24:6961613. [PMID: 36575570 DOI: 10.1093/bib/bbac594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 12/29/2022] Open
Abstract
High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.
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Affiliation(s)
- Jiayin Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China.,Joint Lab for Ocean Research and Education at Dalhousie University, Shandong University and Xiamen University, Qingdao, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
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17
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Gao W, Liu P, Ye Z, Zhou J, Wang X, Huang X, Deng X, Ma L. Divergent prokaryotic microbial assembly, co-existence patterns and functions in surrounding river sediments of a Cu-polymetallic deposit in Tibet. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158192. [PMID: 35988602 DOI: 10.1016/j.scitotenv.2022.158192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The exploitation of polymetallic deposits produces large amounts of mine drainage, which poses great challenges to the surrounding aquatic ecosystem. However, the prokaryotic microbial community assembly and co-existence patterns in the polluted area are poorly understood, especially in high-altitude localities. Herein, we investigated the prokaryotic microbial assembly, co-existence patterns and their potential functional responses in surrounding river sediments of a Cu-polymetallic deposit in Tibet. The sediments from mine drainage and surrounding tributaries exhibited distinct geochemical gradients, especially the changes in Cu content. The microbial community structure changed significantly, accompanied by decreased richness and diversity with increased Cu content. Interestingly, the relative abundances of some potential functional bacteria (e.g., Planctomycetota) actually increased as the Cu levels raised. In low contaminated area, ecological drift was the most important assembly process, whereas deterministic processes gained importance with pollution levels. Meanwhile, negative interactions in co-occurrence networks were more frequent with higher modularity and reduced keystone taxa in high contaminated area. Notably, the functions related to ABC transporters and quorum sensing (QS) were more abundant with high Cu content, which helped bacteria work together to cope with the stressful environment. Taken together, the physicochemical gradients dominated by Cu content drove the distribution, assembly and co-existence patterns of microbial communities in surrounding river sediments of a Cu-polymetallic deposit. These findings provide new insights into the maintenance mechanisms of prokaryotic microbial communities in response to heavy metal stress at high altitudes.
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Affiliation(s)
- Weikang Gao
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Peng Liu
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Zhihang Ye
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Jianwei Zhou
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Xingjie Wang
- Institute of Geological Survey, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Xinping Huang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Xiaoyu Deng
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China
| | - Liyuan Ma
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, School of Environmental Studies, China University of Geosciences, Wuhan 430074, Hubei, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, Hubei, China.
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18
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Goff JL, Szink EG, Thorgersen MP, Putt AD, Fan Y, Lui LM, Nielsen TN, Hunt KA, Michael JP, Wang Y, Ning D, Fu Y, Van Nostrand JD, Poole FL, Chandonia J, Hazen TC, Stahl DA, Zhou J, Arkin AP, Adams MWW. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments. Environ Microbiol 2022; 24:5546-5560. [PMID: 36053980 PMCID: PMC9805006 DOI: 10.1111/1462-2920.16173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/10/2022] [Indexed: 01/09/2023]
Abstract
Bacillus cereus strain CPT56D-587-MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF-matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%-40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species-largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.
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Affiliation(s)
- Jennifer L. Goff
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Elizabeth G. Szink
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Michael P. Thorgersen
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - Andrew D. Putt
- Earth and Planetary SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Yupeng Fan
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Lauren M. Lui
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Torben N. Nielsen
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Kristopher A. Hunt
- Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | | | - Yajiao Wang
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Daliang Ning
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | - Ying Fu
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA
| | | | - Farris L. Poole
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
| | - John‐Marc Chandonia
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Terry C. Hazen
- Earth and Planetary SciencesUniversity of TennesseeKnoxvilleTennesseeUSA,Genome Sciences DivisionOak Ridge National LabOak RidgeTennesseeUSA,Department of Civil and Environmental EngineeringUniversity of TennesseeKnoxvilleTennesseeUSA
| | - David A. Stahl
- Civil and Environmental EngineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Jizhong Zhou
- Institute for Environmental GenomicsUniversity of OklahomaNormanOklahomaUSA,Department of Microbiology and Plant BiologyUniversity of OklahomaNormanOklahomaUSA,School of Civil Engineering and Environmental SciencesUniversity of OklahomaNormanOklahomaUSA,Earth and Environmental SciencesLawrence Berkley National LaboratoryBerkeleyCaliforniaUSA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA,Department of BioengineeringUniversity of California at BerkeleyBerkeleyCaliforniaUSA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensGeorgiaUSA
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19
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Neethu CS, Saravanakumar C, Purvaja R, Robin RS, Ramesh R. Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 311:119937. [PMID: 35977641 DOI: 10.1016/j.envpol.2022.119937] [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: 04/01/2022] [Revised: 07/14/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsBRampR) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.
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Affiliation(s)
- C S Neethu
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - C Saravanakumar
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R Purvaja
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R S Robin
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India
| | - R Ramesh
- National Centre for Sustainable Coastal Management (NCSCM), Ministry of Environment, Forest and Climate Change (MoEFCC), Chennai 600025, India.
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Bärenstrauch M, Vanhove AS, Allégra S, Peuble S, Gallice F, Paran F, Lavastre V, Girardot F. Microbial diversity and geochemistry of groundwater impacted by steel slag leachates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:156987. [PMID: 35772557 DOI: 10.1016/j.scitotenv.2022.156987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m3 steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.
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Affiliation(s)
- Margot Bärenstrauch
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Audrey S Vanhove
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Séverine Allégra
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France
| | - Steve Peuble
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Gallice
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Frédéric Paran
- Mines Saint-Étienne, Centre "Sciences des Processus Industriels et Naturels" (SPIN), Département "Procédés pour l'Environnement et les Géo-ressources" (PEG), UMR 5600 EVS, UMR 5307 LGF, F-42023 Saint-Etienne, France
| | - Véronique Lavastre
- Université de Lyon, Université Jean Monnet Saint-Etienne, Laboratoire de Géologie de Lyon - Terre Planètes Environnement LGL-TPE, CNRS -UMR 5276, F-42023 Saint-Etienne, France
| | - Françoise Girardot
- Université de Lyon, Université Jean Monnet Saint-Etienne, CNRS, EVS-ISTHME UMR 5600, F-42023 Saint-Etienne, France.
