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Liu R, Xu H, Zhao S, Dong C, Li J, Wei G, Li G, Gong L, Yan P, Shao Z. Polyethylene terephthalate (PET)-degrading bacteria in the pelagic deep-sea sediments of the Pacific Ocean. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 352:124131. [PMID: 38734049 DOI: 10.1016/j.envpol.2024.124131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Polyethylene terephthalate (PET) plastic pollution is widely found in deep-sea sediments. Despite being an international environmental issue, it remains unclear whether PET can be degraded through bioremediation in the deep sea. Pelagic sediments obtained from 19 sites across a wide geographic range in the Pacific Ocean were used to screen for bacteria with PET degrading potential. Bacterial consortia that could grow on PET as the sole carbon and energy source were found in 10 of the 19 sites. These bacterial consortia showed PET removal rate of 1.8%-16.2% within two months, which was further confirmed by the decrease of carbonyl and aliphatic hydrocarbon groups using attenuated total reflectance-Fourier-transform infrared analysis (ATR-FTIR). Analysis of microbial diversity revealed that Alcanivorax and Pseudomonas were predominant in all 10 PET degrading consortia. Meanwhile, Thalassospira, Nitratireductor, Nocardioides, Muricauda, and Owenweeksia were also found to possess PET degradation potential. Metabolomic analysis showed that Alcanivorax sp. A02-7 and Pseudomonas sp. A09-2 could turn PET into mono-(2-hydroxyethyl) terephthalate (MHET) even in situ stimulation (40 MPa, 10 °C) conditions. These findings widen the currently knowledge of deep-sea PET biodegrading process with bacteria isolates and degrading mechanisms, and indicating that the marine environment is a source of biotechnologically promising bacterial isolates and enzymes.
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Affiliation(s)
- Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China
| | - Haiming Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Sufang Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Jianyang Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Guangshan Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China
| | - Peisheng Yan
- School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, China; School of Environmental Science, Harbin Institute of Technology, Harbin 150090, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China.
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2
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Chang S, Gui Y, He X, Xue L. Transcriptome analysis of Acinetobacter calcoaceticus HX09 strain with outstanding crude-oil-degrading ability. Braz J Microbiol 2024:10.1007/s42770-024-01392-0. [PMID: 38837015 DOI: 10.1007/s42770-024-01392-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/15/2024] [Indexed: 06/06/2024] Open
Abstract
Microbial remediation plays a pivotal role in the elimination of petroleum pollutants, making it imperative to investigate the capabilities of microorganisms in degrading petroleum. The present study describes the isolation of a promising strain, Acinetobacter sp. HX09, from petroleum-contaminated water. GC-MS analysis revealed a remarkable removal efficiency for short and medium-chain alkanes, with a rate of approximately 64% after a 7-days incubation at 30 °C. Transcriptome analysis of HX09 exhibited a predominant upregulation in gene expression levels by the induce of crude oil. Notably, genes such as alkane 1-monooxygenase, dehydrogenases and fatty acid metabolic enzymes exhibited fold changes range from 3.16 to 1.3. Based on the alkB gene sequences in HX09, the Phyre2 algorithm generated a three-dimensional structure that exhibited similarity to segments of acyl coenzyme desaturases and acyl lipid desaturases. Furthermore, three biodegradation-related gene clusters were predicted in HX09 based on the reference genome sequence. These findings contribute to our understanding of the hydrocarbon-degrading mechanisms employed by Acinetobacter species and facilitate the development of effective remediation strategies for crude oil- polluted environments.
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Affiliation(s)
- Sijing Chang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China.
| | - Yanwen Gui
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Xiaoyan He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
| | - Lingui Xue
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, Gansu, China
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Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
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Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
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Atakpa EO, Yan B, Okon SU, Liu Q, Zhang D, Zhang C. Asynchronous application of modified biochar and exogenous fungus Scedosporium sp. ZYY for enhanced degradation of oil-contaminated intertidal mudflat sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20637-20650. [PMID: 38383925 DOI: 10.1007/s11356-024-32419-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Intertidal mudflats are susceptible to oil pollution due to their proximity to discharges from industries, accidental spills from marine shipping activities, oil drilling, pipeline seepages, and river outflows. The experimental study was divided into two periods. In the first period, microcosm trials were carried out to examine the effect of chemically modified biochar on biological hydrocarbon removal from sediments. The modified biochar's surface area increased from 2.544 to 25.378 m2/g, followed by a corresponding increase in the hydrogen-carbon and oxygen-carbon ratio, indicating improved stability and polarity. In the second period, the effect of exogenous fungus - Scedoporium sp. ZYY on the bacterial community structure was examined in relation to total petroleum hydrocarbon (TPH) removal. The maximum TPH removal efficiency of 82.4% was achieved in treatments with the modified biochar, followed by a corresponding increase in Fluorescein diacetate hydrolysis activity. Furthermore, high-throughput 16S RNA gene sequencing employed to identify changes in the bacterial community of the original sediment and treatments before and after fungal inoculation revealed Proteobacteria as the dominant phylum. In addition, it was observed that Scedoporium sp. ZYY promoted the proliferation of specific TPH-degraders, particularly, Hyphomonas adhaerens which accounted for 77% of the total degrading populations in treatments where TPH removal was highest. Findings in this study provide valuable insights into the effect of modified biochar and the fundamental role of exogenous fungus towards the effective degradation of oil-contaminated intertidal mudflat sediments.
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Affiliation(s)
- Edidiong Okokon Atakpa
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Bozhi Yan
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Samuel Ukpong Okon
- Institute of Port, Coastal, and Offshore Engineering, Ocean College, Zhejiang University, Zhoushan, 316021, China
- Suzhou Industrial Technological Research Institute of Zhejiang University, Suzhou, 215163, China
| | - Qing Liu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, 541006, China
| | - Dongdong Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean College, Zhejiang University, Zhoushan, 316021, Zhejiang, China.
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Wang Q, Hou J, Huang Y, Liu W, Christie P. Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166759. [PMID: 37659531 DOI: 10.1016/j.scitotenv.2023.166759] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L-1 pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.
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Affiliation(s)
- Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ya Huang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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K S, Manian R. Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1441. [PMID: 37946088 DOI: 10.1007/s10661-023-12042-7] [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: 06/14/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.
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Affiliation(s)
- Sumathi K
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Rameshpathy Manian
- Department of Biotechnology, School of Biosciences and Technology, VIT University: Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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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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Ibuprofen: Toxicology and Biodegradation of an Emerging Contaminant. Molecules 2023; 28:molecules28052097. [PMID: 36903343 PMCID: PMC10004696 DOI: 10.3390/molecules28052097] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/26/2023] Open
Abstract
The anti-inflammatory drug ibuprofen is considered to be an emerging contaminant because of its presence in different environments (from water bodies to soils) at concentrations with adverse effects on aquatic organisms due to cytotoxic and genotoxic damage, high oxidative cell stress, and detrimental effects on growth, reproduction, and behavior. Because of its high human consumption rate and low environmental degradation rate, ibuprofen represents an emerging environmental problem. Ibuprofen enters the environment from different sources and accumulates in natural environmental matrices. The problem of drugs, particularly ibuprofen, as contaminants is complicated because few strategies consider them or apply successful technologies to remove them in a controlled and efficient manner. In several countries, ibuprofen's entry into the environment is an unattended contamination problem. It is a concern for our environmental health system that requires more attention. Due to its physicochemical characteristics, ibuprofen degradation is difficult in the environment or by microorganisms. There are experimental studies that are currently focused on the problem of drugs as potential environmental contaminants. However, these studies are insufficient to address this ecological issue worldwide. This review focuses on deepening and updating the information concerning ibuprofen as a potential emerging environmental contaminant and the potential for using bacteria for its biodegradation as an alternative technology.
