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Saibu S, Adebusoye SA, Oyetibo GO. Soil microbiome response to 2-chlorodibenzo-p-dioxin during bioremediation of contaminated tropical soil in a microcosm-based study. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131105. [PMID: 36893594 DOI: 10.1016/j.jhazmat.2023.131105] [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: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
A pristine soil was artificially contaminated with 2-chlorodibenzo-p-dioxin (2-CDD) and separated into three portions. Microcosms SSOC and SSCC were seeded with Bacillus sp. SS2 and a three-member bacterial consortium respectively; SSC was untreated, while heat-sterilized contaminated soil served as overall control. Significant degradation of 2-CDD occurred in all microcosms except for the control where the concentration remained unchanged. Degradation of 2-CDD was highest in SSCC (94.9%) compared to SSOC (91.66%) and SCC (85.9%). There was also a notable reduction in the microbial composition complexity both in species richness and evenness following dioxin contamination, a trend that nearly lasted the study period; particularly in setups SSC and SSOC. Irrespective of the bioremediation strategies, the soil microflora was practically dominated by the Firmicutes and at the genus level, the phylotype Bacillus was the most dominant. Other dominant taxa though negatively impacted were Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria. Overall, this study demonstrated the feasibility of microbial seeding as an effective strategy to cleanup tropical soil contaminated with dioxins and the importance of metagenomics in elucidating the microbial diversities of contaminated soils. Meanwhile, the seeded organisms, owed their success not only to metabolic competence, but survivability, adaptability and ability to compete favourably with autochthonous microflora.
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Affiliation(s)
- Salametu Saibu
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria; Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria.
| | | | - Ganiyu O Oyetibo
- Department of Microbiology, University of Lagos, Akoka, Lagos, Nigeria.
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Thanh LTH, Thi TVN, Shintani M, Moriuchi R, Dohra H, Loc NH, Kimbara K. Isolation and characterization of a moderate thermophilic Paenibacillus naphthalenovorans strain 4B1 capable of degrading dibenzofuran from dioxin-contaminated soil in Vietnam. J Biosci Bioeng 2019; 128:571-577. [DOI: 10.1016/j.jbiosc.2019.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/19/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
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Wu JH, Chen WY, Kuo HC, Li YM. Redox fluctuations shape the soil microbiome in the hypoxic bioremediation of octachlorinated dibenzodioxin- and dibenzofuran-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 248:506-515. [PMID: 30831347 DOI: 10.1016/j.envpol.2019.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/16/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
The biodegradation of polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) has been recently demonstrated in a single reactor under hypoxic conditions. Maintaining hypoxic conditions through periodic aerations results in a marked fluctuation of reduction-oxidation (redox) potential. To further assess the effects of redox fluctuations, we operated two fed-batch continuously stirred tank reactors (CSTRs) with sophisticated redox controls at different anoxic/oxic fluctuations to reduce PCDD/Fs in contaminated soil. The results of long-term reactor operation showed that the CSTR with redox fluctuations at a narrow range (-63 ± 68 mV) (CSTR_A) revealed a higher substrate hydrolysis level and PCDD/F degradation rate than did the CSTR with a redox potential that fluctuated at a broad range (-13 ± 118 mV) (CSTR_B). In accordance with analyses of bacterial 16S rRNA genes, the designated hypoxic conditions with added compost supported survival of bacterial populations at a density of approximately 109 copies/g slurry. The evolved core microbiome was dominated by anoxic/oxic fluctuation-adapted Bacteroidetes, Alphaproteobacteria, and Actinobacteria, with higher species diversity and functionality, including hydrolysis and degradation of dioxin-like compounds in CSTR_A than in CSTR_B. Taken together, the overall results of this study expand the understanding of redox fluctuations in association with the degradation of recalcitrant substrates in soil and the corresponding microbiome.
