1
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Miles SM, Balaberda AL, Leshuk TMC, Peru K, Headley J, Gu F, Ulrich AC. A multi-step approach: Coupling of biodegradation and UV photocatalytic oxidation TiO 2 for the treatment of naphthenic acid fraction compounds in oil sands process-affected water. CHEMOSPHERE 2024; 361:142502. [PMID: 38838863 DOI: 10.1016/j.chemosphere.2024.142502] [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: 03/05/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Bitumen extraction in Alberta's oil sands region uses large volumes of water, leading to an abundance of oil sands process-affected water (OSPW). OSPW contains naphthenic acid fraction compounds (NAFCs) which have been found to contribute to OSPW toxicity. This study utilized a multistep treatment, coupling biological degradation with UV photocatalytic oxidation, and nutrient addition to boost the native microbial community's degradation capacity. OSPW initially contained 40-42 mg/L NAFCs with a toxicity of 3.8-3.9 TU. Initial biodegradation (Step 1) was used to remove the easily biodegradable NAFCs (11-25% removal), followed by a light or heavy dose of oxidation (Step 2) to breakdown the recalcitrant NAFCs (66-82% removal). Lastly, post-oxidation biodegradation with nutrients (Step 3) removed the residual bioavailable NAFCs (16-31% removal). By the end of the multistep treatment, the final NAFC concentrations and toxicity ranged from 5.3 to 6.8 mg/L and 1.1-1.2 TU. Analysis showed that OPSW was limited in phosphorus (below detection limit), and the addition of nutrients improved the degradation of NAFCs. Two treatments throughout the multistep treatment never received nutrients and showed minimal NAFC degradation post-oxidation. The native microbial community survived the stress from UV photocatalytic oxidation as seen by the post-oxidation NAFC biodegradation. Microbial community diversity was reduced considerably following oxidation, but increased with nutrient addition. The microbial community consisted predominately of Proteobacteria (Gammaproteobacteria and Alphaproteobacteria), and the composition shifted depending on the level of oxidation received. Possible NAFC-degrading microbes identified after a light oxidation dose included Pseudomonas, Acinetobacter and Xanthomonadales, while Xanthobacteracea and Rhodococcus were the dominant microbes after heavy oxidation. This experiment confirms that the microbial community is capable of degrading NAFCs and withstanding oxidative stress, and that degradation is further enhanced with the addition of nutrients.
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Affiliation(s)
- Sarah M Miles
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Amy-Lynne Balaberda
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Timothy M C Leshuk
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Department of Chemical Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Kerry Peru
- Water Science and Technology Directorate, Environment and Climate Change Canada, Saskatoon, SK S7N 3H5, Canada
| | - John Headley
- Water Science and Technology Directorate, Environment and Climate Change Canada, Saskatoon, SK S7N 3H5, Canada
| | - Frank Gu
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; Department of Chemical Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada.
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2
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Xu L, Song S, Graham NJD, Yu W. Simultaneous removal of NOM and sulfate in a bioelectrochemical integrated biofilter treating reclaimed water. WATER RESEARCH 2024; 252:121193. [PMID: 38290239 DOI: 10.1016/j.watres.2024.121193] [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: 05/18/2023] [Revised: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024]
Abstract
Biofiltration is an environmentally 'green' technology that is compatible with the recently proposed sustainable development goals, and which has an increasingly important future in the field of water treatment. Here, we explored the impacts of bioelectrochemical integration on a bench-scale slow rate biofiltration system regarding its performance in reclaimed water treatment. Results showed that the short-term (<3 months) integration improved the removal of natural organic matter (NOM) (approximately 8.8%). After long-term (5 months and thereafter) integration, the cathodic charge transfer resistance was found to have a significant reduction from 2662 to 1350 Ω. Meanwhile, bioelectrochemical autotrophic sulfate (SO42-) reduction (over 27.6% reduction) through the syntrophic metabolism between hydrogen oxidation strains (genus Hydrogenophaga) and sulfate-reducing microbes (genera Dethiobacter, Desulfovibrio, and Desulfomicrobium) at the cathodic region was observed. More significantly, the microbial-derived chromophoric humic substances were found to act as electron shuttles at the cathodic region, which might facilitate the process of bioelectrochemical SO42- reduction. Overall, this study provided valuable insights into the potential application of bioelectrochemical-integrated biofilter for simultaneous reduction of NOM and SO42- treating reclaimed water.