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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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Marzuki I, Rosmiati R, Mustafa A, Sahabuddin S, Tarunamulia T, Susianingsih E, Hendrajat EA, Sahrijanna A, Muslimin M, Ratnawati E, Kamariah K, Nisaa K, Herlambang S, Gunawan S, Santi IS, Isnawan BH, Kaseng ES, Septiningsih E, Asaf R, Athirah A, Basri B. Potential Utilization of Bacterial Consortium of Symbionts Marine Sponges in Removing Polyaromatic Hydrocarbons and Heavy Metals, Review. BIOLOGY 2023; 12:86. [PMID: 36671778 PMCID: PMC9855174 DOI: 10.3390/biology12010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/17/2022] [Accepted: 12/08/2022] [Indexed: 01/07/2023]
Abstract
Toxic materials in waste generally contain several components of the global trending pollutant category, especially PAHs and heavy metals. Bioremediation technology for waste management that utilizes microorganisms (bacteria) has not been fully capable of breaking down these toxic materials into simple and environmentally friendly chemical products. This review paper examines the potential application of a consortium of marine sponge symbionts with high performance and efficiency in removing PAHs and heavy metal contaminants. The method was carried out through a review of several related research articles by the author and published by other researchers. The results of the study conclude that the development of global trending pollutant (GTP) bioremediation technology could be carried out to increase the efficiency of remediation. Several types of marine sponge symbiont bacteria, hydrocarbonoclastic (R-1), metalloclastic (R-2), and metallo-hydro-carbonoclastic (R-3), have the potential to be applied to improve waste removal performance. A consortium of crystalline bacterial preparations is required to mobilize into GTP-exposed sites rapidly. Bacterial symbionts of marine sponges can be traced mainly to sea sponges, whose body surface is covered with mucus.
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Affiliation(s)
- Ismail Marzuki
- Department of Chemical Engineering, Fajar University, Makassar 90231, South Sulawesi, Indonesia
| | - Rosmiati Rosmiati
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Akhmad Mustafa
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Sahabuddin Sahabuddin
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Tarunamulia Tarunamulia
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Endang Susianingsih
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Erfan Andi Hendrajat
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Andi Sahrijanna
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Muslimin Muslimin
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Erna Ratnawati
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Kamariah Kamariah
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Khairun Nisaa
- Research Center for Fishery National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Susila Herlambang
- Soil Science Departement of Agriculture Faculty Universitas Pembangunan Nasional Veteran, Yogyakarta 55283, DI Yogyakarta, Indonesia
| | - Sri Gunawan
- Department of Agrotechnology, Institut Pertanian Stiper, Yogyakarta 55283, DI Yogyakarta, Indonesia
| | - Idum Satia Santi
- Department of Agrotechnology, Institut Pertanian Stiper, Yogyakarta 55283, DI Yogyakarta, Indonesia
| | - Bambang Heri Isnawan
- Department of Agrotechnology, Universitas Muhammadiyah Yogyakarta, Bantul 55183, DI Yogyakarta, Indonesia
| | - Ernawati Syahruddin Kaseng
- Agricultural Technology Education Department, Faculty of Engineering, Makassar State University, Makassar 90222, South Sulawesi, Indonesia
| | - Early Septiningsih
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Ruzkiah Asaf
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Admi Athirah
- Research Center for Conservation of Marine and Inland Water Resources, National Research and Innovation Agency, Cibinong 16911, West Java, Indonesia
| | - Basri Basri
- Institute of Health Science (STIK), Makassar 90231, South Sulawesi, Indonesia
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11
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Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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12
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Wang C, Hao Z, Huang C, Wang Q, Yan Z, Bai L, Jiang H, Li D. Drinking water treatment residue recycled to synchronously control the pollution of polycyclic aromatic hydrocarbons and phosphorus in sediment from aquatic ecosystems. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128533. [PMID: 35219062 DOI: 10.1016/j.jhazmat.2022.128533] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Great efforts have long been made to control sediment pollution from persistent organic pollutants and phosphorus for aquatic ecosystem restoration. This study proposed a novel recycling of drinking water treatment residue (DWTR) to synchronously control sediment polycyclic aromatic hydrocarbons (PAHs) and phosphorus pollution based on a 350-day incubation test. The results suggested that DWTR addition reduced approximately 88%- 96% of potential bioavailable PAHs and 76% of mobile phosphorus in sediment. The dominant mechanisms for both reductions by DWTR were immobilization, mainly through increasing sediment amorphous aluminum and iron. The tendency of enhanced PAHs degradation by DWTR was also observed, especially for high molecular weight PAHs (e.g., chrysene, indeno(1, 2, 3-cd)pyrene, and benzo(g, hi)perylene), which decreased by approximately 21.1%- 22.0% of the total. Additionally, accompanying a clear increase in the connections of microbial cooccurrence networks, the variations in bioavailable PAHs, amorphous aluminum and iron, and other properties (e.g., pH, nitrogen, and organic matter) significantly (p < 0.01) enhanced Flavobacterium enrichment, although the enrichment of many other microbes potentially related to PAHs degradation (e.g., C1-B045) decreased after DWTR addition. Therefore, DWTR could promote the construction of a "PAHs immobilization with microbial augmentation" system while immobilizing phosphorus in sediment, indicating the high feasibility of controlling multiple sediment pollution.
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Affiliation(s)
- Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Zheng Hao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenghao Huang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianhong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zaisheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Leilei Bai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Helong Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Dongdong Li
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210008, China
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13
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Cao X, Gao X, Zheng K, Wu S, Wu Y, Meng G, Hu Z, Niu Q, Su J. Efficient pollutants removal and microbial flexibility under high-salt gradient of an oilfield wastewater treatment system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153619. [PMID: 35124032 DOI: 10.1016/j.scitotenv.2022.153619] [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: 12/26/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The treatment of hypersaline oilfield wastewater (HSOW) is a challenge due to its complex composition and low biodegradability, especially in coastal areas. In this study, an HSOW treatment system of gas flotation and biochemistry technology combined with constructed wetland (CW) was investigated. The combined treatment system could efficiently remove COD, NH4+-N and oil under high salinity (1.36-2.21 × 104 mg/L), with average removal rates of 98.5%, 99.9% and 96%, respectively. Meanwhile, different salinity shaped particular community structures and functions. The abundance of Marivita, Parvibaculum, etc. was highly correlated with salinity. Co-occurrence network resulted that the microorganisms were highly interconnected, and formed a functional group of petroleum degrading. Pseudomonas, Rosevarius, Alternaria, etc. were the key genera. Moreover, functional prospected revealed that high salinity reduced the energy metabolism activity. This study will optimize the combined process and provide the basis for further extraction of high-efficiency degradation strains for HSOW enhanced treatment.
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Affiliation(s)
- Xiaoqing Cao
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Xue Gao
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Kai Zheng
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Shan Wu
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Yanan Wu
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Guodong Meng
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Zhen Hu
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Qigui Niu
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China
| | - Jixin Su
- School of Environmental Science and Engineering, Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, Shandong University, Qingdao, Shandong 266237, China.
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14
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Prekrasna I, Pavlovska M, Oleinik I, Dykyi E, Slobodnik J, Alygizakis N, Solomenko L, Stoica E. Bacterial communities of the Black Sea exhibit activity against persistent organic pollutants in the water column and sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113367. [PMID: 35272192 DOI: 10.1016/j.ecoenv.2022.113367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The ability of bacteria to degrade organic pollutants influences their fate in the environment, impact on the other biota and accumulation in the food web. The aim of this study was to evaluate abundance and expression activity of the catabolic genes targeting widespread pollutants, such as polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and hexachloro-cyclohexane (HCH) in the Black Sea water column and sediments. Concentrations of PAHs, PCBs and HCH were determined by gas chromatography (GC) coupled to mass spectrometry (MS) and electron capture (ECD) detectors. bphA1, PAH-RHDα, nahAc, linA and linB that encode biphenyl 2,3 dioxygenase, α-subunits of ring hydroxylating dioxygenases, naphthalene dioxygenase, dehydrochlorinase and halidohydrolase correspondently were quantified by quantitative PCR. More recalcitrant PAHs, PCBs and HCH tended to accumulate in the Black Sea environments. In water samples, 3- and 4-ringed PAHs outnumbered naphthalene, while PAHs with > 4 rings prevailed in the sediments. Congeners with 4-8 chlorines with ortho-position of the substituents were the most abundant among the PCBs. β-HCH was determined at highest concentration in water samples, and total amount of HCH exceeded its legacy Environmental Quality Standard value. bphA1, was the most numerous gene in water layers (105 copies/mL) and sediments (105 copies/mg), followed by linB and PAH-RHDα genes (103 copies/mL; 105 copies/mg). The least abundant genes were linA (103 copies/mL; 104 copies/mg) and nahAc (102 copies/mL; 104 copies/mg). The most widely distributed gene bphА1 was one of the least expressed (10-3-10-2 copies/mL; 10-1 copies/mg). The most actively expressed genes were linB (101-102 copies/mL; 103 copies/mg), PAH-RHDα (101 copies/mL; 102 copies/mg) and linA (10-1-100 copies/mL; 100 copies/mg). Interaction of bacteria with PAHs, PCBs and HCH is evidenced by high copy numbers of the catabolic genes that initiate their degradation. More persistent compounds, such as high-molecular weight PAHs or β-HCH are accumulating in the Black Sea water and sediments, albeit microbial activity is directed against them.