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Affiliation(s)
- Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan.
| | - Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Hung-Chih Kuo
- Department of Environmental Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Yun-Ming Li
- Mass Laboratory, National Chiao-Tung University, Hsinchu, Taiwan
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Huang WY, Ngo HH, Lin C, Vu CT, Kaewlaoyoong A, Boonsong T, Tran HT, Bui XT, Vo TDH, Chen JR. Aerobic co-composting degradation of highly PCDD/F-contaminated field soil. A study of bacterial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:595-602. [PMID: 30641388 DOI: 10.1016/j.scitotenv.2018.12.312] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
This study investigated bacterial communities during aerobic food waste co-composting degradation of highly PCDD/F-contaminated field soil. The total initial toxic equivalent quantity (TEQ) of the soil was 16,004 ng-TEQ kg-1 dry weight. After 42-day composting and bioactivity-enhanced monitored natural attenuation (MNA), the final compost product's TEQ reduced to 1916 ng-TEQ kg-1 dry weight (approximately 75% degradation) with a degradation rate of 136.33 ng-TEQ kg-1 day-1. Variations in bacterial communities and PCDD/F degraders were identified by next-generation sequencing (NGS). Thermophilic conditions of the co-composting process resulted in fewer observed bacteria and PCDD/F concentrations. Numerous organic compound degraders were identified by NGS, supporting the conclusion that PCDD/Fs were degraded during food waste co-composting. Bacterial communities of the composting process were defined by four phyla (Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes). At the genus level, Bacillus (Firmicutes) emerged as the most dominant phylotype. Further studies on specific roles of these bacterial strains are needed, especially for the thermophiles which contributed to the high degradation rate of the co-co-composting treatment's first 14 days.
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Affiliation(s)
- Wen-Yen Huang
- Institute of Marine Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Huu-Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Broadway, NSW 2007, Australia
| | - Chitsan Lin
- Institute of Marine Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan.
| | - Chi-Thanh Vu
- Civil and Environmental Engineering Department, The University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Acharee Kaewlaoyoong
- Department of Safety, Health and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 82445, Taiwan
| | - Totsaporn Boonsong
- Institute of Marine Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Huu-Tuan Tran
- Institute of Marine Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Xuan-Thanh Bui
- Faculty of Environment and Natural Resources, University of Technology, Vietnam National University-Ho Chi Minh City, Vietnam
| | - Thi-Dieu-Hien Vo
- Institute of Marine Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan
| | - Jenq-Renn Chen
- Department of Safety, Health and Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 82445, Taiwan
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pahE, a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria. Appl Environ Microbiol 2019; 85:AEM.02399-18. [PMID: 30478232 DOI: 10.1128/aem.02399-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/09/2018] [Indexed: 11/20/2022] Open
Abstract
The characterization of native polycyclic aromatic hydrocarbon (PAH)-degrading bacteria is significant for understanding the PAH degradation process in the natural environment and developing effective remediation technologies. Most previous investigations of PAH-degrading bacteria in environmental samples employ pahAc, which encodes the α-subunit of PAH ring-hydroxylating dioxygenase, as a functional marker gene. However, the poor phylogenetic resolution and nonspecificity of pahAc result in a misestimation of PAH-degrading bacteria. Here, we propose a PAH hydratase-aldolase-encoding gene, pahE, as a superior biomarker for PAH-degrading bacteria. Comparative phylogenetic analysis of the key enzymes involved in the upper pathway of PAH degradation indicated that pahE evolved dependently from a common ancestor. A phylogenetic tree constructed based on PahE is largely congruent with PahAc-based phylogenies, except for the dispersion of several clades of other non-PAH-degrading aromatic hydrocarbon dioxygenases present in the PahAc tree. Analysis of pure strains by PCR confirmed that pahE can specifically distinguish PAH-degrading bacteria, while pahAc cannot. Illumina sequencing of pahE and pahAc amplicons showed more genotypes and higher specificity and resolution for pahE Novel reads were also discovered among the pahE amplicons, suggesting the presence of novel PAH-degrading populations. These results suggest that pahE is a more powerful biomarker for exploring the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution and environmental microbial ecology.IMPORTANCE PAH contamination has become a worldwide environmental issue because of the potential toxic effects on natural ecosystems and human health. Biotransformation and biodegradation are considered the main natural elimination forms of PAHs from contaminated sites. Therefore, the knowledge of the degradation potential of the microbial community in contaminated sites is crucial for PAH pollution bioremediation. However, the nonspecificity of pahAc as a functional marker of PAH-degrading bacteria has resulted neither in a reliable prediction of PAH degradation potential nor an accurate assessment of degradation. Here, we introduced pahE encoding the PAH hydratase-aldolase as a new and better functional marker gene of PAH-degrading bacteria. This study provides a powerful molecular tool to more effectively explore the ecological role and degradation potential of PAH-degrading bacteria in ecosystems, which is significant to the bioremediation of PAH pollution.