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21
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Tang Z, Song X, Xu M, Yao J, Ali M, Wang Q, Zeng J, Ding X, Wang C, Zhang Z, Liu X. Effects of co-occurrence of PFASs and chlorinated aliphatic hydrocarbons on microbial communities in groundwater: A field study. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128969. [PMID: 35472535 DOI: 10.1016/j.jhazmat.2022.128969] [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: 01/28/2022] [Revised: 04/05/2022] [Accepted: 04/17/2022] [Indexed: 06/14/2023]
Abstract
The effects of per- and polyfluoroalkyl substances (PFASs) and chlorinated aliphatic hydrocarbons (CAHs) co-contamination on the microbial community in the field have not been studied. In this study, we evaluated the presence of PFASs and CAHs in groundwater collected from a fluorochemical plant (FCP), and carried out Illumina MiSeq sequencing to understand the impact of mixed PFASs and CAHs on the indigenous microbial community. The sum concentrations of 20 PFASs in FCP groundwater ranged from 2.05 to 317.40 μg/L, and the highest PFOA concentration was observed in the deep aquifer (60 m below ground surface), co-contaminated by dense non-aqueous-phase liquid (DNAPL). The existence of PFASs and CAHs co-contamination in groundwater resulted in a considerable decrease in the diversity of microbial communities, while the abundance of metabolisms associated with contaminants biodegradation has increased significantly compared to the background wells. Furthermore, Acinetobacter, Pseudomonas and Arthrobacter were the dominant genera in PFASs and CAHs co-contaminated groundwater. The presence of high concentrations of PFASs and CAHs has been positively associated with the genus of Citreitalea. Finally, geochemical parameters, such as ORP, sulfate and nitrate were the key factors to shape up the structure of the microbial community and sources to rich the abundance of the potential functional bacteria.
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Affiliation(s)
- Zhiwen Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Minmin Xu
- Shandong Academy of Environmental Sciences Co., LTD, Jinan 250013, China
| | - Jin Yao
- Zhongke Hualu Soil Remediation Engineering Co., LTD, Dezhou 253500, China
| | - Mukhtiar Ali
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaoyan Ding
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Congjun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhuanxia Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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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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23
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Passarini MRZ, Ottoni JR, Costa PEDS, Hissa DC, Falcão RM, Melo VMM, Balbino VQ, Mendonça LAR, Lima MGDS, Coutinho HDM, Verde LCL. Fungal community diversity of heavy metal contaminated soils revealed by metagenomics. Arch Microbiol 2022; 204:255. [PMID: 35412096 DOI: 10.1007/s00203-022-02860-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Júlia Ronzella Ottoni
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Raul Maia Falcão
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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24
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Wu B, Li J, Peng D, Wang Z, Xu H. Cadmium Exposure Alters Rhizospheric Microbial Community and Transcriptional Expression of Vetiver Grass. FRONTIERS IN PLANT SCIENCE 2022; 13:808844. [PMID: 35283903 PMCID: PMC8914199 DOI: 10.3389/fpls.2022.808844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 01/31/2022] [Indexed: 05/03/2023]
Abstract
Vetiver grass (Chrysopogon zizanioides L.) has been used to remediate cadmium (Cd)-contaminated soil, while there have been few studies on the influence of Cd exposure on the rhizospheric microbial community and transcriptional expression of C. zizanioides. In this study, we investigated the response of the rhizospheric microbial community and transcriptional expression of C. zizanioides in 20 mg/kg Cd-contaminated soil. The results showed that Cd levels in the roots and shoots of C. zizanioides reached 250.80 and 73.40 mg/kg, respectively. The Cd exposure changed the rhizospheric bacterial community, resulting in the significant enrichment of Sphingomonas, Lysobacter, and Gemmatimonadetes in Cd-contaminated soil. In addition, 880 and 3,419 differentially expressed genes were identified in the plant roots and shoots, respectively, in response to Cd stress. Among these, the overexpressed genes associated with redox homeostasis, glutathione (GSH) metabolism, cell wall biosynthesis, and transmembrane transport pathways were found to participate in Cd detoxification in C. zizanioides. These findings could be useful for understanding the selective variation of the rhizospheric microbial community and the detoxification mechanisms of C. zizanioides in Cd phytoremediation.
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Affiliation(s)
- Bin Wu
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
- State Key Laboratory of Geohazard Prevention and Geoenvironment Protection, Chengdu University of Technology, Chengdu, China
| | - Jia Li
- College of Ecology and Environment, Chengdu University of Technology, Chengdu, China
| | - Dinghua Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ziru Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Heng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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25
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He LX, He LY, Gao FZ, Wu DL, Ye P, Cheng YX, Chen ZY, Hu LX, Liu YS, Chen J, Ying GG. Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152042. [PMID: 34856250 DOI: 10.1016/j.scitotenv.2021.152042] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Increasing use of feed and medicine in mariculture could cause negative environmental impacts such as habitat modification, microbial disease development and antibiotic resistance. Here we investigated contamination of antibiotics and antibiotic resistance genes (ARGs), and composition of microbial community in grouper mariculture systems in Hainan province, China. Results showed detection of various antibiotic residues with the dominance of fluoroquinolones and tetracyclines in the six grouper cultivation systems. The concentrations of the detected antibiotics in the grouper mariculture water were significantly higher than those in the original seawater. Some of the detected antibiotics such as enrofloxacin, ciprofloxacin, ofloxacin, oxytetracycline and erythromycin in the mariculture water and/or sediment would pose high resistance selection risks. Sulfonamides resistance genes sul1 and sul2 were found to be predominant in water and sediment, while tetracycline resistance genes were prevalent in fish gill and gut. The dominant bacterial phyla in water and sediments were Bacteroides, Actinomycetes, and Proteobacteria, while the dominant ones in fish gill and gut were the Proteobacteria. Genera of Vibrio and Mycobacterium in the core microbiota were important zoonotic pathogens, and there was a significant positive correlation between Vibrio and ARGs. Phyla of Proteobacteria, Actinomyces, and Cyanobacteria were positively correlated to ARGs, indicating that these microorganisms are potential hosts of ARGs. The putative functions of microbiome related to antibiotic resistance and human diseases were significantly higher in fish than in the mariculture environment. This study suggests that mariculture system is a reservoir of ARGs, and the use of antibiotics in mariculture could induce the increase of antibiotic resistance and the prevalence of opportunistic pathogens.
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Affiliation(s)
- Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Pu Ye
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Yu-Xiao Cheng
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Zi-Yin Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Li-Xin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Jun Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; Guangdong Provincial Engineering Technology Research Center for Life and Health of River & Lake, Pearl River Hydraulic Research Institute, Pearl River Water Resources Commission of the Ministry of Water Resources, Guangzhou 510611, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, University Town, Guangzhou 510006, China.