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Affiliation(s)
- Ievgeniia Prekrasna
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | - Mariia Pavlovska
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine; National University of Life and Environmental Sciences of Ukraine, 15, Heroiv Oborony Str., 03041 Kyiv, Ukraine
| | - Iurii Oleinik
- Ukrainian Scientific Center of Ecology of the Sea, 89 Frantsuzsky Blvd., 65009 Odessa, Ukraine
| | - Evgen Dykyi
- State Institution National Antarctic Scientific Center, Taras Shevchenko Blvd., 16, 01601 Kyiv, Ukraine
| | | | - Nikiforos Alygizakis
- Environmental Institute, Okruzna 784/42, 97241 Kos, Slovak Republic; Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens Greece
| | - Liudmyla Solomenko
- National University of Life and Environmental Sciences of Ukraine, 15, Heroiv Oborony Str., 03041 Kyiv, Ukraine
| | - Elena Stoica
- National Institute for Marine Research and Development "Grigore Antipa", Blvd. Mamaia no. 300, RO-900581 Constanţa 3, Romania.
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15
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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16
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Tomco PL, Duddleston KN, Driskill A, Hatton JJ, Grond K, Wrenn T, Tarr MA, Podgorski DC, Zito P. Dissolved organic matter production from herder application and in-situ burning of crude oil at high latitudes: Bioavailable molecular composition patterns and microbial community diversity effects. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127598. [PMID: 34798546 DOI: 10.1016/j.jhazmat.2021.127598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/09/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Chemical herders and in-situ burning (ISB) are designed to mitigate the effects that oil spills may have on the high latitude marine environment. Little information exists on the water solubilization of petroleum residues stemming from chemically herded ISB and whether these bioavailable compounds have measurable impacts on marine biota. In this experiment, we investigated the effects of Siltech OP40 and crude oil ISB on a) petroleum-derived dissolved organic matter (DOMHC) composition and b) seawater microbial community diversity over 28 days at 4 °C in aquarium-scale mesocosms. Ultra-high resolution mass spectrometry and fluorescence spectroscopy revealed increases in aromaticity over time, with ISB and ISB+OP40 samples having higher % aromatic classes in the initial incubation periods. ISB+OP40 contained a nearly 12-fold increase in the number of DOMHC formulae relative to those before ISB. 16S rRNA gene sequencing identified differences in microbial alpha diversity between seawater, ISB, OP40, and ISB+OP40. Microbial betadiversity shifts were observed that correlated strongly with aromatic/condensed relative abundance and incubation time. Proteobacteria, specifically from the genera Marinomonas and Perlucidibaca experienced -22 and +24 log2-fold changes in ISB+OP40 vs. seawater, respectively. These findings provide an important opportunity to advance our understanding of chemical herders and ISB in the high latitude marine environment.
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Affiliation(s)
- Patrick L Tomco
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA.
| | - Khrystyne N Duddleston
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
| | - Adrienne Driskill
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
| | - Jasmine J Hatton
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
| | - Kirsten Grond
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
| | - Toshia Wrenn
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA
| | - Matthew A Tarr
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| | - David C Podgorski
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA; Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA; Pontchartrain Institute for Environmental Sciences, Shea Penland Coastal Education and Research Facility, University of New Orleans, New Orleans, LA 70148, USA
| | - Phoebe Zito
- Department of Chemistry, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA; Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; Chemical Analysis & Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA
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17
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Iwabuchi T. Phenanthrene-degrading Sphingobium xenophagum are widely distributed in the western Pacific Ocean. Can J Microbiol 2022; 68:315-328. [PMID: 35044838 DOI: 10.1139/cjm-2021-0177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Six phenanthrene-degrading bacteria were isolated from surface sea water sampled from the western Pacific Ocean. They were identified as Sphingobium xenophagum (formerly Sphingomonas xenophaga) based on morphological, biochemical, and chemical characteristics and 16S rRNA sequences. Salinity ranges for the growth of these isolates were broader than those of seven reported Sphingomonas strains isolated from soil, and the optimum NaCl concentration in the growth medium was higher than that for soil sphingomonads. These isolates also exhibited higher phenanthrene-degrading activity in briny conditions than that of a phenanthrene-degrading Sphingomonas strain isolated from soil. A DNA fragment carrying nah genes, which are encoded on the naphthalene-catabolic plasmid NAH of Pseudomonas putida PpG7, hybridised less strongly with the total DNA of all isolates. Certain genes for phenanthrene degradation were also preliminarily characterised in all isolates. This is the first demonstration that S. xenophagum strains, that are able to degrade phenanthrene, are widely distributed in marine environments, and the growth and phenanthrene-degrading activity of these strains are adapted to briny conditions. Results also suggest that genes for phenanthrene degradation, which are dissimilar to the nah genes, were also ubiquitously distributed in marine strains.
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Affiliation(s)
- Tokuro Iwabuchi
- Tokyo University of Technology, 13097, Faculty of Bioscience and Biotechnology, 1404-1 Katakura, Hachioji, Tokyo, Japan, 192-0914;
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18
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Gomes A, Christensen JH, Gründger F, Kjeldsen KU, Rysgaard S, Vergeynst L. Biodegradation of water-accommodated aromatic oil compounds in Arctic seawater at 0 °C. CHEMOSPHERE 2022; 286:131751. [PMID: 34399257 DOI: 10.1016/j.chemosphere.2021.131751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 06/28/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Oil spills in Arctic marine environments are expected to increase concurrently with the expansion of shipping routes and petroleum exploitation into previously inaccessible ice-dominated regions. Most research on oil biodegradation focusses on the bulk oil, but the fate of the water-accommodated fraction (WAF), mainly composed of toxic aromatic compounds, is largely underexplored. To evaluate the bacterial degradation capacity of such dissolved aromatics in Greenlandic seawater, microcosms consisting of 0 °C seawater polluted with WAF were investigated over a 3-month period. With a half-life (t1/2) of 26 days, m-xylene was the fastest degraded compound, as measured by gas chromatography - mass spectrometry. Substantial slower degradation was observed for ethylbenzene, naphthalenes, phenanthrene, acenaphthylene, acenaphthene and fluorenes with t1/2 of 40-105 days. Colwellia, identified by 16S rRNA gene sequencing, was the main potential degrader of m-xylene. This genus occupied up to 47 % of the bacterial community until day 10 in the microcosms. Cycloclasticus and Zhongshania aliphaticivorans, potentially utilizing one-to three-ringed aromatics, replaced Colwellia between day 10 and 96 and occupied up to 6 % and 23 % of the community, respectively. Although most of the WAF can ultimately be eliminated in microcosms, our results suggest that the restoration of an oil-impacted Arctic environment may be slow as most analysed compounds had t1/2 of over 2-3 months and the detrimental effects of a spill towards the marine ecosystem likely persist during this time.
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Affiliation(s)
- Ana Gomes
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Friederike Gründger
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Centre for Earth Observation Science, CHR Faculty of Environment Earth and Resources, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Leendert Vergeynst
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark; Aarhus University Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark.
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19
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Méndez García M, García de Llasera MP. A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149035. [PMID: 34303250 DOI: 10.1016/j.scitotenv.2021.149035] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.
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Affiliation(s)
- Manuel Méndez García
- Facultad de Química, Departamento de Química Analítica, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D. F. 04510, Mexico
| | - Martha Patricia García de Llasera
- Facultad de Química, Departamento de Química Analítica, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, D. F. 04510, Mexico.
