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Zhang X, Meng H, Yang Y, Lan W, Wang W, Lam PKS, Li XY, Gu JD. Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1705-1718. [PMID: 33433766 DOI: 10.1007/s10646-020-02332-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 105 to 1.28 × 106 gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH4+-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH4+-N, (NO3- + NO2-)-N, and NH4+/NOX were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.
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Affiliation(s)
- Xiaowei Zhang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People's Republic of China
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu, 210023, The People's Republic of China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, The People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Inspection and Quarantine, Food Inspection and Quarantine Center of Shenzhen Customs, 1011 Fuqiang Road, Shenzhen, 518045, The People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Agro-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, 163319, People's Republic of China
| | - Paul K S Lam
- Department of Chemistry, State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, The People's Republic of China
| | - Xiao-Yan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, The People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, The People's Republic of China.
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Wu J, Hong Y, Liu X, Hu Y. Variations in nitrogen removal rates and microbial communities over sediment depth in Daya Bay, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117267. [PMID: 33965803 DOI: 10.1016/j.envpol.2021.117267] [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: 12/13/2020] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Depth-related variations in the activities, abundances, and community composition of denitrification and anaerobic ammonia oxidation (anammox) bacteria in coastal sediment cores remain poorly understood. In this study, we used 15N-labelled incubation, quantitative polymerase chain reaction (qPCR), and high-throughput sequencing techniques to reveal the structure and function of denitrifiers and anammox bacteria in sediment cores (almost 100 cm depth) collected in winter and summer from four locations in Daya Bay. The results indicated that the activities and abundances of both denitrifiers and anammox bacteria were detected even in deeper sediments with low concentrations of dissolved inorganic nitrogen (DIN). The potential rates, abundances, and community compositions of denitrifiers and anammox bacteria only varied spatially. In the surface sediment (top 2 cm), denitrifiers had significantly higher activities and abundances than anammox bacteria, but the relative contribution of anammox bacteria to nitrogen loss increased to >60% in the subsurface sediments. Phylogenetic analysis revealed that nirS-type denitrifiers were affiliated to 10 different clusters and Candidatus Scalindua dominated the anammox community in the whole sediments. Furthermore, both denitrification and anammox bacterial communities in the subsurface sediments were distinct from those in the surface sediments. Coupled nitrification and denitrification or anammox may play significant roles in removing fixed N, and the availability of electronic acceptors (e.g. nitrite and nitrate) strongly influenced the N loss activities in the subsurface sediment, emphasising its role as a sink for buried N.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Xiaohan Liu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yaohao Hu
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
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Wu J, Hong Y, Wilson SJ, Song B. Microbial nitrogen loss by coupled nitrification to denitrification and anammox in a permeable subterranean estuary at Gloucester Point, Virginia. MARINE POLLUTION BULLETIN 2021; 168:112440. [PMID: 33971455 DOI: 10.1016/j.marpolbul.2021.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The nitrogen (N) loss processes have not been well examined in subterranean estuaries (STEs) between land and sea. We utilized a 15N isotope tracer method, q-PCR, and high-throughput sequencing to reveal the activities, abundances, and community compositions of N loss communities in a STE in Gloucester Point, Virginia, US. The highest activities, abundances and diversity of denitrifiers and anammox bacteria were detected at 50-60 cm depth in the aerobic-anaerobic transition zone (AATZ) characterized by sharp redox gradients. nirS-denitrifiers and anammox bacteria were affiliated to 10 different clusters and three genera, respectively. Denitrification and anammox played equal roles with an estimated N loss of 13.15 mmol N m-3 day-1. A positive correlation between ammonia oxidizing prokaryote abundances and DO as well as NOx- suggested that nitrification produces NOx- which supports the hotspot of denitrification and anammox within the AATZ. Overall, these results highlight the roles of N loss communities in STEs.
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Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
| | - Stephanie J Wilson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, USA.
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Nie S, Zhang Z, Mo S, Li J, He S, Kashif M, Liang Z, Shen P, Yan B, Jiang C. Desulfobacterales stimulates nitrate reduction in the mangrove ecosystem of a subtropical gulf. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144562. [PMID: 33460836 DOI: 10.1016/j.scitotenv.2020.144562] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
The amount of nitrogen compounds discharged into the natural environment has increased drastically due to frequent human activities and led to worsening pollution. The mangrove ecosystem can remove nitrogen pollution, in this regard, few studies had focused on the relationship among nitrogen cycling genes, environmental factors, and taxonomic composition. In this study, shotgun metagenomic sequencing and quantitative polymerase chain reaction were used to understand the nitrogen cycle in the subtropical mangrove ecosystem in the Beibu Gulf of China. Eight nitrogen cycling pathways were annotated. Nitrogen metabolism activities were significantly higher in the wet season than those in the dry season. The most abundant genes were those related to the synthesis and degradation of organic nitrogen, followed by the genes involved in nitrate reduction (denitrification, dissimilation/assimilation nitrate reduction). Furthermore, dissimilation nitrate reduction was the main nitrate reduction pathway. Desulfobacterales plays an important role in nitrogen cycling and contributes 12% of the genes of nitrogen pathways on average; as such, a strong coupling relationship exists among nitrogen cycling, sulfur cycling, and carbon cycling in the mangrove ecosystem. Nitrogen pollution in the mangrove wetland can be efficiently alleviated by nitrate reduction of Desulfobacterales. Nevertheless, only 50% of genes can be matched among the known species, suggesting that many unknown microorganisms in the mangrove ecosystem can perform nitrogen cycling. Total phosphorus, available iron, and total organic carbon are the key environmental factors that influence the distribution of nitrogen cycling genes, related pathways, and the taxonomic composition. Our study clearly illustrates how the mangrove ecosystem mitigates nitrogen pollution through Desulfobacterales. This finding could provide a research reference for the whole nitrogen cycling in the mangrove ecosystem.