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Farda B, Djebaili R, Vaccarelli I, Del Gallo M, Pellegrini M. Actinomycetes from Caves: An Overview of Their Diversity, Biotechnological Properties, and Insights for Their Use in Soil Environments. Microorganisms 2022; 10:453. [PMID: 35208907 PMCID: PMC8875103 DOI: 10.3390/microorganisms10020453] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/21/2022] Open
Abstract
The environmental conditions of caves shape microbiota. Within caves' microbial communities, actinomycetes are among the most abundant bacteria. Cave actinomycetes have gained increasing attention during the last decades due to novel bioactive compounds with antibacterial, antioxidant and anticancer activities. However, their potential role in soil environments is still unknown. This review summarises the literature dealing with actinomycetes from caves, underlining for the first time their potential roles in soil environments. We provide an overview of their diversity and biotechnological properties, underling their potential role in soil environments applications. The contribution of caves' actinomycetes in soil fertility and bioremediation and crops biostimulation and biocontrol are discussed. The survey on the literature show that several actinomycetes genera are present in cave ecosystems, mainly Streptomyces, Micromonospora, and Nocardiopsis. Among caves' actinomycetes, Streptomyces is the most studied genus due to its ubiquity, survival capabilities, and metabolic versatility. Despite actinomycetes' outstanding capabilities and versatility, we still have inadequate information regarding cave actinomycetes distribution, population dynamics, biogeochemical processes, and metabolisms. Research on cave actinomycetes needs to be encouraged, especially concerning environmental soil applications to improve soil fertility and health and to antagonise phytopathogens.
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Affiliation(s)
| | - Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy; (B.F.); (I.V.); (M.D.G.)
| | | | | | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy; (B.F.); (I.V.); (M.D.G.)
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Liu X, Wang H, Li L, Deng C, Chen Y, Ding H, Yu Z. Do microplastic biofilms promote the evolution and co-selection of antibiotic and metal resistance genes and their associations with bacterial communities under antibiotic and metal pressures? JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127285. [PMID: 34597934 DOI: 10.1016/j.jhazmat.2021.127285] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/30/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Microplastic (MP) biofilms with heterogeneous bacterial compositions and structure have become a hotspot of antibiotic resistance genes (ARGs) in aquatic environments. The evolutionary features of ARGs and their related factors including class 1 integron (intI1), metal resistance genes (MRGs), and bacterial communities in MP biofilms under exogenous pressures and how they compared with natural substrates (NS) are unclear. The individual and combined pressures of sulfamethoxazole, tetracycline, and zinc were used to drive the dynamic evolution of ARGs, intI1, MRGs, and bacterial communities in the MP and NS biofilms. The exogenous pressures from the combined selection of sulfamethoxazole, tetracycline, and zinc and their increasing concentrations both significantly enhanced the abundances of ARGs on the MP compared to the NS. Meanwhile, the selective pressures resulted in obvious dissimilarities between the MP and NS bacterial communities. The core bacterial taxa and the co-occurrence patterns of ARGs and bacterial genera in the biofilms of MP and NS were obviously different, and more potential ARG host bacteria selectively colonized the MP. Metal pressure also enhanced the enrichment of ARGs in the MP biofilms by promoting the spread of intI1 via the co-selection mechanism.
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Affiliation(s)
- Xiaowei Liu
- School of Biology, Food, and Environment, Hefei University, Hefei 230601, China; International (Sino-German) Joint Research Center for Biomass of Anhui Province, Hefei 230601, China.
| | - Huixiang Wang
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
| | - Lanlan Li
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chengxun Deng
- School of Biology, Food, and Environment, Hefei University, Hefei 230601, China; International (Sino-German) Joint Research Center for Biomass of Anhui Province, Hefei 230601, China
| | - Yihan Chen
- School of Resources and Environmental Engineering, Hefei University of Technology, Hefei 230009, China
| | - Haitao Ding
- School of Biology, Food, and Environment, Hefei University, Hefei 230601, China; International (Sino-German) Joint Research Center for Biomass of Anhui Province, Hefei 230601, China
| | - Zhimin Yu
- School of Biology, Food, and Environment, Hefei University, Hefei 230601, China; International (Sino-German) Joint Research Center for Biomass of Anhui Province, Hefei 230601, China
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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Responses of Bacterial Taxonomical Diversity Indicators to Pollutant Loadings in Experimental Wetland Microcosms. WATER 2022. [DOI: 10.3390/w14020251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Urbanization results in higher stormwater loadings of pollutants such as metals and nutrients into surface waters. This directly impacts organisms in aquatic ecosystems, including microbes. Sediment microbes are known for pollution reduction in the face of contamination, making bacterial communities an important area for bioindicator research. This study explores the pattern of bacterial responses to metal and nutrient pollution loading and seeks to evaluate whether bacterial indicators can be effective as a biomonitoring risk assessment tool for wetland ecosystems. Microcosms were built containing sediments collected from wetlands in the urbanizing Pike River watershed in southeastern Wisconsin, USA, with metals and nutrients added at 7 day intervals. Bacterial DNA was extracted from the microcosm sediments, and taxonomical profiles of bacterial communities were identified up to the genera level by sequencing 16S bacterial rRNA gene (V3–V4 region). Reduction of metals (example: 90% for Pb) and nutrients (example: 98% for NO3−) added in water were observed. The study found correlations between diversity indices of genera with metal and nutrient pollution as well as identified specific genera (including Fusibacter, Aeromonas, Arthrobacter, Bacillus, Bdellovibrio, and Chlorobium) as predictive bioindicators for ecological risk assessment for metal pollution.
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30
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Sharma V, Malla MA, Kori RK, Yadav RS, Azam Z. Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.