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Affiliation(s)
- Lei Xu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shian Song
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Wenzheng Yu
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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3
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Asiedu E, Zhao K, Anwar MN, Ross M, Balaberda AL, Ulrich AC. Biodegradation in oil sands process-affected water: A comprehensive laboratory analysis of the in situ biodegradation of dissolved organic acids. CHEMOSPHERE 2024; 349:141018. [PMID: 38141671 DOI: 10.1016/j.chemosphere.2023.141018] [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: 09/14/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023]
Abstract
Oil sands process-affected water (OSPW) is a by-product of the extraction of bitumen, and volumes of OSPW have accumulated across the Alberta oil sands region due to the governments zero-discharge policy. Some dissolved organics in OSPW, including toxic naphthenic acids (NAs), can be biodegraded in oxic conditions, thereby reducing the toxicity of OSPW. While there has been much focus on degradation of NAs, the biodegradation of other dissolved organic chemicals by endogenous organisms remains understudied. Here, using the HPLC-ultrahigh resolution Orbitrap mass spectrometry, we examined the microbial biodegradation of dissolved organic acids in OSPW. Non-targeted analysis enabled the estimation of biodegradation rates for unique heteroatomic chemical classes detected in negative ion mode. The microcosm experiments were conducted with and without nutrient supplementation, and the changes in the microbial community over time were investigated. Without added nutrients, internal standard-adjusted intensities of all organics, including NAs, were largely unchanged. The addition of nutrients increased the biodegradation rate of O2- and SO2- chemical classes. While anoxic biodegradation can occur in tailings ponds and end pit lakes, microbial community analyses confirmed that the presence of oxygen stimulated biodegradation of the OSPW samples studied. We detected several aerobic hydrocarbon-degrading microbes (e.g., Pseudomonas and Brevundimonas), and microbes capable of degrading sulfur-containing hydrocarbons (e.g., Microbacterium). Microbial community diversity decreased over time with nutrient addition. Overall, the results from this study indicate that toxic dissolved organics beyond NAs can be biodegraded by endogenous organisms in OSPW, but reaffirms that biological treatment strategies require careful consideration of how nutrients and dissolved oxygen may impact efficacy.
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Affiliation(s)
- Evelyn Asiedu
- Division of Analytical & Environmental Toxicology, Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Kankan Zhao
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Mian Nabeel Anwar
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Matthew Ross
- Department of Physical Sciences, MacEwan University, Edmonton, Alberta, T5J 2P2, Canada
| | - Amy-Lynne Balaberda
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada.
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4
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Hussain NAS, Stafford JL. Abiotic and biotic constituents of oil sands process-affected waters. J Environ Sci (China) 2023; 127:169-186. [PMID: 36522051 DOI: 10.1016/j.jes.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 06/17/2023]
Abstract
The oil sands in Northern Alberta are the largest oil sands in the world, providing an important economic resource for the Canadian energy industry. The extraction of petroleum in the oil sands begins with the addition of hot water to the bituminous sediment, generating oil sands process-affected water (OSPW), which is acutely toxic to organisms. Trillions of litres of OSPW are stored on oil sands mining leased sites in man-made reservoirs called tailings ponds. As the volume of OSPW increases, concerns arise regarding the reclamation and eventual release of this water back into the environment. OSPW is composed of a complex and heterogeneous mix of components that vary based on factors such as company extraction techniques, age of the water, location, and bitumen ore quality. Therefore, the effective remediation of OSPW requires the consideration of abiotic and biotic constituents within it to understand short and long term effects of treatments used. This review summarizes selected chemicals and organisms in these waters and their interactions to provide a holistic perspective on the physiochemical and microbial dynamics underpinning OSPW .
