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Liu Y, Chen S, Xie Z, Zhang L, Wang J, Fang J. Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench. Microorganisms 2023; 11:microorganisms11030630. [PMID: 36985204 PMCID: PMC10052102 DOI: 10.3390/microorganisms11030630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.
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Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen 518000, China
| | - Zhe Xie
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Li Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Correspondence: (J.W.); (J.F.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, Shanghai Ocean University, Shanghai 200120, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
- Department of Natural Sciences, Hawaii Pacific University, Honolulu, HI 96813, USA
- Correspondence: (J.W.); (J.F.)
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Liu F, Ji M, Xiao L, Wang X, Diao Y, Dan Y, Wang H, Sang W, Zhang Y. Organics composition and microbial analysis reveal the different roles of biochar and hydrochar in affecting methane oxidation from paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 843:157036. [PMID: 35772551 DOI: 10.1016/j.scitotenv.2022.157036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/20/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar and hydrochar, as valuable and eco-friendly soil remediation materials from greenwaste, have potential to enhance methane oxidation in paddy soil. But the mechanism of biomass carbon on the improvement of methane-oxidizing bacteria communities in paddy soil has not been adequately elucidated. In the present study, the effect of different-temperature rice straw-based biomass carbon (RB400, RB600, RH250 and RH300) on methane oxidation were investigated by analyzing the soil dissolved organic matter (DOM), physicochemical properties and changes in microbial community structure. The results of the 17-day incubation experiment showed that the methane oxidation rate increased under all types of biomass carbon in the first 6 days. The enhancement of methane oxidation rate was more pronounced for biochar compared to hydrochar, with RB600 being the most effective treatment. The result of excitation-emission matrix (EEM) fluorescence spectroscopy showed that less DOM were released from the soil in the biochar treatments compared to the hydrochar treatments and protein-like were detected only in the hydrochar group. Microbial analysis further showed that hydrochar inhibited the growth of Bacillus, Methylobacter, and Methylocystis, while RB600 significantly increased the relative abundance of methanotrophs (responsible for methane oxidation), such as Methylocystis and Methylobacter, which was consistent with their different effects on the methane oxidation rate. Moreover, from the analysis of principal component analysis (PCA) and canonical correspondence analysis (CCA), Methylobacter and Methylocystis were negatively respond to H/C of biomass carbon. The present study provides a deeper understanding of the effect of biomass carbon obtained by different processes on methane oxidation when applied to soil from the perspective of organic matter and microbial communities.
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Affiliation(s)
- Feihong Liu
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Mengyuan Ji
- Department of Biology, University of Padua, 35131 Padova, Italy
| | - Lurui Xiao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaoxia Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yinzhu Diao
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yitong Dan
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Huan Wang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Wenjing Sang
- Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
| | - Yalei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
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Liu YF, Chen J, Liu ZL, Shou LB, Lin DD, Zhou L, Yang SZ, Liu JF, Li W, Gu JD, Mu BZ. Anaerobic Degradation of Paraffins by Thermophilic Actinobacteria under Methanogenic Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:10610-10620. [PMID: 32786606 DOI: 10.1021/acs.est.0c02071] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microbial anaerobic alkane degradation is a key process in subsurface oil reservoirs and anoxic environments contaminated with petroleum, with a major impact on global carbon cycling. However, the thermophiles capable of water-insoluble paraffins (>C17) degradation under methanogenic conditions has remained understudied. Here, we established thermophilic (55 °C) n-paraffins-degrading (C21-C30) cultures from an oil reservoir. After over 900 days of incubation, the even-numbered n-paraffins were biodegraded to methane. The bacterial communities are dominated by a novel class-level lineage of actinobacteria, 'Candidatus Syntraliphaticia'. These 'Ca. Syntraliphaticia'-like metagenome-assembled genomes (MAGs) encode a complete alkylsuccinate synthases (ASS) gene operon, as well as hydrogenases and formate dehydrogenase, and several enzymes potentially involved in alkyl-CoA oxidation and the Wood-Ljungdahl pathway. Metatranscriptomic analysis suggests that n-paraffins are activated via fumarate addition reaction, and oxidized into carbon dioxide, hydrogen/formate and acetate by 'Ca. Syntraliphaticia', that could be further converted to methane by the abundant hydrogenotrophic and acetoclastic methanogens. We also found a divergent methyl-CoM reductase-like complex (MCR) and a canonical MCR in two MAGs representing 'Ca. Methanosuratus' (within candidate phylum Verstraetearchaeota), indicating the capability of methane and short-chain alkane metabolism in the oil reservoir. Ultimately, this result offers new insights into the degradability and the mechanisms of n-paraffins under methanogenic conditions at high temperatures.