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31
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Zhang C, Yao D, Su Z, Chen H, Hao P, Liao Y, Guo Y, Yang D. Copper/Zinc-Modified Palygorskite Protects Against Salmonella Typhimurium Infection and Modulates the Intestinal Microbiota in Chickens. Front Microbiol 2021; 12:739348. [PMID: 34956111 PMCID: PMC8696032 DOI: 10.3389/fmicb.2021.739348] [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: 07/13/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022] Open
Abstract
Palygorskite (Pal), a clay nanoparticle, has been demonstrated to be a vehicle for drug delivery. Copper has antibacterial properties, and zinc is an essential micronutrient for intestinal health in animals and humans. However, whether copper/zinc-modified Pal (Cu/Zn-Pal) can protect chickens from Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) infection remains unclear. In this study, three complexes (Cu/Zn-Pal-1, Cu/Zn-Pal-2, and Cu/Zn-Pal-3) were prepared, and Cu/Zn-Pal-1 was shown to be the most effective at inhibiting the growth of S. Typhimurium in vitro, whereas natural Pal alone had no inhibitory effect. In vivo, Cu/Zn-Pal-1 reduced S. Typhimurium colonization in the intestine of infected chickens and relieved S. Typhimurium-induced organ and intestinal mucosal barrier damage. Moreover, this reduction in Salmonella load attenuated intestinal inflammation and the oxidative stress response in challenged chickens. Additionally, Cu/Zn-Pal-1 modulated the intestinal microbiota in infected chickens, which was characterized by the reduced abundance of Firmicutes and the increased abundance of Proteobacteria and Bacteroidetes. Our results indicated that the Cu/Zn-Pal-1 complex may be an effective feed supplement for reducing S. Typhimurium colonization of the gut.
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Affiliation(s)
- Chaozheng Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Dawei Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zenan Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huan Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Pan Hao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yun Liao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yiwen Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Deji Yang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Zhao H, Lin J, Wang X, Shi J, Dahlgren RA, Xu J. Dynamics of Soil Microbial N-Cycling Strategies in Response to Cadmium Stress. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14305-14315. [PMID: 34617741 DOI: 10.1021/acs.est.1c04409] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Globally increasing trace metal contamination of soils requires a better mechanistic understanding of metal-stress impacts on microbially mediated nutrient cycling. Herein, a 5-month laboratory experiment was employed to assess the effects of cadmium (Cd) on soil microbial N-cycling processes and associated functional gene abundance, with and without urea amendment. In non-N-amended soils, Cd progressively stimulated microbial populations for N acquisition from initial dissolved organic N (DON) to later recalcitrant organic N. The acceleration of N catabolism was synchronously coupled with C catabolism resulting in increased CO2/N2O fluxes and adenosine triphosphate (ATP) contents. The abundance of microbes deemed inefficient in N catabolism was gradually repressed after an initial stimulation period. We posit that enhanced exergonic N processes diminished the need for endergonic activities as a survival strategy for N communities experiencing metal stress. With urea amendment, Cd exhibited an initial stimulation effect on soil nitrification and a later a promotion effect on mineralization, along with an increase in the associated microbial populations. In N-amended soils, Cd accelerated N/C transformation processes, but decreased N2O and CO2 fluxes by 19 and 14%, respectively. This implies that under eutrophic conditions, Cd synchronously altered microbial C/N metabolism from a dominance of catabolic to anabolic processes. These results infer a nutrient-based adjustment of microbial N-cycling strategies to enhance their metal resistance.
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Affiliation(s)
- Haochun Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jiahui Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Xuehua Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jiachun Shi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, California 95616, United States
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. JOURNAL OF HAZARDOUS MATERIALS 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
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Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
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34
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Nayak T, Sengupta I, Dhal PK. A new era of radiation resistance bacteria in bioremediation and production of bioactive compounds with therapeutic potential and other aspects: An in-perspective review. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2021; 237:106696. [PMID: 34265519 DOI: 10.1016/j.jenvrad.2021.106696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms that survive in extreme environmental conditions are known as 'extremophiles'. Recently, extremophiles draw an impression in biotechnology/pharmaceutical researches/industries because of their novel molecules, known as 'extremolytes'. The intriguing phenomenon of microbial radiation resistance probably arose independently throughout their evolution of selective pressures (e.g. UV, X-ray, Gamma radiation etc.). Radiation produces multiple types of damage/oxidation to nucleic acids, proteins and other crucial cellular components. Most of the literature on microbial radiation resistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures isolation and their application on bioremediation/therapeutic field. There is much less information other than bioremediation and therapeutic application of such promising microbes we called as 'new era'. Here we discus origin and diversity of radiation resistance bacteria as well as selective mechanisms by which microorganisms can sustain in radiation rich environment. Potential uses of these radiations resistant microbes in the field of bioremediation, bioactive compounds and therapeutic industry. Last but not the least, which is the new aspect of radiation resistance microbes. Our review suggest that resistance to chronic radiation is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap molecular mechanisms of resistance to radiation and other stressors. These stress tolerance potential make them potential for radionuclides remediation, their extremolytes can be useful as anti-oxidant and anti-proliferative agents. In current scenario they can be useful in various fields from natural dye synthesis to nanoparticles production and anti-cancer treatment.
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Affiliation(s)
- Tilak Nayak
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Indraneel Sengupta
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, 700032, India.
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35
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Wang Y, Ma F, Yang J, Guo H, Su D, Yu L. Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis. Int J Mol Sci 2021; 22:ijms221910435. [PMID: 34638775 PMCID: PMC8508750 DOI: 10.3390/ijms221910435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative transcriptome analysis of YN2 grown on dioxane and citrate to elucidate its genetic degradation mechanism and investigated the transcriptomes of different dioxane degradation stages (T0, T24, T48). We also analyzed the transcriptional response of YN2 over time during which the carbon source switched from citrate to dioxane. The results indicate that strain YN2 was a methylotroph, which provides YN2 a major advantage as a pollutant degrader. A large number of genes involved in dioxane metabolism were constitutively expressed prior to dioxane exposure. Multiple genes related to the catabolism of each intermediate were upregulated by treatment in response to dioxane. Glyoxylate metabolism was essential during dioxane degradation by YN2, and the key intermediate glyoxylate was metabolized through three routes: glyoxylate carboligase pathway, malate synthase pathway, and anaplerotic ethylmalonyl-CoA pathway. Genes related to quorum sensing and transporters were significantly upregulated during the early stages of degradation (T0, T24) prior to dioxane depletion, while the expression of genes encoding two-component systems was significantly increased at late degradation stages (T48) when total organic carbon in the culture was exhausted. This study is the first to report the participation of genes encoding glyoxalase, as well as methylotrophic genes xoxF and mox, in dioxane metabolism. The present study reveals multiple genetic and transcriptional strategies used by YN2 to rapidly increase biomass during growth on dioxane, achieve high degradation efficiency and tolerance, and adapt to dioxane exposure quickly, which provides useful information regarding the molecular basis for efficient dioxane biodegradation.