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Affiliation(s)
- Nora A S Hussain
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2N8, Canada
| | - James L Stafford
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2N8, Canada.
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5
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Teng T, Liang J, Wu Z, Jin P, Zhang D. Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 864:161139. [PMID: 36572297 DOI: 10.1016/j.scitotenv.2022.161139] [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: 10/16/2022] [Revised: 12/04/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.
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Affiliation(s)
- Tingting Teng
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China; College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Jidong Liang
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China.
| | - Zijun Wu
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China
| | - Pengkang Jin
- Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University, Xi'an 710000, PR China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun 130021, PR China; Key Laboratory of Groundwater Resources and Environment Ministry of Education, Jilin University, Changchun 130021, PR China
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6
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Imam A, Suman SK, Singh P, Vempatapu BP, Tripathi D, Ray A, Kanaujia PK. Proteomic response of Pseudomonas aeruginosa IIPIS-8 during rapid and efficient degradation of naphthalene. ENVIRONMENTAL RESEARCH 2023; 216:114511. [PMID: 36265600 DOI: 10.1016/j.envres.2022.114511] [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: 07/18/2022] [Revised: 09/05/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the ecosystem and are of significant concern due to their toxicity and mutagenicity. Bioremediation of PAHs is a popular and benign approach that ameliorates the environment. This study investigated the biodegradation and proteome response of Pseudomonas aeruginosa IIPIS-8 for two-ringed PAH: naphthalene (NAP) to understand proteome alteration during its bioremediation. Rapid biodegradation was observed up to 98 ± 1.26% and 84 ± 1.03%, respectively, for initial concentrations of 100 mg L-1 and 500 mg L-1 of NAP. Degradation followed first-order kinetics with rate constants of 0.12 h-1 and 0.06 h-1 and half-life (t1/2) of 5.7 h and 11.3 h, respectively. Additionally, the occurrence of key ring cleavage and linear chain intermediates, 2,3,4,5,6, -pentamethyl acetophenone, 1-octanol 2-butyl, and hexadecanoic acid supported complete NAP degradation. Proteomics study of IIPIS-8 throws light on the impact of protein expression, in which 415 proteins were quantified in sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) analysis, of which 97 were found to be significantly up-regulated and 75 were significantly down-regulated by ≥ 2-fold change (p values ≤ 0.05), during the NAP degradation. The study also listed the up-regulation of several enzymes, including oxido-reductases, hydrolases, and catalases, potentially involved in NAP degradation. Overall, differential protein expression, through proteomics study, demonstrated IIPIS-8's capability to efficiently assimilate NAP in their metabolic pathways even in a high concentration of NAP.
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Affiliation(s)
- Arfin Imam
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India; Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Sunil Kumar Suman
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India.
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Bhanu Prasad Vempatapu
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
| | - Deependra Tripathi
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India
| | - Anjan Ray
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India
| | - Pankaj K Kanaujia
- Analytical Sciences Division, CSIR-Indian Institute of Petroleum, Haridwar Road, Dehradun, 248005, Uttarakhand, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, 201002, India.