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Liu X, Wang W, Hu H, Lu X, Zhang L, Xu P, Tang H. 2-Hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid biosynthesis from dibenzofuran using lateral dioxygenation in a Pseudomonas putida strain B6-2 (DSM 28064). BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0209-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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7
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Valle A, Fernández M, Ramírez M, Rovira R, Gabriel D, Cantero D. A comparative study of eubacterial communities by PCR-DGGE fingerprints in anoxic and aerobic biotrickling filters used for biogas desulfurization. Bioprocess Biosyst Eng 2018; 41:1165-1175. [DOI: 10.1007/s00449-018-1945-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/22/2018] [Indexed: 12/31/2022]
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Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13111146. [PMID: 27869691 PMCID: PMC5129356 DOI: 10.3390/ijerph13111146] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 11/17/2022]
Abstract
Pentachlorophenol (PCP) is a toxic and persistent wood and cellulose preservative extensively used in the past decades. The production process of PCP generates polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs) as micropollutants. PCDD/Fs are also known to be very persistent and dangerous for human health and ecosystem functioning. Several physico-chemical and biological technologies have been used to remove PCP and PCDD/Fs from the environment. Bacterial degradation appears to be a cost-effective way of removing these contaminants from soil while causing little impact on the environment. Several bacteria that cometabolize or use these pollutants as their sole source of carbon have been isolated and characterized. This review summarizes current knowledge on the metabolic pathways of bacterial degradation of PCP and PCDD/Fs. PCP can be successfully degraded aerobically or anaerobically by bacteria. Highly chlorinated PCDD/Fs are more likely to be reductively dechlorinated, while less chlorinated PCDD/Fs are more prone to aerobic degradation. The biochemical and genetic basis of these pollutants’ degradation is also described. There are several documented studies of effective applications of bioremediation techniques for the removal of PCP and PCDD/Fs from soil and sediments. These findings suggest that biodegradation can occur and be applied to treat these contaminants.
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Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
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Affiliation(s)
- Jaya Chakraborty
- 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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10
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Foyer CH, Lam HM, Nguyen HT, Siddique KHM, Varshney RK, Colmer TD, Cowling W, Bramley H, Mori TA, Hodgson JM, Cooper JW, Miller AJ, Kunert K, Vorster J, Cullis C, Ozga JA, Wahlqvist ML, Liang Y, Shou H, Shi K, Yu J, Fodor N, Kaiser BN, Wong FL, Valliyodan B, Considine MJ. Neglecting legumes has compromised human health and sustainable food production. NATURE PLANTS 2016. [PMID: 28221372 DOI: 10.1007/978-981-13-0253-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.