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20
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Lofthus S, Bakke I, Greer CW, Brakstad OG. Biodegradation of weathered crude oil by microbial communities in solid and melted sea ice. MARINE POLLUTION BULLETIN 2021; 172:112823. [PMID: 34454387 DOI: 10.1016/j.marpolbul.2021.112823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Oil spilled in the Arctic may drift into ice-covered areas and become trapped until the ice melts. To determine if exposure to oil during freezing may have a priming effect on degradation of the oil, weathered dispersed oil (2-3 mg/L) was frozen into solid ice for 200 days at -10 °C, then melted and incubated for 64 days at 4 °C. No degradation was measured in oil frozen into ice prior to melting. Both total amount of oil and target compounds were biotransformed by the microbial community from the melted ice. However, oil released from melted ice was degraded at a slower rate than oil incubated in fresh seawater at the same temperature (4 °C), and by a different microbial community. These data suggest negligible biodegradation of oil frozen in sea ice, while oil-degrading bacteria surviving in the ice may contribute to biodegradation when the ice melts.
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Affiliation(s)
- Synnøve Lofthus
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway; SINTEF Ocean AS, Climate and Environment, Trondheim, Norway.
| | - Ingrid Bakke
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Centre, Montreal, Quebec, Canada
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21
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An Intracellular Sensing and Signal Transduction System That Regulates the Metabolism of Polycyclic Aromatic Hydrocarbons in Bacteria. mSystems 2021; 6:e0063621. [PMID: 34609168 PMCID: PMC8547461 DOI: 10.1128/msystems.00636-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many bacteria utilize polycyclic aromatic hydrocarbon (PAH) as carbon and energy sources for growth. These bacteria play an important role in the amelioration of PAH pollution in various environments. However, it is unclear how bacteria sense PAHs and how PAH degradation pathways are regulated via signal transduction. Here, we investigated these mechanisms in Cycloclasticus, a ubiquitous PAH-degrading bacterium in marine environments. We identified the key genes involved in intracellular PAH sensing, signal transduction, and the differential regulation of degradation pathways for each PAH examined. Our results showed that PAHs bind specifically to a diguanylate cyclase PdgC, leading to the generation of cyclic dimeric GMP (c-di-GMP), which subsequently binds to two CRP/FNR family regulators, DPR-1 and DPR-2. c-di-GMP activates the transcription of DPR-1 and DPR-2 to positively regulate degradation pathways specific to pyrene and phenanthrene/naphthalene, respectively. This is the first report of an intracellular signal transduction pathway associated with PAH degradation in bacteria. Our results improve our understanding of the intracellular responses to PAHs. The existence of the identified genes in other bacteria indicates that the strategy described here is widely used by other PAH-degrading bacteria. IMPORTANCE Polycyclic aromatic hydrocarbons (PAHs) are widely distributed and have been found indoors, in the atmosphere, in terrestrial soils, in marine waters and sediments, and even in outer space. Bacteria degrade PAHs via degradation pathways. PAH signal sensing and transduction, as well as the regulation of PAH degradation pathways, are crucial for bacterial PAH biodegradation. However, prior to this study, these processes were poorly known. This study employed multiple molecular approaches to better understand the regulatory networks controlling PAH metabolism in bacteria. This report illustrates, for the first time, PAH-specific intracellular sensing, signal transduction, and metabolic regulatory pathways. Our results will help to increase our understanding of the hydrocarbon-metabolism regulatory network as well as the regulatory intricacies that control microbial biodegradation of organic matter. These key data should be considered to improve the rational design and efficiency of recombinant biodegradable, bacterial biosensors, and biocatalysts in modern green chemistry.
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22
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Saraiva JP, Bartholomäus A, Kallies R, Gomes M, Bicalho M, Coelho Kasmanas J, Vogt C, Chatzinotas A, Stadler P, Dias O, Nunes da Rocha U. OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes. Life Sci Alliance 2021; 4:4/12/e202101167. [PMID: 34580179 PMCID: PMC8500227 DOI: 10.26508/lsa.202101167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/01/2022] Open
Abstract
OrtSuite predicts synergistic species interactions using the genomic potential of microbial communities The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known. OrtSuite is an open-source software available at https://github.com/mdsufz/OrtSuite.
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Affiliation(s)
- João Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | | | - René Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Marta Gomes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Marcos Bicalho
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jonas Coelho Kasmanas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Mathematics and Computer Sciences, University of Sao Paulo, Sao Carlos, Brazil.,Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, University of Leipzig, Leipzig, Germany
| | - Carsten Vogt
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, and Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Santa Fe Institute, Santa Fe, NM, USA
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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23
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Muriel-Millán LF, Millán-López S, Pardo-López L. Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics. Appl Microbiol Biotechnol 2021; 105:7171-7185. [PMID: 34515846 DOI: 10.1007/s00253-021-11569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad Universitaria, CDMX, Mexico.
| | - Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
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24
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Xu T, Liu T, Jiang D, Yuan Z, Jia X. Attainment and characterization of a microbial consortium that efficiently degrades biphenyl and related substances. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Zhou H, Chen C, Zhou S, Bu K, Li P, Lin X, Jiang L, Zhang C. Performance and microbial community analysis of a bio-contact oxidation reactor during the treatment of low-COD and high-salinity oilfield produced water. BIORESOURCE TECHNOLOGY 2021; 335:125267. [PMID: 33992912 DOI: 10.1016/j.biortech.2021.125267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
The multistage bio-contact oxidation reactor (BCOR) is a widely used biological strategy to treat wastewater, however, little is known about the performance and microbial community information of BCOR during the treatment of low-COD and high-salinity oilfield produced water. In this study, the performance of a multistage BCOR in treating produced water was investigated. The result suggested the BCOR could efficiently remove COD, BOD5, NH4+-N, and oil pollutants. Besides, high-throughput sequencing analysis revealed that oil content was the main variable in shaping the community structure. The highest total relative abundance of potential pollutants degraders in first BCOR stage suggested significant role of this stage in pollutants removal. In addition, the correlation analysis disclosed the key functional genera during the degradation process, including Rhodobacter, Citreibacter, and Roseovarius. Moreover, network analysis revealed that the microbial taxa within same module had strong ecological linkages and specific functions.
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Affiliation(s)
- Hanghai Zhou
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Chunlei Chen
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Shaoxiong Zhou
- Xinjiang Keli New Technology Development Co., Ltd., Karamay 834000, Xinjiang, China
| | - Kuiyong Bu
- Xinjiang Keli New Technology Development Co., Ltd., Karamay 834000, Xinjiang, China
| | - Pingyuan Li
- Xinjiang Keli New Technology Development Co., Ltd., Karamay 834000, Xinjiang, China
| | - Xiaoyun Lin
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Lijia Jiang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China
| | - Chunfang Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan 316021, Zhejiang, China.
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26
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Dong C, Lai Q, Liu X, Gu L, Zhang Y, Xie Z, Wang D, Shao Z. Alcanivorax profundimaris sp. nov., a Novel Marine Hydrocarbonoclastic Bacterium Isolated from Seawater and Deep-Sea Sediment. Curr Microbiol 2021; 78:1053-1060. [PMID: 33599831 DOI: 10.1007/s00284-020-02322-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
Two novel Alcanivorax-related strains, designated ST75FaO-1T and 521-1, were isolated from the seawater of the South China Sea and the deep-sea sediment of the West Pacific Ocean, respectively. Both strains are Gram-stain-negative, rod-shaped, and non-motile, and grow at 10-40 °C, pH 5.0-10.0, in the presence of 1.0-15.0% (w/v) NaCl. Their 16S rRNA gene sequences showed 99.9% similarity. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that both strains belong to the genus Alcanivorax, and share 92.9-98.1% sequence similarity with all valid type strains of this genus, with the highest similarity being to type strain Alcanivorax venustensis DSM 13974T (98.0-98.1%). Digital DNA-DNA hybridization (dDDH) and average nucleotide identity values between strains ST75FaO-1T and 521-1 were 75.7% and 97.1%, respectively, while the corresponding values with A. venustensis DSM 13974T were only 25.4-25.6% and 82.4-82.7%, respectively. The two strains contained similar major cellular fatty acids including C16:0, C18:1 ω7c/ω6c, C19:0 cyclo ω8c, C16:1 ω7c/ω6c, C12:0 3-OH, and C12:0. The genomic G + C content of strains ST75FaO-1T and 521-1 were 66.3% and 66.1%, respectively. Phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and one unidentified polar lipid were present in both strains. On the basis of phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Alcanivorax, for which the name Alcanivorax profundimaris sp. nov. is proposed. The type strain is ST75FaO-1T (= MCCC 1A17714T = KCTC 82142T).