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Affiliation(s)
- Yingning Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
- Correspondence:
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Haijuan Guo
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056107, China;
| | - Delin Su
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Lan Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
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Chandler L, Harford AJ, Hose GC, Humphrey CL, Chariton A, Greenfield P, Davis J. Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117318. [PMID: 34052601 DOI: 10.1016/j.envpol.2021.117318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg2+) and sulfate (SO42-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO42-, Mg2+ and Na+. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.
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Affiliation(s)
- Lisa Chandler
- Research Institute for the Environment and Livelihoods, College of Engineering, IT & Environment, Charles Darwin University, Darwin, Northern Territory, Australia; Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia.
| | - Andrew J Harford
- Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Chris L Humphrey
- Supervising Scientist Branch, Department of Agriculture, Water and the Environment, Darwin, Northern Territory, Australia
| | - Anthony Chariton
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Paul Greenfield
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Jenny Davis
- Research Institute for the Environment and Livelihoods, College of Engineering, IT & Environment, Charles Darwin University, Darwin, Northern Territory, Australia
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37
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Shi W, Tang S, Huang W, Zhang S, Li Z. Distribution Characteristics of C-N-S Microorganism Genes in Different Hydraulic Zones of High-Rank Coal Reservoirs in Southern Qinshui Basin. ACS OMEGA 2021; 6:21395-21409. [PMID: 34471743 PMCID: PMC8387991 DOI: 10.1021/acsomega.1c02169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/02/2021] [Indexed: 06/03/2023]
Abstract
Microbial decomposition of carbon and biogenic methane in coal is one of the most important issues in CBM exploration. Using metagenomic technologies, the microbial C-N-S functional genes in different hydraulic zones of high-rank coal reservoirs were systematically studied, demonstrating the high sensitivity of this ecosystem to hydrodynamic conditions. The results show that the hydrodynamic strength of coal reservoir #3 in the Shizhuangnan block gradually weakened from east to west, forming a transitional feature from a runoff area to a stagnant area. Compared with runoff areas, stagnant areas have higher reservoir pressure, gas content, and ion concentrations. The relative abundance of genes associated with C, N, and S cycling increased from the runoff area to the stagnant area, including cellulose-degrading genes (e.g., cellulose 1,4-beta-cellobiosidase), methane metabolism genes (e.g., mcr, fwd, mtd, mer, and mtr), N-cycling genes (e.g., nifDKH, amoB, narGHI, napAB, nirK, norC, and nosZ), and S-cycling genes (e.g., dsrAB, sir, cysN, sat, aprAB, and PAPSS). This indicates that the stagnant zone had a more active microbial C-N-S cycle. The machine learning model shows that these significantly different genes could be used as effective indices to distinguish runoff and stagnant areas. Carbon and hydrogen isotopes indicate that methane in the study area was thermally generated. Methanogens compete with anaerobic heterotrophic bacteria to metabolize limited substrates, resulting in a low abundance of methanogens. In addition, the existence of methane-oxidizing bacteria suggests that biogenic methane was consumed by methanotrophic bacteria, which is the main reason why biogenic methane in the study area was not effectively preserved. In addition, weakened hydrodynamic conditions increased genes involved in nutrient cycling, including organic matter decomposition, methanogenesis, denitrification, and sulfate reduction, which contributed to the increase in CO2 and consumption of sulfate and nitrate from runoff areas to stagnant areas.
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Affiliation(s)
- Wei Shi
- MOE
Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, China University of Geosciences, Beijing 100083, China
- MOLR
Key Lab of Shale Gas Resources Survey and Strategic Evaluation, China University of Geosciences, Beijing 100083, China
- School
of Energy Resources, China University of
Geosciences (Beijing), Beijing 100083, China
| | - Shuheng Tang
- MOE
Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, China University of Geosciences, Beijing 100083, China
- MOLR
Key Lab of Shale Gas Resources Survey and Strategic Evaluation, China University of Geosciences, Beijing 100083, China
- School
of Energy Resources, China University of
Geosciences (Beijing), Beijing 100083, China
| | - Wenhui Huang
- MOE
Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, China University of Geosciences, Beijing 100083, China
- MOLR
Key Lab of Shale Gas Resources Survey and Strategic Evaluation, China University of Geosciences, Beijing 100083, China
- School
of Energy Resources, China University of
Geosciences (Beijing), Beijing 100083, China
| | - Songhang Zhang
- MOE
Key Lab of Marine Reservoir Evolution and Hydrocarbon Enrichment Mechanism, China University of Geosciences, Beijing 100083, China
- MOLR
Key Lab of Shale Gas Resources Survey and Strategic Evaluation, China University of Geosciences, Beijing 100083, China
- School
of Energy Resources, China University of
Geosciences (Beijing), Beijing 100083, China
| | - Zhongcheng Li
- China
United Coalbed Methane Corporation Ltd., Beijing 100011, China
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Lehosmaa K, Muotka T, Pirttilä AM, Jaakola I, Rossi PM, Jyväsjärvi J. Bacterial communities at a groundwater-surface water ecotone: gradual change or abrupt transition points along a contamination gradient? Environ Microbiol 2021; 23:6694-6706. [PMID: 34382316 DOI: 10.1111/1462-2920.15708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/11/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023]
Abstract
Microbial communities contribute greatly to groundwater quality, but the impacts of land-use practices on bacteria in groundwaters and groundwater-dependent ecosystems remain poorly known. With 16S rRNA gene amplicon sequencing, we assessed bacterial community composition at the groundwater-surface water ecotone of boreal springs impacted by urbanization and agriculture, using spring water nitrate-N as a surrogate of contamination. We also measured the rate of a key ecosystem process, organic matter decomposition. We documented a recurrent pattern across all major bacterial phyla where diversity started to decrease at unexpectedly low nitrate-N concentrations (100-300 μg L-1 ). At 400 NO3 - -N μg L-1 , 25 bacterial exact sequence variants showed a negative response, resulting in a distinct threshold in bacterial community composition. Chthonomonas, Acetobacterales and Hyphomicrobium were the most sensitive taxa, while only three taxa (Duganella, Undibacterium and Thermoanaerobaculaceae) were enriched due to increased contamination. Decomposition rate responded unimodally to increasing nitrate-N concentration, with a peak rate at ~400 NO3 - -N μg L-1 , parallelly with a major shift in bacterial community composition. Our results emphasize the utility of bacterial communities in the assessment of groundwater-dependent ecosystems. They also call for a careful reconsideration of threshold nitrate values for defining groundwater ecosystem health and protecting their microbial biodiversity.