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Affiliation(s)
- Christine H Foyer
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- School of Plant Biology, Faculty of Science, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Rajeev K Varshney
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Greater Hyderabad, India
| | - Timothy D Colmer
- School of Plant Biology, Faculty of Science, The University of Western Australia, Perth, Western Australia 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Wallace Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Helen Bramley
- Plant Breeding Institute, Faculty of Agriculture and Environment, The University of Sydney, Narrabri, New South Wales 2390, Australia
| | - Trevor A Mori
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
- School of Medicine and Pharmacology, Royal Perth Hospital Unit, The University of Western Australia, Perth, Western Australia 6000, Australia
| | - Jonathan M Hodgson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
- School of Medicine and Pharmacology, Royal Perth Hospital Unit, The University of Western Australia, Perth, Western Australia 6000, Australia
| | - James W Cooper
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Anthony J Miller
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, NR4 7UH, UK
| | - Karl Kunert
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Juan Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, Ohio 44106-7080, USA
| | - Jocelyn A Ozga
- Plant BioSystems Division, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Mark L Wahlqvist
- Fuli Institute of Food Science, Zhejiang University, Hangzhou, 310058, China
- Monash Asia Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Yan Liang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huixia Shou
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kai Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jingquan Yu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Nandor Fodor
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Brent N Kaiser
- Centre for Carbon Water and Food, Faculty of Agriculture and Environment, The University of Sydney, Brownlow Hill, New South Wales 2570, Australia
| | - Fuk-Ling Wong
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
| | - Michael J Considine
- School of Plant Biology, Faculty of Science, The University of Western Australia, Perth, Western Australia 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
- The Department of Agriculture and Food, Western Australia, South Perth, Western Australia 6151, Australia
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Chen WY, Wu JH, Lin SC, Chang JE. Bioremediation of polychlorinated-p-dioxins/dibenzofurans contaminated soil using simulated compost-amended landfill reactors under hypoxic conditions. JOURNAL OF HAZARDOUS MATERIALS 2016; 312:159-168. [PMID: 27037469 DOI: 10.1016/j.jhazmat.2016.03.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/08/2016] [Accepted: 03/22/2016] [Indexed: 06/05/2023]
Abstract
Compost-amended landfill reactors were developed to reduce polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) in contaminated soils. By periodically recirculating leachate and suppling oxygen, the online monitoring of the oxidation reduction potential confirmed that the reactors were maintained under hypoxic conditions, with redox levels constantly fluctuating between -400 and +80mV. The subsequent reactor operation demonstrated that PCDD/F degradation in soil could be facilitated by amending compost originating from the cow manure and waste sludge and that the degradation might be affected by the availability of easily degradable substrates in the soil and compost. The pyrosequencing analysis of V4/V5 regions of bacterial 16S rRNA genes suggested that species richness of the soil microbial community was increased by a factor of 1.37-1.61. Although the bacterial community varied with the compost origin and changed markedly during reactor operation, it was dominated by Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes. The aerotolerant anaerobic Sedimentibacter and Propionibacterium spp., and the uncultured Chloroflexi group could be temporarily induced to a high abundance by amending the cow manure compost; the bacterial growths were associated with the rapid degradation of PCDD/Fs. Overall, the novel bioremediation method for PCDD/F-contaminated soils using hypoxic conditions was effective, simple, energy saving, and thus easily practicable.
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Affiliation(s)
- Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University, No.1, University Road, East District, Tainan City 701, Taiwan, ROC
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, No.1, University Road, East District, Tainan City 701, Taiwan, ROC.
| | - Shih-Chiang Lin
- Department of Environmental Engineering, National Cheng Kung University, No.1, University Road, East District, Tainan City 701, Taiwan, ROC
| | - Juu-En Chang
- Department of Environmental Engineering, National Cheng Kung University, No.1, University Road, East District, Tainan City 701, Taiwan, ROC
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Changes in microbial community structures due to varying operational conditions in the anaerobic digestion of oxytetracycline-medicated cow manure. Appl Microbiol Biotechnol 2016; 100:6469-6479. [DOI: 10.1007/s00253-016-7469-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 03/06/2016] [Accepted: 03/08/2016] [Indexed: 01/26/2023]
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13
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
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14
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Kim BJ, Kim JM, Kim BR, Lee SY, Kim G, Jang YH, Ryoo S, Jeon CO, Jin HM, Jeong J, Lee SH, Lim JH, Kook YH, Kim BJ. Mycobacterium anyangense sp. nov., a rapidly growing species isolated from blood of Korean native cattle, Hanwoo (Bos taurus coreanae). Int J Syst Evol Microbiol 2015; 65:2277-2285. [PMID: 25870258 DOI: 10.1099/ijs.0.000255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
From the whole blood of Korean native cattle, Hanwoo (Bos taurus coreanae), a previously undescribed, rapidly growing, scotochromogenic isolate of the genus Mycobacterium is reported. Its 16S rRNA gene sequence, and the sequences of three other genes (hsp65, recA and rpoB) were unique and phylogenetic analysis based on 16S rRNA gene sequence (1420 bp) placed the organism into the rapidly growing Mycobacterium group close to Mycobacterium smegmatis (98.5% sequence similarity). However, phylogenetic analyses based on three different gene sequences (hsp65, recA and rpoB) revealed its location to be distinct from the branch of rapidly growing species. Culture and biochemical characteristics were generally similar to those of Mycobacterium fortuitum. Unique matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS profiles of lipids, unique fatty acid profile, unique mycolic acids profiles and a low DNA-DNA relatedness to M. fortuitum (23.6%) and M. smegmatis (39.7%) strongly supported the taxonomic status of this strain as a representative of a novel species of rapidly growing mycobacteria named Mycobacterium anyangense. The type strain is strain QIA-38(T) ( = JCM 30275(T) = KCTC 29443(T)).