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Li Gu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China
| | - Yu Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Zhangxian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Dazhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, Fujian, People's Republic of China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
- Fujian Key Laboratory of Marine Genetic Resources, No. 184, Daxue Road, Siming District, Xiamen, 361005, Fujian, People's Republic of China.
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27
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Characterisation of hydrocarbon degradation, biosurfactant production, and biofilm formation in Serratia sp. Tan611: a new strain isolated from industrially contaminated environment in Algeria. Antonie van Leeuwenhoek 2021; 114:411-424. [PMID: 33587226 DOI: 10.1007/s10482-021-01527-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/22/2021] [Indexed: 10/22/2022]
Abstract
A novel bacterial strain was isolated from industrially contaminated waste water. In the presence of crude oil, this strain was shown to reduce the rate of total petroleum hydrocarbons (TPH) up to 97.10% in 24 h. This bacterium was subsequently identified by 16S rRNA gene sequence analysis and affiliated to the Serratia genus by the RDP classifier. Its genome was sequenced and annotated, and genes coding for catechol 1,2 dioxygenase and naphthalene 1,2-dioxygenase system involved in aromatic hydrocarbon catabolism, and LadA-type monooxygenases involved in alkane degradation, were identified. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of crude oil after biological treatment showed that Serratia sp. Tan611 strain was able to degrade n-alkanes (from C13 to C25). This bacterium was also shown to produce a biosurfactant, the emulsification index (E24) reaching 43.47% and 65.22%, against vegetable and crude oil, respectively. Finally, the formation of a biofilm was increased in the presence of crude oil. These observations make Serratia sp. Tan611 a good candidate for hydrocarbon bioremediation.
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28
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Li Q, Li J, Jiang L, Sun Y, Luo C, Zhang G. Diversity and structure of phenanthrene degrading bacterial communities associated with fungal bioremediation in petroleum contaminated soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123895. [PMID: 33264959 DOI: 10.1016/j.jhazmat.2020.123895] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/14/2020] [Accepted: 08/29/2020] [Indexed: 06/12/2023]
Abstract
Fungal bioremediation is a promising technique for the cleanup of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). However, due to limited understanding of the composition and dynamics of the native PAH-degrading microorganisms in contaminated sites, its application has been difficult. In the present study, DNA stable-isotope probing was performed to identify indigenous phenanthrene (PHE)-degrading bacteria and determine their diversity during the fungal bioremediation process. The results showed a total of 14 operational taxonomic units (OTUs) enriched in the heavy DNA fractions, which were related to seven genera (Sphingomonas, Sphingobacterium, Acidovorax, Massilia, Flavobacterium, Cupriavidus, Aeromicrobium, and unclassified Chitinophagaceae). Along with enhanced efficiency of PHE removal, the number and diversity of indigenous PHE-degrading bacteria in soil bioaugmented with fungi were significantly increased. Furthermore, based on the results of linear model analysis, we found that PHE degraders affiliated with the genus Sphingomonas were significantly enriched during fungal bioremediation. Moreover, fungal bioaugmentation promoted indigenous functional Proteobacteria involved in PAH degradation through co-metabolism, suggesting that PAH biodegradation was attributable to cooperative metabolism by fungi and indigenous bacteria. Our findings provide new insights into the diversity of PHE-degrading communities and support a more comprehensive view of the fungal bioremediation process.
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Affiliation(s)
- Qiqian Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; College of Chemical and Biological Engineering, Hechi University, Yizhou, 546300, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Yingtao Sun
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China; College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
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29
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Suárez-Moo P, Lamelas A, Garcia-Bautista I, Barahona-Pérez LF, Sandoval-Flores G, Valdes-Lozano D, Toledano-Thompson T, Polanco-Lugo E, Valdez-Ojeda R. Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico. PeerJ 2020; 8:e10339. [PMID: 33354414 PMCID: PMC7731659 DOI: 10.7717/peerj.10339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
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Affiliation(s)
- Pablo Suárez-Moo
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Itza Garcia-Bautista
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | | | - Gloria Sandoval-Flores
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autonoma de Tamaulipas, Merida, Yucatan, Mexico
| | - David Valdes-Lozano
- Centro de Investigación y de Estudios Avanzados, Insituto Politecnico Nacional, Merida, Yucatan, Mexico
| | - Tanit Toledano-Thompson
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | - Erik Polanco-Lugo
- Campus de Ciencias Biológicas y Agropecuarias,, Universidad Autonoma de Yucatan, Merida, Yucatan, Mexico
| | - Ruby Valdez-Ojeda
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
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30
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Li X, Zhang X, Li L, Lin C, Dong W, Shen W, Yong X, Jia H, Wu X, Zhou J. Anaerobic biodegradation of pyrene by Klebsiella sp. LZ6 and its proposed metabolic pathway. ENVIRONMENTAL TECHNOLOGY 2020; 41:2130-2139. [PMID: 30522413 DOI: 10.1080/09593330.2018.1556348] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Pyrene is one of the polycyclic aromatic hydrocarbons, which are a potential threat to ecosystems due to their mutagenicity, carcinogenicity, and teratogenicity. In this study, several bacteria were isolated from oil contaminated sludge and their capacity to biodegrade pyrene was investigated. Of these bacteria, the monoculture strain LZ6 showed the highest pyrene anaerobic biodegradation rate of 33% after 30 days when the initial concentration was 50 mg/L, and was identified as Klebsiella sp. LZ6 by morphological observation, the GENIII technology of Biolog, and 16S rDNA gene sequence analysis. The influence of various culture parameters on the biodegradation of pyrene were evaluated, and Klebsiella sp. LZ6 all showed the high degradation rate at an inoculum of 10-20% (v/v), pH 6.0-8.4, temperature 30-38°C, and initial pyrene concentration of 50-150 mg/L. The intermediate metabolites of the anaerobic biodegradation were analyzed by GC-MS. Several metabolites were identified, such as pyrene, 4,5-dihydro-, phenanthrene, dibenzo-p-dioxin, and 4-hydroxycinnamate acid. The anaerobic metabolic pathway for the degradation of pyrene was inferred by the products. It seems that pyrene was first reduced to pyrene,4,5-dihydro- by the adding of two hydrogen atoms, and then the carbon-carbon bond cleavage at saturated carbon atoms generated phenanthrene.
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Affiliation(s)
- Xiang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xueying Zhang
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Lian Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Chaoba Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Weiliang Dong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Weiran Shen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- College of Environment, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xiaoyu Yong
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Xiayuan Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Jun Zhou
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
- Bioenergy Research Institute, Nanjing Tech University, Nanjing, People's Republic of China
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Highlighting the Crude Oil Bioremediation Potential of Marine Fungi Isolated from the Port of Oran (Algeria). DIVERSITY 2020. [DOI: 10.3390/d12050196] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
While over hundreds of terrestrial fungal genera have been shown to play important roles in the biodegradation of hydrocarbons, few studies have so far focused on the fungal bioremediation potential of petroleum in the marine environment. In this study, the culturable fungal communities occurring in the port of Oran in Algeria, considered here as a chronically-contaminated site, have been mainly analyzed in terms of species richness. A collection of 84 filamentous fungi has been established from seawater samples and then the fungi were screened for their ability to utilize and degrade crude oil. A total of 12 isolates were able to utilize crude oil as a unique carbon source, from which 4 were defined as the most promising biodegrading isolates based on a screening test using 2,6-dichlorophenol indophenol as a proxy to highlight their ability to metabolize crude oil. The biosurfactant production capability was also tested and, interestingly, the oil spreading and drop-collapse tests highlighted that the 4 most promising isolates were also those able to produce the highest quantity of biosurfactants. The results generated in this study demonstrate that the most promising fungal isolates, namely Penicillium polonicum AMF16, P. chrysogenum AMF47 and 2 isolates (AMF40 and AMF74) affiliated to P. cyclopium, appear to be interesting candidates for bioremediation of crude oil pollution in the marine environment within the frame of bioaugmentation or biostimulation processes.