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Affiliation(s)
- Shiqing Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zufan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinhui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Sheng He
- Guangxi Birth Defects Prevention and Control Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530033, China
| | - Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhengwu Liang
- Guangxi Liyuanbao Science and Technology Co., Ltd, Nanning 530033, China
| | - Peihong Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai 536000, China.
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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Shen LD, Tian MH, Cheng HX, Liu X, Yang YL, Liu JQ, Xu JB, Kong Y, Li JH, Liu Y. Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114623. [PMID: 33618455 DOI: 10.1016/j.envpol.2020.114623] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 06/12/2023]
Abstract
Nitrite (NO2-)- and nitrate (NO3-)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO2-- and NO3--dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 107 to 2.8 × 108 copies g-1 dry sediment) than upstream sediments (2.4 × 107 to 3.5 × 107 copies g-1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 105 to 4.8 × 105 copies g-1 dry sediment). The 13CH4 tracer experiments suggested the occurrence of NO2-- and NO3--dependent AOM activities, and their rates were 4.7-14.1 and 0.8-2.6 nmol CO2 g-1 (dry sediment) d-1, respectively. Further, the rates of NO2--dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO3- concentration was the key factor affecting the spatial variations of abundance and activity of NO2--dependent anaerobic methanotrophs. Overall, our results showed different responses of NO2-- and NO3--dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hai-Xiang Cheng
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jiang-Bing Xu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yun Kong
- College of Resources and Environment, Yangtze University, Hubei, Wuhan, 430100, China
| | - Jian-Hui Li
- College of Chemistry and Materials Engineering, Quzhou University, Quzhou, 324000, China
| | - Yan Liu
- Wuxijiang National Wetland Park Service, Quzhou, 324000, China
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Chen S, Li N, Chang S, Chen D, Xie S, Guo Q. Evaluating the response of anaerobic ammonium-oxidizing bacteria to heavy metal spill in freshwater sediment. ECOTOXICOLOGY (LONDON, ENGLAND) 2019; 28:1003-1008. [PMID: 31471821 DOI: 10.1007/s10646-019-02099-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria can play an important role in nitrogen elimination in the environment. However, the effect of heavy metals on anammox bacteria in aquatic ecosystem remains largely unknown. The present study investigated the variability of anammox bacterial community in a freshwater reservoir after a severe heavy metal spill. The richness (Chao1 richness estimator = 2-18), diversity (Shannon index = 0.26-2.04) and community structure of anammox bacteria changed considerably with sampling date, while anammox bacterial abundance (from 1.38 × 105 to 3.09 × 105 anammox bacterial 16S rRNA gene copies per gram dry sediment) was less responsive to metal spill. Anammox bacterial communities were mainly composed of Brocadia- and Anammoxoglobus-like bacteria as well as novel phylotype, however, there relative abundance varied among sampling dates. This work could add the knowledge of the response of anammox bacteria to heavy metal contamination.
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Affiliation(s)
- Sili Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Ningning Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Sha Chang
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Dinghao Chen
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Qingwei Guo
- South China Institute of Environmental Sciences (SCIES), Ministry of Ecology and Environment, Guangzhou, 510655, China.
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Qin H, Han C, Jin Z, Wu L, Deng H, Zhu G, Zhong W. Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake. J Appl Microbiol 2018. [DOI: 10.1111/jam.13758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- H. Qin
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control; School of Geography Science; Nanjing Normal University; Nanjing China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
| | - C. Han
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control; School of Geography Science; Nanjing Normal University; Nanjing China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
| | - Z. Jin
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
- School of Environment; Nanjing Normal University; Nanjing China
| | - L. Wu
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control; School of Geography Science; Nanjing Normal University; Nanjing China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
| | - H. Deng
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
- School of Environment; Nanjing Normal University; Nanjing China
| | - G. Zhu
- Nanjing Institute for Geography and Limnology; Chinese Academy of Sciences; Nanjing China
| | - W. Zhong
- Jiangsu Provincial Key Laboratory of Materials Cycling and Pollution Control; School of Geography Science; Nanjing Normal University; Nanjing China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application; Nanjing China
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Xue Y, Yu Z, Chen H, Yang JR, Liu M, Liu L, Huang B, Yang J. Cyanobacterial bloom significantly boosts hypolimnelic anammox bacterial abundance in a subtropical stratified reservoir. FEMS Microbiol Ecol 2017; 93:4111147. [DOI: 10.1093/femsec/fix118] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/09/2017] [Indexed: 11/14/2022] Open
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