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Affiliation(s)
- Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Jae-Myung Kim
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - GaNa Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yun-Ho Jang
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Soyoon Ryoo
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Che-Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hyun-Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Seon Ho Lee
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Ji-Hun Lim
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
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15
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Teng Y, Wang X, Li L, Li Z, Luo Y. Rhizobia and their bio-partners as novel drivers for functional remediation in contaminated soils. FRONTIERS IN PLANT SCIENCE 2015; 6:32. [PMID: 25699064 PMCID: PMC4318275 DOI: 10.3389/fpls.2015.00032] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 01/13/2015] [Indexed: 05/20/2023]
Abstract
Environmental pollutants have received considerable attention due to their serious effects on human health. There are physical, chemical, and biological means to remediate pollution; among them, bioremediation has become increasingly popular. The nitrogen-fixing rhizobia are widely distributed in the soil and root ecosystems and can increase legume growth and production by supplying nitrogen, resulting in the reduced need for fertilizer applications. Rhizobia also possess the biochemical and ecological capacity to degrade organic pollutants and are resistant to heavy metals, making them useful for rehabilitating contaminated soils. Moreover, rhizobia stimulate the survival and action of other biodegrading bacteria, thereby lowering the concentration of pollutants. The synergistic action of multiple rhizobial strains enhances both plant growth and the availability of pollutants ranging from heavy metals to persistent organic pollutants. Because phytoremediation has some restrictions, the beneficial interaction between plants and rhizobia provides a promising option for remediation. This review describes recent advances in the exploitation of rhizobia for the rehabilitation of contaminated soil and the biochemical and molecular mechanisms involved, thereby promoting further development of this novel bioremediation strategy into a widely accepted technique.
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Affiliation(s)
- Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
- *Correspondence: Ying Teng, Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road No. 71, Nanjing, Jiangsu 210008, China e-mail:
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Lina Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of SciencesNanjing, China
| | - Yongming Luo
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of SciencesYantai, China
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16
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Chen WY, Wu JH, Chang JE. Pyrosequencing analysis reveals high population dynamics of the soil microcosm degrading octachlorodibenzofuran. Microbes Environ 2014; 29:393-400. [PMID: 25491754 PMCID: PMC4262363 DOI: 10.1264/jsme2.me14001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A deeper understanding of the microbial community structure is very important in bioremediation for polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs). However, this has been insufficiently addressed in previous studies. To obtain more information, we pyrosequenced the V4/V5 regions of the 16S rRNA genes of bacterial communities transited from polluted soil to batch microcosms that rapidly degraded high concentrations of octachlorodibenzofuran (OCDF). The analysis results contained an average of 11,842 reads per sample, providing the first detailed description of bacterial communities associated with PCDD/Fs. The community composition markedly changed to be concomitant with the degradation of OCDF, indicating that a distinctive population structure developed rapidly in the microcosm. Although oxygen gas was provided weekly to the microcosm, the growth of potential degraders, Sphingomonas, Pseudomonas, Rhodococcus, and Clostridium, was observed, but in consistently low quantities. While anaerobic Sedimentibacter initially emerged as an abundant pioneer, several aerobic participants, such as the genera Brevundimonas, Pseudoxanthomonas, and Lysobacter, exhibited a large increase in their 16S rRNA gene copies within the timeframe, which showed a temporal population dynamic, and indicated their collaborative contributions to the degradation of OCDF under hypoxic conditions. These results have provided a deeper insight into the microbial community structure and population dynamics of the OCDF-degrading microcosm.