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Lofthus S, Bakke I, Tremblay J, Greer CW, Brakstad OG. Biodegradation of weathered crude oil in seawater with frazil ice. MARINE POLLUTION BULLETIN 2020; 154:111090. [PMID: 32319919 DOI: 10.1016/j.marpolbul.2020.111090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
As ice extent in the Arctic is declining, oil and gas activities will increase, with higher risk of oil spills to the marine environment. To determine biotransformation of dispersed weathered oil in newly formed ice, oil dispersions (2-3 ppm) were incubated in a mixture of natural seawater and frazil ice for 125 days at -2 °C. Dispersed oil in seawater without frazil ice were included in the experimental setup. Presence or absence of frazil ice was a strong driver for microbial community structures and affected the rate of oil degradation. n-alkanes were degraded faster in the presence of frazil ice, the opposite was the case for naphthalenes and 2-3 ring PAHs. No degradation of 4-6 ring PAHs was observed in any of the treatments. The total petroleum oil was not degraded to any significant degree, suggesting that oil will freeze into the ice matrix and persist throughout the icy season.
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Affiliation(s)
- Synnøve Lofthus
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway; SINTEF Ocean AS, Environment and New Resources, Trondheim, Norway.
| | - Ingrid Bakke
- Norwegian University of Science and Technology, Department of Biotechnology and Food Science, Trondheim, Norway
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada
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The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems. ISME JOURNAL 2020; 14:1994-2006. [PMID: 32355200 PMCID: PMC7368058 DOI: 10.1038/s41396-020-0662-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/24/2020] [Accepted: 04/15/2020] [Indexed: 11/08/2022]
Abstract
Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly 13C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.
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Valencia-Agami SS, Cerqueda-García D, Putzeys S, Uribe-Flores MM, García-Cruz NU, Pech D, Herrera-Silveira J, Aguirre-Macedo ML, García-Maldonado JQ. Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale. Microorganisms 2019; 7:microorganisms7100441. [PMID: 31614583 PMCID: PMC6843455 DOI: 10.3390/microorganisms7100441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/28/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r2 = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r2 = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.
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Affiliation(s)
- Sonia S Valencia-Agami
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Sébastien Putzeys
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - María Magdalena Uribe-Flores
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Norberto Ulises García-Cruz
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Lerma Campeche, Campeche 24500, Mexico.
| | - Jorge Herrera-Silveira
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - M Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
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Complete Genome Sequence of Cycloclasticus sp. Strain PY97N, Which Includes Two Heavy Metal Resistance Genomic Islands. Microbiol Resour Announc 2019; 8:8/40/e00771-19. [PMID: 31582435 PMCID: PMC6776764 DOI: 10.1128/mra.00771-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the complete genome sequence of fluoranthene-consuming Cycloclasticus sp. strain PY97N. This strain has one circular chromosome with a G+C content of 42.06%. Moreover, two genomic islands were identified as putative conjugative elements. These genomic details are expected to inform our understanding of the remarkable catabolic capacities of organisms of the Cycloclasticus lineage. We present the complete genome sequence of fluoranthene-consuming Cycloclasticus sp. strain PY97N. This strain has one circular chromosome with a G+C content of 42.06%. Moreover, two genomic islands were identified as putative conjugative elements. These genomic details are expected to inform our understanding of the remarkable catabolic capacities of organisms of the Cycloclasticus lineage.
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36
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Zhang S, Hu Z, Wang H. Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment. ENVIRONMENT INTERNATIONAL 2019; 129:308-319. [PMID: 31150973 DOI: 10.1016/j.envint.2019.05.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/15/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.
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Affiliation(s)
- Shuangfei Zhang
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou 515063, China.
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37
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Uribe‐Flores M, Cerqueda‐García D, Hernández‐Nuñez E, Cadena S, García‐Cruz N, Trejo‐Hernández M, Aguirre‐Macedo M, García‐Maldonado J. Bacterial succession and co‐occurrence patterns of an enriched marine microbial community during light crude oil degradation in a batch reactor. J Appl Microbiol 2019; 127:495-507. [DOI: 10.1111/jam.14307] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/15/2019] [Accepted: 05/06/2019] [Indexed: 12/17/2022]
Affiliation(s)
- M.M. Uribe‐Flores
- Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - D. Cerqueda‐García
- Consorcio de Investigación del Golfo de México (CIGoM) Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - E. Hernández‐Nuñez
- CONACYT – Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - S. Cadena
- Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - N.U. García‐Cruz
- Consorcio de Investigación del Golfo de México (CIGoM) Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - M.R. Trejo‐Hernández
- Centro de Investigación en Biotecnología Universidad Autónoma del Estado de Morelos Cuernavaca, Morelos Mexico
| | - M.L. Aguirre‐Macedo
- Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
| | - J.Q. García‐Maldonado
- CONACYT – Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV) Unidad Mérida Mérida Mexico
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Haleyur N, Shahsavari E, Jain SS, Koshlaf E, Ravindran VB, Morrison PD, Osborn AM, Ball AS. Influence of bioaugmentation and biostimulation on PAH degradation in aged contaminated soils: Response and dynamics of the bacterial community. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 238:49-58. [PMID: 30844545 DOI: 10.1016/j.jenvman.2019.02.115] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) represent a group of hazardous compounds that are ubiquitous and persistent. The main aim of this study was to investigate the degradation of PAHs in chronically contaminated, aged and weathered soils obtained from a former gas plant of Australia. Biostimulation and bioaugmentation using individual isolates (Rhodococcus sp. (NH2), Achromobacter sp. (NH13), Oerskovia paurometabola (NH11), Pantoea sp. (NH15), Sejongia sp. (NH20), Microbacterium maritypicum (NH30) and Arthrobacter equi (NH21)) and a consortium of these isolates were tested during mesocosm studies. A significant reduction (99%) in PAH concentration was observed in all the treatments. In terms of the abundance of PAH-degrading genes and microbial community structure during PAH degradation, qPCR results revealed that Gram-positive bacteria were dominant over other bacterial communities in all the treatments. 16S sequencing results revealed that the inoculated organisms did not establish themselves during the treatment. However, substantial bacterial community changes during the treatments were observed, suggesting that the natural community exhibited sufficient resilience and diversity to enable an active, but changing degrading community at all stages of the degradation process. Consequently, biostimulation is proposed as the best strategy to remediate PAHs in aged, weathered and chronically contaminated soils.
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Affiliation(s)
- Nagalakshmi Haleyur
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
| | - Esmaeil Shahsavari
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Sohni Singh Jain
- Department of Electrical and Biomedical Engineering, School of Engineering, RMIT University, Bundoora West, VIC, 3083, Australia
| | - Eman Koshlaf
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Vivek B Ravindran
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Paul D Morrison
- Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - A Mark Osborn
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia
| | - Andrew S Ball
- School of Science, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia; Centre for Environmental Sustainability and Remediation, RMIT University, Bundoora, Melbourne, VIC, 3083, Australia.
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Wang Z, Wang W, Li Y, Yang Q. Co-metabolic degradation of naphthalene and pyrene by acclimated strain and competitive inhibition kinetics. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 54:505-513. [PMID: 30909840 DOI: 10.1080/03601234.2019.1586033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A dominant strain named Ochrobactrum sp. was isolated from soils contaminated with coal tar. The batch experiments were carried out to study the co-metabolic degradation of pyrene by Ochrobactrum MB-2 with naphthalene as the main substrate and the effects of several significant parameters such as naphthalene concentration, pH and temperature on removal efficiency were explored. The results showed that Ochrobactrum MB-2 effectively degraded naphthalene and that the addition of naphthalene favored the degradation of pyrene. The maximum elimination efficiency of naphthalene (10 mg L-1) and pyrene (1 mg L-1) was achieved at pH 7 and 25 °C, and the corresponding values were 99 and 41%, respectively. A competitive inhibition model based on the Michaelis-Menten equation was used to characterize the inhibitory effect of pyrene on naphthalene degradation. The values of the half-saturation coefficient for naphthalene (KS) and dissociation constant of enzyme-inhibitor complex (KC) were determined to be 4.93 and 1.38 mg L-1, respectively.