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Affiliation(s)
- Yi-Fan Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Jing Chen
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Zhong-Lin Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Li-Bin Shou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Dan-Dan Lin
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Lei Zhou
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Shi-Zhong Yang
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Jin-Feng Liu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Li
- National Engineering Laboratory for Industrial Wastewater Treatment, School of Resources and Environmental Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, P.R. China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, P.R. China
| | - Bo-Zhong Mu
- State Key Laboratory of Bioreactor Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P.R. China
- Engineering Research Center of MEOR, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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Catania V, Lopresti F, Cappello S, Scaffaro R, Quatrini P. Innovative, ecofriendly biosorbent-biodegrading biofilms for bioremediation of oil- contaminated water. N Biotechnol 2020; 58:25-31. [PMID: 32485241 DOI: 10.1016/j.nbt.2020.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/24/2023]
Abstract
Immobilization of microorganisms capable of degrading specific contaminants significantly promotes bioremediation processes. In this study, innovative and ecofriendly biosorbent-biodegrading biofilms have been developed in order to remediate oil-contaminated water. This was achieved by immobilizing hydrocarbon-degrading gammaproteobacteria and actinobacteria on biodegradable oil-adsorbing carriers, based on polylactic acid and polycaprolactone electrospun membranes. High capacities for adhesion and proliferation of bacterial cells were observed by scanning electron microscopy. The bioremediation efficiency of the systems, tested on crude oil and quantified by gas chromatography, showed that immobilization increased hydrocarbon biodegradation by up to 23 % compared with free living bacteria. The resulting biosorbent biodegrading biofilms simultaneously adsorbed 100 % of spilled oil and biodegraded more than 66 % over 10 days, with limited environmental dispersion of cells. Biofilm-mediated bioremediation, using eco-friendly supports, is a low-cost, low-impact, versatile tool for bioremediation of aquatic systems.
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Affiliation(s)
- Valentina Catania
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, blg. 16, 90128, Palermo, Italy
| | - Francesco Lopresti
- Dept. of Engineering, University of Palermo, Viale delle Scienze, blg. 6, 90128, Palermo, Italy
| | - Simone Cappello
- Institute for Biological Resources and Marine Biotechnology, National Research Council (CNR) of Messina, Spianata San Raineri, 86, 98121, Messina, Italy
| | - Roberto Scaffaro
- Dept. of Engineering, University of Palermo, Viale delle Scienze, blg. 6, 90128, Palermo, Italy
| | - Paola Quatrini
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, blg. 16, 90128, Palermo, Italy.
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Sowani H, Kulkarni M, Zinjarde S. Harnessing the catabolic versatility of Gordonia species for detoxifying pollutants. Biotechnol Adv 2019; 37:382-402. [DOI: 10.1016/j.biotechadv.2019.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/12/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
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Djahnit N, Chernai S, Catania V, Hamdi B, China B, Cappello S, Quatrini P. Isolation, characterization and determination of biotechnological potential of oil-degrading bacteria from Algerian centre coast. J Appl Microbiol 2019; 126:780-795. [PMID: 30586234 DOI: 10.1111/jam.14185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/31/2018] [Accepted: 12/20/2018] [Indexed: 11/26/2022]
Abstract
AIMS The Algerian coastline is exposed to several types of pollution, including hydrocarbons. The aim of this work was to isolate oil-degrading bacteria and to explore the intrinsic bioremediation potential of part of its contaminated harbour. METHODS AND RESULTS A collection of 119 strains, capable to grow on mineral medium supplemented with hydrocarbons, were obtained from polluted sediment and seawater collected from Sidi Fredj harbour (Algiers). Twenty-three strains were selected for further studies. Sequencing of the 16S rRNA gene showed that most isolates belong to genera of hydrocarbonoclastic bacteria (Alcanivorax), generalist hydrocarbons degraders (Marinobacter, Pseudomonas, Gordonia, Halomonas, Erythrobacter and Brevibacterium) and other bacteria not known as hydrocarbon degraders (Xanthomarina) but were able to degrade hydrocarbons. Strains related to Marinobacter and Alcanivorax were frequently isolated from our samples and resulted the most effective in degrading crude oil. Screening of catabolic genes alkB and xylA revealed the presence of alkB gene in several bacterial strains; one isolate harboured both catabolic genes while other isolates carried none of the studied genes. However, they grew in the presence of crude oil implying the existence of other biodegradation pathways. CONCLUSIONS The samples of seawater and sediment from the Algerian coast contain high level of hydrocarbon-degrading bacteria that could be interesting and useful for future bioremediation purposes. SIGNIFICANCE AND IMPACT OF THE STUDY This investigation demonstrates the diversity of hydrocarbon-degrading bacteria from a marine-contaminated area in Algeria, and their variable biodegradation abilities.
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Affiliation(s)
- N Djahnit
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - S Chernai
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - V Catania
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - B Hamdi
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - B China
- Sciensano, J. Wytsmanstreet, Brussels, Belgium
| | - S Cappello
- Istituto per l'Ambiente Marino Costiero (IAMC) - C.N.R. U.O.S. di Messina Sp., Messina, Italy
| | - P Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
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Polycaprolactone-based scaffold for oil-selective sorption and improvement of bacteria activity for bioremediation of polluted water. Eur Polym J 2017. [DOI: 10.1016/j.eurpolymj.2017.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Catania V, Sarà G, Settanni L, Quatrini P. Bacterial communities in sediment of a Mediterranean marine protected area. Can J Microbiol 2017; 63:303-311. [DOI: 10.1139/cjm-2016-0406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) “Capo Gallo–Isola delle Femmine” was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.
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Affiliation(s)
- Valentina Catania
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Gianluca Sarà
- Dipartimento di Scienze della Terra e del Mare (DISTEM), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Luca Settanni
- Dipartimento di Scienze Agrarie e Forestali (SAF), Università degli Studi di Palermo, Viale delle Scienze Ed.4 - 90128 Palermo, Italia
| | - Paola Quatrini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
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BACTERIA OF NOCАRDIA GENUS AS OBJECT OF BIOTECHNOLOGY. BIOTECHNOLOGIA ACTA 2013. [DOI: 10.15407/biotech6.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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