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Affiliation(s)
- Wei-Yu Chen
- Department of Environmental Engineering, National Cheng Kung University
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17
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
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18
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Narihiro T, Kamagata Y. Cultivating yet-to-be cultivated microbes: the challenge continues. Microbes Environ 2013; 28:163-5. [PMID: 23727826 PMCID: PMC4070670 DOI: 10.1264/jsme2.me2802rh] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 6, Tsukuba, Ibaraki 305–8566, Japan.
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19
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Yoshida N, Ye L, Liu F, Li Z, Katayama A. Evaluation of biodegradable plastics as solid hydrogen donors for the reductive dechlorination of fthalide by Dehalobacter species. BIORESOURCE TECHNOLOGY 2013; 130:478-485. [PMID: 23313696 DOI: 10.1016/j.biortech.2012.11.139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/29/2012] [Accepted: 11/30/2012] [Indexed: 06/01/2023]
Abstract
Biodegradable plastics (BPs) were evaluated for their applicability as sustainable and solid H(2) donors for microbial reductive dechlorination of 4,5,6,7-tetrachlorophthalide (fthalide). After a screening test of several BPs, the starch-based plastic (SP) that produced the highest levels of H(2) was selected for its use as the sole H(2) donor in this reaction. Fthalide dechlorination was successfully accomplished by combining an H(2)-producing SP culture and a KFL culture containing Dehalobacter species, supplemented with 0.13% and 0.5% SP, respectively. The efficiency of H(2) use in dechlorination was evaluated in a combined culture containing the KFL culture and strain Clostridium sp. Ma13, a new isolate that produces H(2) from SP. Results obtained with this culture indicated increased H(2)-fraction for fthalide dechlorination much more in this culture than in compared with a KFL culture supplemented with 20mM lactate, which are 0.75 H(2)·glucose(-1) and 0.015 H(2)·lactate(-1) in mol ratio, respectively.
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Affiliation(s)
- Naoko Yoshida
- Electronics-Inspired Interdisciplinary Research Institute (EIIRIS), Toyohashi University of Technology, Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan.
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20
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Thi Vu H, Itoh H, Ishii S, Senoo K, Otsuka S. Identification and phylogenetic characterization of cobalamin biosynthetic genes of Ensifer adhaerens. Microbes Environ 2012; 28:153-5. [PMID: 23257908 PMCID: PMC4070679 DOI: 10.1264/jsme2.me12069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Ensifer adhaerens CSBa was screened as a cobalamin producer. The draft genome sequence revealed that the strain possesses 22 cobalamin biosynthetic genes (cob genes). The cob gene arrangement on the genome of E. adhaerens CSBa was similar to that of other Ensifer species, and most similar to that of Pseudomonas denitrificans SC510. The cobN sequence phylogeny was generally congruent with that of the 16S rRNA gene, and it is suggeted that E. adhaerens CSBa might have inherited the cob genes from common ancestors of the Ensifer species. It was also suggested that the cob genes can be laterally transferred.
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Affiliation(s)
- Hoan Thi Vu
- Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
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Kaiya S, Rubaba O, Yoshida N, Yamada T, Hiraishi A. Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes. J GEN APPL MICROBIOL 2012; 58:211-24. [PMID: 22878739 DOI: 10.2323/jgam.58.211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6‒0.9 μm in width and 1.2‒3.0 μm in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3‒60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585T = KCTC 23252T).
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Affiliation(s)
- Shinichi Kaiya
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi 4418580, Japan
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