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Affiliation(s)
- Zhen Wang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Wenjing Wang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Yalong Li
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
| | - Qi Yang
- a School of Water Resources and Environment , China University of Geosciences , Beijing , China
- b Beijing Key Laboratory of Water Resource & Environmental Engineering , China University of Geosciences , Beijing , China
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Kosek K, Kozioł K, Luczkiewicz A, Jankowska K, Chmiel S, Polkowska Ż. Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:1585-1596. [PMID: 30446169 DOI: 10.1016/j.scitotenv.2018.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 06/09/2023]
Abstract
Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L-1 (R12) and 3901 ng L-1 (R13) in June, and 2179 ng L-1 (R12) and 1349 ng L-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L-1 in June and 0.35 mg L-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.
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Affiliation(s)
- Klaudia Kosek
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Krystyna Kozioł
- Institute of Geography, Faculty of Geography and Biology, Pedagogical University in Cracow, Podchorążych 2, Cracow 30-084, Poland; Institute of Geophysics, Polish Academy of Sciences, 64 Księcia Janusza St., Warsaw 01-452, Poland
| | - Aneta Luczkiewicz
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Katarzyna Jankowska
- Department of Water and Waste-Water Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Stanisław Chmiel
- Faculty of Earth Sciences and Spatial Management, Maria Curie-Skłodowska University, 2 C-D Kraśnicka Ave., Lublin 20-718, Poland
| | - Żaneta Polkowska
- Department of Analytical Chemistry, Faculty of Chemistry, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Lu H, Wang W, Li F, Zhu L. Mixed-surfactant-enhanced phytoremediation of PAHs in soil: Bioavailability of PAHs and responses of microbial community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:658-666. [PMID: 30759591 DOI: 10.1016/j.scitotenv.2018.10.385] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/22/2018] [Accepted: 10/28/2018] [Indexed: 06/09/2023]
Abstract
The present study was conducted to explore the mechanisms of surfactant-enhanced phytoremediation of soils contaminated with polycyclic aromatic hydrocarbons (PAHs), focusing on the bioavailability of PAHs and microbial diversity. We investigated the remediation efficiencies of phenanthrene and pyrene after the addition of mixed surfactants (sodium dodecyl benzene sulfonate (SDBS) and Tween 80) of different ratios (1:1, 1:2, and 2:1) at the concentration of 100 mg/kg to soils cultured with ryegrass (Lolium multiflorum L.). The fractions of phenanthrene and pyrene were determined using a sequential extraction method, and the microbial diversity was evaluated using 16S rRNA gene high-throughput sequencing. The results showed that mixed surfactants could enhance the remediation efficiencies of PAHs, and mainly occurred in the initial 21 days. Mixed surfactants at the ratio of 1:1 (HM1) showed the best remediation efficiency in enhancing the dissipation of pyrene in 21 days. Mixed surfactants showed little effects on the removal of phenanthrene. In general, HM1 significantly decreased the bioavailable, bound and residual fractions of pyrene; additionally, higher abundances of PAH-degradation bacteria and degradation-related genes were observed. Pearson correlation analysis among PAH degraders, degradation-related genes and bioavailable fraction of PAHs was performed. Our results indicated that mixed surfactants could promote the transformation of pyrene from the bound and residual fractions to bioavailable fractions and enhance the abundances of PAH degradation bacteria and PAH degradation-related genes, thereby enhancing the degradation of pyrene.
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Affiliation(s)
- Hainan Lu
- Dept Environm Sci, Zhejiang Univ, Hangzhou 310058, Zhejiang, China; Zhejiang Prov Key Lab Organ Pollut Proc Control, Hangzhou 310058, Zhejiang, China
| | - Wei Wang
- Dept Environm Sci, Zhejiang Univ, Hangzhou 310058, Zhejiang, China; Zhejiang Prov Key Lab Organ Pollut Proc Control, Hangzhou 310058, Zhejiang, China
| | - Feng Li
- Dept Environm Sci & Engn, Xiangtan Univ, Xiangtan 411105, China
| | - Lizhong Zhu
- Dept Environm Sci, Zhejiang Univ, Hangzhou 310058, Zhejiang, China; Zhejiang Prov Key Lab Organ Pollut Proc Control, Hangzhou 310058, Zhejiang, China.
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n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil. Chin J Chem Eng 2019. [DOI: 10.1016/j.cjche.2018.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Vergeynst L, Christensen JH, Kjeldsen KU, Meire L, Boone W, Malmquist LMV, Rysgaard S. In situ biodegradation, photooxidation and dissolution of petroleum compounds in Arctic seawater and sea ice. WATER RESEARCH 2019; 148:459-468. [PMID: 30408732 DOI: 10.1016/j.watres.2018.10.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
In pristine sea ice-covered Arctic waters the potential of natural attenuation of oil spills has yet to be uncovered, but increasing shipping and oil exploitation may bring along unprecedented risks of oil spills. We deployed adsorbents coated with thin oil films for up to 2.5 month in ice-covered seawater and sea ice in Godthaab Fjord, SW Greenland, to simulate and investigate in situ biodegradation and photooxidation of dispersed oil. GC-MS-based chemometric methods for oil fingerprinting were used to identify characteristic signatures for dissolution, biodegradation and photooxidation. In sub-zero temperature seawater, fast degradation of n-alkanes was observed with estimated half-life times of ∼7 days. PCR amplicon sequencing and qPCR quantification of bacterial genes showed that a biofilm with a diverse microbial community colonised the oil films, yet a population related to the psychrophilic hydrocarbonoclastic gammaproteobacterium Oleispira antarctica seemed to play a key role in n-alkane degradation. Although Oleispira populations were also present in sea ice, we found that biofilms in sea ice had 25 to 100 times lower bacterial densities than in seawater, which explained the non-detectable n-alkane degradation in sea ice. Fingerprinting revealed that photooxidation, but not biodegradation, transformed polycyclic aromatic compounds through 50 cm-thick sea ice and in the upper water column with removal rates up to ∼1% per day. Overall, our results showed a fast biodegradation of n-alkanes in sea ice-covered seawater, but suggested that oils spills will expose the Arctic ecosystem to bio-recalcitrant PACs over prolonged periods of time.
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Affiliation(s)
- Leendert Vergeynst
- Arctic Research Centre, Aarhus University, Aarhus, Denmark; Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Urup Kjeldsen
- Section for Microbiology and Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lorenz Meire
- Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk, Greenland; Department of Estuarine and Delta Systems, Royal Netherlands Institute of Sea Research, Utrecht University, Yerseke, Netherlands
| | - Wieter Boone
- Centre for Earth Observation Science, University of Manitoba, Winnipeg, Canada
| | - Linus M V Malmquist
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Aarhus University, Aarhus, Denmark; Centre for Earth Observation Science, University of Manitoba, Winnipeg, Canada
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Wang W, Wang L, Shao Z. Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 PMCID: PMC6193391 DOI: 10.1128/aem.01261-18 10.1016/j.biotechadv.2015.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 06/12/2023] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by CycloclasticusCycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in CycloclasticusIMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lin Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, SOA, Xiamen, China
- Xiamen Key Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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45
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Polycyclic Aromatic Hydrocarbon (PAH) Degradation Pathways of the Obligate Marine PAH Degrader Cycloclasticus sp. Strain P1. Appl Environ Microbiol 2018; 84:AEM.01261-18. [PMID: 30171002 DOI: 10.1128/aem.01261-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteria play an important role in the removal of polycyclic aromatic hydrocarbons (PAHs) from polluted environments. In marine environments, Cycloclasticus is one of the most prevalent PAH-degrading bacterial genera. However, little is known regarding the degradation mechanisms for multiple PAHs by Cycloclasticus Cycloclasticus sp. strain P1 was isolated from deep-sea sediments and is known to degrade naphthalene, phenanthrene, pyrene, and other aromatic hydrocarbons. Here, six ring-hydroxylating dioxygenases (RHDs) were identified in the complete genome of Cycloclasticus sp. P1 and were confirmed to be involved in PAH degradation by enzymatic assays. Further, five gene clusters in its genome were identified to be responsible for PAH degradation. Degradation pathways for naphthalene, phenanthrene, and pyrene were elucidated in Cycloclasticus sp. P1 based on genomic and transcriptomic analysis and characterization of an interconnected metabolic network. The metabolic pathway overlaps in many steps in the degradation of pyrene, phenanthrene, and naphthalene, which were validated by the detection of metabolic intermediates in cultures. This study describes a pyrene degradation pathway for Cycloclasticus. Moreover, the study represents the integration of a PAH metabolic network that comprises pyrene, phenanthrene, and naphthalene degradation pathways. Taken together, these results provide a comprehensive investigation of PAH metabolism in Cycloclasticus IMPORTANCE PAHs are ubiquitous in the environment and are carcinogenic compounds and tend to accumulate in food chains due to their low bioavailability and poor biodegradability. Cycloclasticus is an obligate marine PAH degrader and is widespread in marine environments, while the PAH degradation pathways remain unclear. In this report, the degradation pathways for naphthalene, phenanthrene, and pyrene were revealed, and an integrated PAH metabolic network covering pyrene, phenanthrene, and naphthalene was constructed in Cycloclasticus This overlapping network provides streamlined processing of PAHs to intermediates and ultimately to complete mineralization. Furthermore, these results provide an additional context for the prevalence of Cycloclasticus in oil-polluted marine environments and pelagic settings. In conclusion, these analyses provide a useful framework for understanding the cellular processes involved in PAH metabolism in an ecologically important marine bacterium.