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7
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Diversity and Metabolic Potential of a PAH-Degrading Bacterial Consortium in Technogenically Contaminated Haplic Chernozem, Southern Russia. Processes (Basel) 2022. [DOI: 10.3390/pr10122555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemically recalcitrant carcinogenic and mutagenic compounds with primarily anthropogenic origin. The investigation of the effects of emissions from energy enterprises on soil microbiomes is of a high priority for modern soil science. In this study, metagenomic profiling of technogenic contaminated soils was carried out based on bioinformatic analysis of shotgun metagenome data with PAH-degrading genes identification. The use of prokaryotic consortia has been often used as one of the bio-remediation approaches to degrade PAHs with different molecular weight. Since the process of PAH degradation predominantly includes non-culturable or yet-to-be cultured species, metagenomic approaches are highly recommended for studying the composition and metabolic abilities of microbial communities. In this study, whole metagenome shotgun sequencing of DNA from two soils with varying PAH levels was performed. In the control site, the total content of 12 priority PAHs was 262 µg kg−1. The background soil levels in the polluted site for PAHs with 3 or more rings exceeded this, at 800 µg kg−1. The abundance of genes and taxa associated with PAH degradation in these two sites were estimated. Despite differences in PAH concentrations up to 1200 µg kg−1, individual and operon-organized PAH degradation genes were almost equally abundant and diverse in pristine and highly contaminated areas. The most numerous taxa in both spots were actinobacteria from Terrabacteria group. In addition to well-known PAH degraders such as Gordonia and Rhodococcus, genes corresponding to the PAH degradation were found in Azoarcus, Burkholderia and Variovorax. The data shows non-specificity and multifunctionality of metabolic pathways encoded in the genes of PAH-degrading microorganisms.
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8
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Zhou Z, Jiao C, Liang Y, Du A, Zhang J, Xiong J, Chen G, Zhu H, Lu L. Study on Degradation of 1,2,4-TrCB by Sugarcane Cellulose-TiO2 Carrier in an Intimate Coupling of Photocatalysis and Biodegradation System. Polymers (Basel) 2022; 14:polym14214774. [PMID: 36365767 PMCID: PMC9658834 DOI: 10.3390/polym14214774] [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] [Received: 10/11/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022] Open
Abstract
1,2,4 trichlorobenzene (1,2,4-TrCB) is a persistent organic pollutant with chemical stability, biological toxicity, and durability, which has a significant adverse impact on the ecological environment and human health. In order to solve the pollution problem, bagasse cellulose is used as the basic framework and nano TiO2 is used as the photocatalyst to prepare composite carriers with excellent performance. Based on this, an intimate coupling of photocatalysis and biodegradation (ICPB) system combining photocatalysis and microorganisms is constructed. We use the combined technology for the first time to deal with the pollution problem of 1,2,4-TrCB. The biofilm in the composite carrier can decompose the photocatalytic products so that the removal rate of 1,2,4-TrCB is 68.01%, which is 14.81% higher than those of biodegradation or photocatalysis alone, and the mineralization rate is 50.30%, which is 11.50% higher than that of photocatalysis alone. The degradation pathways and mechanisms of 1,2,4-TrCB are explored, which provide a theoretical basis and potential application for the efficient degradation of 1,2,4-TrCB and other refractory organics by the ICPB system.
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Affiliation(s)
- Zhenqi Zhou
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Chunlin Jiao
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Yinna Liang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Ang Du
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Jiaming Zhang
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
| | - Jianhua Xiong
- School of Resources, Environment and Materials, Guangxi University, Nanning 530004, China
- Correspondence:
| | - Guoning Chen
- Guangxi Bossco Environmental Protection Technology Co., Ltd., Nanning 530007, China
| | - Hongxiang Zhu
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Clean Pulp & Papermaking and Pollution Control, Nanning 530004, China
| | - Lihai Lu
- Guangxi Bossco Environmental Protection Technology Co., Ltd., Nanning 530007, China
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9