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Affiliation(s)
- Kaisa Lehosmaa
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Timo Muotka
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Anna Maria Pirttilä
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Iikka Jaakola
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
| | - Pekka M Rossi
- Water, Energy and Environmental Engineering Research Group, University of Oulu, Oulu, FI-90014, Finland
| | - Jussi Jyväsjärvi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, FI-90014, Finland
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Jeevanandam V, Osborne J. Understanding the fundamentals of microbial remediation with emphasize on metabolomics. Prep Biochem Biotechnol 2021; 52:351-363. [PMID: 34338137 DOI: 10.1080/10826068.2021.1946694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The post-genomic tool metabolomics is a great advancement in science and technology which acquires novel strategies and pathways to analyze various biological compounds. Metabolomics aids in retrieving the qualitative and quantitative data from the various biological system. The current review is focused on the application of metabolomics in bioremediation and helps to focus on the xenobiotic compounds which are discharged into the environment and have long term impact. The microbial based biodegradation can be effectively used along with the combination of metabolomic approach for a better understanding of the breakdown of certain recalcitrant. Additionally, this review also discusses the candidate gene approach which helps to comprehend the functional analysis of microbial genes in response to different contaminants. Therefore, this review intends to discuss the metabolomics in bioremediation by studying the complete set of metabolites involved during the process of degradation and their interaction with the environment.
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Affiliation(s)
- Vaishnavi Jeevanandam
- Department of Biosciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Jabez Osborne
- Department of Biosciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
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Chen Z, Liu WS, Zhong X, Zheng M, Fei YH, He H, Ding K, Chao Y, Tang YT, Wang S, Qiu R. Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China. WATER RESEARCH 2021; 201:117331. [PMID: 34153824 DOI: 10.1016/j.watres.2021.117331] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.
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Affiliation(s)
- Ziwu Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Xi Zhong
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Mengyuan Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying-Heng Fei
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Huan He
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Kengbo Ding
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China.
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Shizhong Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Huang CC, Liang CM, Yang TI, Chen JL, Wang WK. Shift of bacterial communities in heavy metal-contaminated agricultural land during a remediation process. PLoS One 2021; 16:e0255137. [PMID: 34297781 PMCID: PMC8301633 DOI: 10.1371/journal.pone.0255137] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/09/2021] [Indexed: 02/01/2023] Open
Abstract
Anthropogenic activities accompanied by heavy metal waste threaten the environment. Heavy metal pollution alters the soil microbial community composition, and the microorganisms that adapt to this stress increase in abundance. The remediation process of contaminated soil not only reduces the concentration of heavy metals but also alters the bacterial communities. High-throughput 16S rDNA sequencing techniques were applied to understand the changes in soil microbial communities. Using the remediation approach of the soil mixing, the concentrations of heavy metals in the contaminated areas were diluted and the soil environment was changed. The change of soil environment as a disturbance contributed to the alteration of microbial diversity of the remediated areas. The pH and heavy metals (Cr, Cu, Ni, and Zn) were the most influential factors driving the changes in community structure. The bacterial community structure was significantly different among sample areas. The decrease of heavy metals in soil may be the important factors that changed the microbial composition. This study provides the better understanding of the changes in composition of microbial communities affected by the remediation process in heavy metal-contaminated soil.
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Affiliation(s)
- Chi-Chun Huang
- Endemic Species Research Institute, Jiji, Nantou, Taiwan
| | - Chih-Ming Liang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Ting-I Yang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Jiann-Long Chen
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
| | - Wei-Kuang Wang
- Department of Environmental Engineering and Science, Feng Chia University, Taichung, Taiwan
- * E-mail:
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Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. mSystems 2021; 6:e0053721. [PMID: 34184913 PMCID: PMC8269241 DOI: 10.1128/msystems.00537-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 05/26/2021] [Indexed: 01/21/2023] Open
Abstract
Viruses are ubiquitous microbiome components, shaping ecosystems via strain-specific predation, horizontal gene transfer and redistribution of nutrients through host lysis. Viral impacts are important in groundwater ecosystems, where microbes drive many nutrient fluxes and metabolic processes; however, little is known about the diversity of viruses in these environments. We analyzed four groundwater plasmidomes (the entire plasmid content of an environment) and identified 200 viral sequences, which clustered into 41 genus-level viral clusters (approximately equivalent to viral genera) including 9 known and 32 putative new genera. We used publicly available bacterial whole-genome sequences (WGS) and WGS from 261 bacterial isolates from this groundwater environment to identify potential viral hosts. We linked 76 of the 200 viral sequences to a range of bacterial phyla, the majority associated with Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria. The publicly available WGS enabled mapping bacterial hosts to several viral sequences. The WGS of groundwater isolates increased the depth of host prediction by allowing host identification at the strain level. The latter included 4 viruses that were almost entirely (>99% query coverage, >99% identity) identified as integrated in the genomes of Pseudomonas, Acidovorax, and Castellaniella strains, resulting in high-confidence host assignments. Lastly, 21 of these viruses carried putative auxiliary metabolite genes for metal and antibiotic resistance, which might drive their infection cycles and/or provide selective advantage to infected hosts. Exploring the groundwater virome provides a necessary foundation for integration of viruses into ecosystem models where they are key players in microbial adaption to environmental stress. IMPORTANCE To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications. Using this method, we detected several novel phage genera along with those previously established. Our approach of using the whole-genome sequences of hundreds of bacterial isolates from the same site enabled us to make host assignments with high confidence, several at strain levels. Certain phage genes suggest that they provide an environment-specific selective advantage to their bacterial hosts. Our study lays the foundation for future research on directed phage isolations using specific bacterial host strains to further characterize groundwater phages, their life cycles, and their effects on groundwater microbiome and biogeochemistry.