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46
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Yang R, Liu G, Chen T, Zhang W, Zhang G, Chang S. The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil. Stand Genomic Sci 2018; 13:23. [PMID: 30338026 PMCID: PMC6180392 DOI: 10.1186/s40793-018-0328-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 09/28/2018] [Indexed: 12/02/2022] Open
Abstract
Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.
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Affiliation(s)
- Ruiqi Yang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
| | - Sijing Chang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000 Gansu Province China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000 China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049 China
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47
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Żur J, Piński A, Marchlewicz A, Hupert-Kocurek K, Wojcieszyńska D, Guzik U. Organic micropollutants paracetamol and ibuprofen-toxicity, biodegradation, and genetic background of their utilization by bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:21498-21524. [PMID: 29923050 PMCID: PMC6063337 DOI: 10.1007/s11356-018-2517-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/07/2018] [Indexed: 05/26/2023]
Abstract
Currently, analgesics and nonsteroidal anti-inflammatory drugs (NSAIDs) are classified as one of the most emerging group of xenobiotics and have been detected in various natural matrices. Among them, monocyclic paracetamol and ibuprofen, widely used to treat mild and moderate pain are the most popular. Since long-term adverse effects of these xenobiotics and their biological and pharmacokinetic activity especially at environmentally relevant concentrations are better understood, degradation of such contaminants has become a major concern. Moreover, to date, conventional wastewater treatment plants (WWTPs) are not fully adapted to remove that kind of micropollutants. Bioremediation processes, which utilize bacterial strains with increased degradation abilities, seem to be a promising alternative to the chemical methods used so far. Nevertheless, despite the wide prevalence of paracetamol and ibuprofen in the environment, toxicity and mechanism of their microbial degradation as well as genetic background of these processes remain not fully characterized. In this review, we described the current state of knowledge about toxicity and biodegradation mechanisms of paracetamol and ibuprofen and provided bioinformatics analysis concerning the genetic bases of these xenobiotics decomposition.
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Affiliation(s)
- Joanna Żur
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Artur Piński
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Ariel Marchlewicz
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Katarzyna Hupert-Kocurek
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Danuta Wojcieszyńska
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Urszula Guzik
- Department of Biochemistry, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
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Brakstad OG, Davies EJ, Ribicic D, Winkler A, Brönner U, Netzer R. Biodegradation of dispersed oil in natural seawaters from Western Greenland and a Norwegian fjord. Polar Biol 2018. [DOI: 10.1007/s00300-018-2380-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Dong C, Liu R, Lai Q, Liu Y, Shao Z. Thalassospira marina sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2018; 68:2943-2948. [PMID: 30028290 DOI: 10.1099/ijsem.0.002925] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10-40 °C, pH 5-10 and in the presence of 0-15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira, and shared 97.5-98.3 % sequence similarity to all other validly type strains of the genus Thalassospira, and the highest similarity was to the type strain Thalassospira povalilyticaZumi 95T (98.3 %), followed by Thalassospira australica NP3b2T (98.2 %). The digital DNA-DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilyticaZumi 95T and T. australica NP3b2T were only 20.5-20.7 % and 20.4-20.5 %, respectively. The two strains possess similar major cellular fatty acids including C18 : 1ω7c, C16 : 0, C19 : 0ω8c cyclo, C18 : 1 2-OH and C17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).
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Affiliation(s)
- Chunming Dong
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Yang Liu
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, The Third Institute of Oceanography, State Oceanic Administration; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources; Fujian Collaborative Innovation Center of Marine Biological Resources; South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Xiamen 361005, PR China
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50
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Noh J, Kim H, Lee C, Yoon SJ, Chu S, Kwon BO, Ryu J, Kim JJ, Lee H, Yim UH, Giesy JP, Khim JS. Bioaccumulation of Polycyclic Aromatic Hydrocarbons (PAHs) by the Marine Clam, Mactra veneriformis, Chronically Exposed to Oil-Suspended Particulate Matter Aggregates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7910-7920. [PMID: 29898595 DOI: 10.1021/acs.est.7b06692] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Dispersion and biodegradation of petroleum hydrocarbons are significantly enhanced by formation of oil-suspended particulate matter aggregates (OSAs), but little is known about their adverse effects on benthic invertebrates or microbes. In this study, we investigated: (1) bioaccumulation of polycyclic aromatic hydrocarbons (PAHs) by the marine bivalve, Mactra veneriformis and (2) changes in composition and relative abundances of microbes, during 50-d of an OSAs feeding experiment. Total concentrations of PAHs increased more rapidly during the first week of exposure, peaked at Day 30, then gradually declined to the end of experiment. While bioaccumulation of PAHs by clams varied among the 20 target compounds, two major groups of PAHs were identified by cluster analysis. One group including 3-methylphenanthrene, 1,6-dimethylphenanthrene, 1,2,6,9-tetramethylphenanthrene, and benzo[ a]anthracene showed a fairly constant rate of accumulation, while the second group including 2-methyldibenzothiophene, 2,4-dimethyldibenzothiophene, 2,4,7-trimethyldibenzothiophene, 3-methylchrysene, 6-ethylchrysene, and 1,3,6-trimethylchrysene exhibited a bell-shaped pattern. Bioaccumulation of PAHs by clams was dependent on changes in abundance of Gammaproteobacteria, indicating active degradations of hydrocarbons by selected species. Six key species included: Porticoccus litoralis, Porticoccus hydrocarbonoclasticus, Cycloclasticus spirillensus, Alcanivorax borkumensis, Alcanivorax dieselolei, and Alkalimarinus sediminis. These results are the first to demonstrate interactions of OSAs and macrofauna/microbe in oil cleanup operations.
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Affiliation(s)
- Junsung Noh
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Hosang Kim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Changkeun Lee
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seo Joon Yoon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Seungoh Chu
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Bong-Oh Kwon
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
| | - Jongseong Ryu
- Department of Marine Biotechnology , Anyang University , Ganghwa-gun , Incheon Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering , Korea University , Seoul , Republic of Korea
| | - Un Hyuk Yim
- Oil and POPs Research Group , Korea Institute of Ocean Science and Technology , Geoje , Republic of Korea
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre , University of Saskatchewan , Saskatoon , Saskatchewan Canada
- Department of Zoology, and Center for Integrative Toxicology , Michigan State University , East Lansing , Michigan United States
- School of Biological Sciences , University of Hong Kong , Hong Kong , SAR China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment , Nanjing University , Nanjing , People's Republic of China
| | - Jong Seong Khim
- School of Earth and Environmental Sciences & Research Institute of Oceanography , Seoul National University , Seoul , Republic of Korea
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