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Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions. Antonie Van Leeuwenhoek 2022; 115:1113-1128. [PMID: 35841500 PMCID: PMC9363352 DOI: 10.1007/s10482-022-01759-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022]
Abstract
In the present study, the bacterial community structure of enrichment cultures degrading benzene under microaerobic conditions was investigated through culturing and 16S rRNA gene Illumina amplicon sequencing. Enrichments were dominated by members of the genus Rhodoferax followed by Pseudomonas and Acidovorax. Additionally, a pale amber-coloured, motile, Gram-stain-negative bacterium, designated B7T was isolated from the microaerobic benzene-degrading enrichment cultures and characterized using a polyphasic approach to determine its taxonomic position. The 16S rRNA gene and whole genome-based phylogenetic analyses revealed that strain B7T formed a lineage within the family Comamonadaceae, clustered as a member of the genus Ideonella and most closely related to Ideonella dechloratans CCUG 30977T. The sole respiratory quinone is ubiquinone-8. The major fatty acids are C16:0 and summed feature 3 (C16:1ω7c/iso-C15:0 2-OH). The DNA G + C content of the type strain is 68.8 mol%. The orthologous average nucleotide identity (OrthoANI) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain B7T and closest relatives were below the threshold values for species demarcation. The genome of strain B7T, which is approximately 4.5 Mb, contains a phenol degradation gene cluster, encoding a multicomponent phenol hydroxylase (mPH) together with a complete meta-cleavage pathway including a I.2.C-type catechol 2,3-dioxygenase (C23O) gene. As predicted by the genome, the type strain is involved in aromatic hydrocarbon-degradation: benzene, toluene and ethylbenzene are degraded aerobically and also microaerobically as sole source of carbon and energy. Based on phenotypic characteristics and phylogenetic analysis, strain B7T is a member of the genus Ideonella and represents a novel species for which the name Ideonella benzenivorans sp. nov. is proposed. The type strain of the species is strain B7T (= LMG 32,345T = NCAIM B.02664T).
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10
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Bedics A, Banerjee S, Bóka K, Tóth E, Benedek T, Kriszt B, Táncsics A. Pinisolibacter aquiterrae sp. nov., a novel aromatic hydrocarbon-degrading bacterium isolated from benzene-, and xylene-degrading enrichment cultures, and emended description of the genus Pinisolibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005229] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-reaction-negative strains, designated as B13T and MA2-2, were isolated from two different aromatic hydrocarbon-degrading enrichment cultures and characterized using a polyphasic approach to determine their taxonomic position. The two strains had identical 16S rRNA gene sequences and were most closely related to
Pinisolibacter ravus
E9T (97.36 %) and
Siculibacillus lacustris
SA-279T (96.33 %). Cells were facultatively aerobic rods and motile with a single polar flagellum. The strains were able to degrade ethylbenzene as sole source of carbon and energy. The assembled genome of strain B13T had a total length of 4.91 Mb and the DNA G+C content was 68.8 mol%. The predominant fatty acids (>5 % of the total) of strains B13T and MA2-2 were C18 : 1
ω7c/C18 : 1
ω6c, C16 : 1
ω7c/C16 : 1
ω6c and C16 : 0. The major ubiquinone of strain B13T was Q10, while the major polar lipids were phosphatidyl-N-methylethanolamine, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and a phospholipid. Based on phenotypic characteristics and phylogenetic data, it is concluded that strains B13T and MA2-2 are members of the genus
Pinisolibacter
and represent a novel species for which the name Pinisolibacter aquiterrae sp. nov. is proposed. The type strain of the species is strain B13T (=LMG 32346T=NCAIM B.02665T).
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Affiliation(s)
- Anna Bedics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Sinchan Banerjee
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Tibor Benedek
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
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11
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Jurelevicius D, Pereira RDS, da Mota FF, Cury JC, de Oliveira IC, Rosado AS, Mason OU, Jansson JK, Seldin L. Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica. GEOBIOLOGY 2022; 20:98-111. [PMID: 34545693 DOI: 10.1111/gbi.12472] [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: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.