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Affiliation(s)
- Ankita Kothari
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anatori Prieto
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Drishti Soneja
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah Spencer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Xiaoqin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Matthew W. Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
- Department of Microbiology & Immunology, Montana State University, Bozeman, Montana, USA
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Energy Biosciences Institute, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Eric J. Alm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Broad Institute of MIT Cambridge, Cambridge, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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43
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Zou HY, He LY, Gao FZ, Zhang M, Chen S, Wu DL, Liu YS, He LX, Bai H, Ying GG. Antibiotic resistance genes in surface water and groundwater from mining affected environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145516. [PMID: 33571766 DOI: 10.1016/j.scitotenv.2021.145516] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 05/05/2023]
Abstract
Mining activities are known to generate a large amount of mine tailings and acid mine drainage which contain varieties of heavy metals. Heavy metals play an important role in co-selection for bacterial antibiotic resistance. However, the characteristics of antibiotic resistance genes (ARGs) in mining-affected water environments are still unclear. Here we investigated the pollution of metals, profiles of ARGs, mobile genetic elements (MGEs) and microbial community in mining-affected surface water and groundwater. The results showed that in the tested water samples, the concentrations of Zn and Mn were the highest, and Ni was the lowest. Higher abundances of ARGs with great proportion of sulfonamides, chloramphenicols and tetracyclines resistance genes were found in mining-affected water when compared with those without mining activities. Additionally, there were positive correlations between heavy metals (especially Ni, Zn and Mn) and these ARGs. Linear regression analysis suggested that MGEs were positively correlated with ARGs. In addition, total phosphorus was correlated with ARGs (p < 0.05). The microbial community was different between the mining-affected water and the reference (p < 0.05). Proteobacteria, Bacteroidetes and Actinobacteria were dominant phyla in the surface water and groundwater. Network analysis showed that many ARGs were significantly associated with these dominant bacteria, which suggested they might be potential hosts for these ARGs. These findings provide a clear evidence that the mining activities in the study area had a significant impact on surface water and groundwater to different degrees.
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Affiliation(s)
- Hai-Yan Zou
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Liang-Ying He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Fang-Zhou Gao
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Min Zhang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Shuai Chen
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Dai-Ling Wu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - You-Sheng Liu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Lu-Xi He
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Hong Bai
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, China; School of Environment, South China Normal University, Guangzhou 510006, China.
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Wang X, Lan B, Fei H, Wang S, Zhu G. Heavy metal could drive co-selection of antibiotic resistance in terrestrial subsurface soils. JOURNAL OF HAZARDOUS MATERIALS 2021; 411:124848. [PMID: 33858075 DOI: 10.1016/j.jhazmat.2020.124848] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Terrestrial surface ecosystems are important sinks for antibiotic resistance genes (ARGs) due to the continuous discharge of contaminants from human-impacted ecosystems. However, the abundance and resistance types of ARGs and their influencing factors in terrestrial subsurface soils are not well known. In this study, we investigated the abundance and diversity of ARGs, and their correlations with metal resistance genes (MRGs), mobile genetic elements (MGEs), bacteria, and heavy metals in subsurface soils using high throughput quantitative PCR and metagenomic sequencing approaches. Abundant and diverse ARGs were detected with high spatial heterogeneity among sampling sites. Vertically, there was no significant difference in ARG profiles between the aquifer and non-aquifer soils. Heavy metals were key factors shaping ARG profiles in soils with high heavy metal contents, while they showed no significant effect in low contents. Moreover, heavy metals could trigger the proliferation of antibiotic resistance by increasing MGE abundance or influencing bacterial communities. Metagenomic analysis also revealed the widespread co-occurrence of ARGs and MRGs, with heavy metals possibly enhancing the co-selection of ARGs and MRGs in soils with high heavy metal contents. This study highlighted the heavy metal-driven co-selection of ARGs and revealed the occurrence of ARG pollution in terrestrial subsurface soils.
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Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bangrui Lan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hexin Fei
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Abstract
Metabolites have essential roles in microbial communities, including as mediators of nutrient and energy exchange, cell-to-cell communication, and antibiosis. However, detecting and quantifying metabolites and other chemicals in samples having extremes in salt or mineral content using liquid chromatography-mass spectrometry (LC-MS)-based methods remains a significant challenge. Here, we report a facile method based on in situ chemical derivatization followed by extraction for analysis of metabolites and other chemicals in hypersaline samples, enabling for the first time direct LC-MS-based exometabolomics analysis in sample matrices containing up to 2 M total dissolved salts. The method, MetFish, is applicable to molecules containing amine, carboxylic acid, carbonyl, or hydroxyl functional groups, and it can be integrated into either targeted or untargeted analysis pipelines. In targeted analyses, MetFish provided limits of quantification as low as 1 nM, broad linear dynamic ranges (up to 5 to 6 orders of magnitude) with excellent linearity, and low median interday reproducibility (e.g., 2.6%). MetFish was successfully applied in targeted and untargeted exometabolomics analyses of microbial consortia, quantifying amino acid dynamics in the exometabolome during community succession; in situ in a native prairie soil, whose exometabolome was isolated using a hypersaline extraction; and in input and produced fluids from a hydraulically fractured well, identifying dramatic changes in the exometabolome over time in the well. IMPORTANCE The identification and accurate quantification of metabolites using electrospray ionization-mass spectrometry (ESI-MS) in hypersaline samples is a challenge due to matrix effects. Clean-up and desalting strategies that typically work well for samples with lower salt concentrations are often ineffective in hypersaline samples. To address this gap, we developed and demonstrated a simple yet sensitive and accurate method—MetFish—using chemical derivatization to enable mass spectrometry-based metabolomics in a variety of hypersaline samples from varied ecosystems and containing up to 2 M dissolved salts.
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Lopez‐Fernandez M, Jroundi F, Ruiz‐Fresneda MA, Merroun ML. Microbial interaction with and tolerance of radionuclides: underlying mechanisms and biotechnological applications. Microb Biotechnol 2021; 14:810-828. [PMID: 33615734 PMCID: PMC8085914 DOI: 10.1111/1751-7915.13718] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 11/26/2022] Open
Abstract
Radionuclides (RNs) generated by nuclear and civil industries are released in natural ecosystems and may have a hazardous impact on human health and the environment. RN-polluted environments harbour different microbial species that become highly tolerant of these elements through mechanisms including biosorption, biotransformation, biomineralization and intracellular accumulation. Such microbial-RN interaction processes hold biotechnological potential for the design of bioremediation strategies to deal with several contamination problems. This paper, with its multidisciplinary approach, provides a state-of-the-art review of most research endeavours aimed to elucidate how microbes deal with radionuclides and how they tolerate ionizing radiations. In addition, the most recent findings related to new biotechnological applications of microbes in the bioremediation of radionuclides and in the long-term disposal of nuclear wastes are described and discussed.