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Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael da Silva Pereira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Juliano C Cury
- Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Ivan Cardoso de Oliveira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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12
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Li J, Luo C, Zhang D, Zhao X, Dai Y, Cai X, Zhang G. The catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation in oil-contaminated soil. Environ Microbiol 2021; 23:7042-7055. [PMID: 34587314 DOI: 10.1111/1462-2920.15790] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 01/21/2023]
Abstract
Rhizoremediation is a potential technique for polycyclic aromatic hydrocarbon (PAH) remediation; however, the catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation remain unclear. To address these issues, stable-isotope-probing coupled with metagenomics and molecular ecological network analyses were first used to investigate the phenanthrene rhizoremediation by three different prairie grasses in this study. All rhizospheres exhibited a significant increase in phenanthrene removal and markedly modified the diversity of phenanthrene degraders by increasing their populations and interactions with other microbes. Of all the active phenanthrene degraders, Marinobacter and Enterobacteriaceae dominated in the bare and switchgrass rhizosphere respectively; Achromobacter was markedly enriched in ryegrass and tall fescue rhizospheres. Metagenomes of 13 C-DNA illustrated several complete pathways of phenanthrene degradation for each rhizosphere, which clearly explained their unique rhizoremediation mechanisms. Additionally, propanoate and inositol phosphate of carbohydrates were identified as the dominant factors that drove PAH rhizoremediation by strengthening the ecological networks of soil microbial communities. This was verified by the results of rhizospheric and non-rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites.
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Affiliation(s)
- 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.,CAS Center for Excellence in Deep Earth Science, 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.,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China.,Joint Institute of Environmental Research & Education, South China Agricultural University, Guangzhou, 510642, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, China
| | - Xuan Zhao
- 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.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yeliang Dai
- 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.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xixi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, 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.,CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China
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13
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Abstract
Oil sands surface mining in Alberta has generated over a billion cubic metres of waste, known as tailings, consisting of sands, silts, clays, and process-affected water that contains toxic organic compounds and chemical constituents. All of these tailings will eventually be reclaimed and integrated into one of two types of mine closure landforms: end pit lakes (EPLs) or terrestrial landforms with a wetland feature. In EPLs, tailings deposits are capped with several metres of water while in terrestrial landforms, tailings are capped with solid materials, such as sand or overburden. Because tailings landforms are relatively new, past research has heavily focused on the geotechnical and biogeochemical characteristics of tailings in temporary storage ponds, referred to as tailings ponds. As such, the geochemical stability of tailings landforms remains largely unknown. This review discusses five mechanisms of geochemical change expected in tailings landforms: consolidation, chemical mass loading via pore water fluxes, biogeochemical cycling, polymer degradation, and surface water and groundwater interactions. Key considerations and knowledge gaps with regard to the long-term geochemical stability of tailings landforms are identified, including salt fluxes and subsequent water quality, bioremediation and biogenic greenhouse gas emissions, and the biogeochemical implications of various tailings treatment methods meant to improve geotechnical properties of tailings, such as flocculant (polyacrylamide) and coagulant (gypsum) addition.
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14
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Ramdass AC, Rampersad SN. Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad. Microorganisms 2021; 9:1167. [PMID: 34071489 PMCID: PMC8230346 DOI: 10.3390/microorganisms9061167] [Citation(s) in RCA: 5] [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: 05/15/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 11/29/2022] Open
Abstract
Trinidad and Tobago is the largest producer of oil and natural gas in Central America and the Caribbean. Natural crude oil seeps, in addition to leaking petroleum pipelines, have resulted in chronic contamination of the surrounding terrestrial environments since the time of petroleum discovery, production, and refinement in Trinidad. In this study, we isolated microbes from soils chronically contaminated with crude oil using a culture-dependent approach with enrichment. The sampling of eight such sites located in the southern peninsula of Trinidad revealed a diverse microbial composition and novel oil-degrading filamentous fungi and yeast as single-isolate degraders and naturally occurring consortia, with specific bacterial species not previously reported in the literature. Multiple sequence comparisons and phylogenetic analyses confirmed the identity of the top degraders. The filamentous fungal community based on culturable species was dominated by Ascomycota, and the recovered yeast isolates were affiliated with Basidiomycota (65.23%) and Ascomycota (34.78%) phyla. Enhanced biodegradation of petroleum hydrocarbons is maintained by biocatalysts such as lipases. Five out of seven species demonstrated extracellular lipase activity in vitro. Our findings could provide new insights into microbial resources from chronically contaminated terrestrial environments, and this information will be beneficial to the bioremediation of petroleum contamination and other industrial applications.