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Affiliation(s)
- Margarita Lopez‐Fernandez
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Institute of Resource EcologyHelmholtz‐Zentrum Dresden‐RossendorfBautzner Landstraße 400Dresden01328Germany
| | - Fadwa Jroundi
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
| | - Miguel A. Ruiz‐Fresneda
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
- Present address:
Departamento de Cristalografía y Biología EstructuralCentro Superior de Investigaciones Científicas (CSIC)Instituto de Química‐Física Rocasolano (IQFR)Calle Serrano 119Madrid28006Spain
| | - Mohamed L. Merroun
- Department of MicrobiologyUniversity of GranadaAvenida Fuentenueva s/nGranada18071Spain
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47
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Wang C, Wang Y, Liu P, Sun Y, Song Z, Hu X. Characteristics of bacterial community structure and function associated with nutrients and heavy metals in coastal aquaculture area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 275:116639. [PMID: 33578318 DOI: 10.1016/j.envpol.2021.116639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 05/20/2023]
Abstract
Coastal aquaculture area has become one of the critical zones that are more susceptible to the influence of human activity. Many aquaculture operations invariably result in the accumulation of nutrients and heavy metals in the coastal ecosystem. Our study investigated sediment bacterial community structure and function across 23 sites under the influence of nutrients and heavy metals in the coastal aquaculture area. The habitat environment of the sediment was described by analyzing physicochemical characteristics. Sediment bacterial community structure and diversity were investigated by 16S rRNA sequencing. The sequencing data presented that Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria and Chloroflexi were predominant at phylum level. Variations in the bacterial community composition and diversity were significant (P < 0.01) among different groups (according to the distance from the bank side) which indicated that specific environmental conditions had shaped distinct bacterial community. Specifically, bacterial diversity and composition were significantly influenced by the temperature, salinity, pH, dissolved oxygen (DO), TOC, TON, nitrite, nitrate and heavy metals (P < 0.05). Results related to functional prediction demonstrated that carbon, nitrogen and sulfur metabolism were the dominant processes in the coastal aquaculture area. In the meantime, the potential pathogens such as Arcobacter was found in site S3, which indicated the possible threat to the cultured species in this area. Overall, variations in bacterial communities caused by nutrients and heavy metals can affect biogeochemical cycles, which may provide an indication for the protection of coastal aquaculture environments.
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Affiliation(s)
- Caixia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266237, China
| | - Yibo Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengyuan Liu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zenglei Song
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264403, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266237, China.
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48
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Garner E, Davis BC, Milligan E, Blair MF, Keenum I, Maile-Moskowitz A, Pan J, Gnegy M, Liguori K, Gupta S, Prussin AJ, Marr LC, Heath LS, Vikesland PJ, Zhang L, Pruden A. Next generation sequencing approaches to evaluate water and wastewater quality. WATER RESEARCH 2021; 194:116907. [PMID: 33610927 DOI: 10.1016/j.watres.2021.116907] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 05/24/2023]
Abstract
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
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Affiliation(s)
- Emily Garner
- Wadsworth Department of Civil and Environmental Engineering, West Virginia University, 1306 Evansdale Drive, Morgantown, WV 26505, United States.
| | - Benjamin C Davis
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Erin Milligan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Matthew Forrest Blair
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ishi Keenum
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Ayella Maile-Moskowitz
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Jin Pan
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Mariah Gnegy
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Krista Liguori
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Suraj Gupta
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Aaron J Prussin
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Linsey C Marr
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Peter J Vikesland
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, 225 Stranger Street, Blacksburg, VA 24061, United States
| | - Amy Pruden
- Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States.
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49
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Heavy-metal resistance mechanisms developed by bacteria from Lerma-Chapala basin. Arch Microbiol 2021; 203:1807-1823. [PMID: 33491161 DOI: 10.1007/s00203-020-02140-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 11/08/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
Heavy-metal (HM) contamination is a huge environmental problem in many countries including Mexico. Currently, microorganisms with multiple heavy-metal resistance and/or plant-promoting characteristics have been widely used for bioremediation of HM-contaminated soils. The aim of the study was isolated bacteria with multiple heavy-metal resistance and to determinate the resistance mechanism developed by these organisms. A total of 138 aerobic bacteria were isolated from soil and sediments surrounding the Lerma-Chapala basin located in the boundary of the States of Michoacán and Jalisco states of Mexico. One hundred and eight strains showed at least 1 plant growth-promoting features. The Lerma-Chapala basin bacteria were also resistant to high concentrations of HMs including the metalloid arsenic. Sequence analysis of 16S RNA genes reveled that these bacteria were mainly affiliated to the phyla Proteobacteria (38%), Firmicutes (31%) and Actinobacteria (25%), covering 21 genera with Bacillus as the most abundant one. Among them, at least 27 putative novel species were detected in the genera Acinetobacter, Arthrobacter, Bacillus, Agrobacterium, Dyadobacter, Enterobacter, Exiguobacterium, Kluyvera, Micrococcus, Microbacterium and Psychrobacter. In addition, these bacteria developed various heavy-metal-resistance mechanisms, such as biosorption/bioaccumulation, immobilization and detoxification. Therefore, the bacteria isolated from soils and sediments of Lerma-Chapala basin could be used in bioremediation strategies.
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50
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Hao X, Zhu J, Rensing C, Liu Y, Gao S, Chen W, Huang Q, Liu YR. Recent advances in exploring the heavy metal(loid) resistant microbiome. Comput Struct Biotechnol J 2020; 19:94-109. [PMID: 33425244 PMCID: PMC7771044 DOI: 10.1016/j.csbj.2020.12.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/18/2022] Open
Abstract
Heavy metal(loid)s exert selective pressure on microbial communities and evolution of metal resistance determinants. Despite increasing knowledge concerning the impact of metal pollution on microbial community and ecological function, it is still a challenge to identify a consistent pattern of microbial community composition along gradients of elevated metal(loid)s in natural environments. Further, our current knowledge of the microbial metal resistome at the community level has been lagging behind compared to the state-of-the-art genetic profiling of bacterial metal resistance mechanisms in a pure culture system. This review provides an overview of the core metal resistant microbiome, development of metal resistance strategies, and potential factors driving the diversity and distribution of metal resistance determinants in natural environments. The impacts of biotic factors regulating the bacterial metal resistome are highlighted. We finally discuss the advances in multiple technologies, research challenges, and future directions to better understand the interface of the environmental microbiome with the metal resistome. This review aims to highlight the diversity and wide distribution of heavy metal(loid)s and their corresponding resistance determinants, helping to better understand the resistance strategy at the community level.
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Affiliation(s)
- 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
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - 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
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, 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
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, 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
| | - Yu-Rong 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
- Corresponding authors at: State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
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