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Affiliation(s)
| | - Sephra N. Rampersad
- Biochemistry Research Laboratory (Rm216), Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, Trinidad and Tobago, West Indies;
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15
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Mahjoubi M, Aliyu H, Neifar M, Cappello S, Chouchane H, Souissi Y, Masmoudi AS, Cowan DA, Cherif A. Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14. Sci Rep 2021; 11:8124. [PMID: 33854112 PMCID: PMC8046798 DOI: 10.1038/s41598-021-87487-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 02/12/2021] [Indexed: 02/02/2023] Open
Abstract
Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.
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Affiliation(s)
- Mouna Mahjoubi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Habibu Aliyu
- grid.7892.40000 0001 0075 5874Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Mohamed Neifar
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Simone Cappello
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM)-CNR of Messina, Sp. San Raineri, 86, 98122 Messina, Italy
| | - Habib Chouchane
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Yasmine Souissi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Ahmed Salaheddine Masmoudi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Don A. Cowan
- grid.49697.350000 0001 2107 2298Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002 South Africa
| | - Ameur Cherif
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
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16
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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17
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Salam LB, Obayori OS. Remarkable shift in structural and functional properties of an animal charcoal-polluted soil accentuated by inorganic nutrient amendment. J Genet Eng Biotechnol 2020; 18:70. [PMID: 33175233 PMCID: PMC7658278 DOI: 10.1186/s43141-020-00089-9] [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: 08/07/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
Abstract
Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-020-00089-9.
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Affiliation(s)
- Lateef Babatunde Salam
- Department of Biological Sciences, Microbiology unit, Summit University, Offa, Kwara, Nigeria.
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18
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Wright RJ, Langille MGI, Walker TR. Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere. ISME JOURNAL 2020; 15:789-806. [PMID: 33139870 PMCID: PMC8027867 DOI: 10.1038/s41396-020-00814-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/22/2022]
Abstract
It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role that biofilms colonizing plastics in the environment—termed the “Plastisphere”—may play in the transportation and ecological impact of these plastics. By collecting and re-analyzing all raw 16S rRNA gene sequencing and metadata from 2,229 samples within 35 studies, we have performed the first meta-analysis of the Plastisphere in marine, freshwater, other aquatic (e.g., brackish or aquaculture) and terrestrial environments. We show that random forest models can be trained to differentiate between groupings of environmental factors as well as aspects of study design, but—crucially—also between plastics when compared with control biofilms and between different plastic types and community successional stages. Our meta-analysis confirms that potentially biodegrading Plastisphere members, the hydrocarbonoclastic Oceanospirillales and Alteromonadales are consistently more abundant in plastic than control biofilm samples across multiple studies and environments. This indicates the predilection of these organisms for plastics and confirms the urgent need for their ability to biodegrade plastics to be comprehensively tested. We also identified key knowledge gaps that should be addressed by future studies.
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Affiliation(s)
- Robyn J Wright
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Canada. .,Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada.
| | - Morgan G I Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
| | - Tony R Walker
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Canada
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19
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Chen LX, Méheust R, Crits-Christoph A, McMahon KD, Nelson TC, Slater GF, Warren LA, Banfield JF. Large freshwater phages with the potential to augment aerobic methane oxidation. Nat Microbiol 2020; 5:1504-1515. [PMID: 32839536 PMCID: PMC7674155 DOI: 10.1038/s41564-020-0779-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/21/2020] [Indexed: 12/31/2022]
Abstract
There is growing evidence that phages with unusually large genomes are common across various microbiomes, but little is known about their genetic inventories or potential ecosystem impacts. In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bacteria that oxidize methane. Of manually curated genomes, 22 (18 are complete), ranging from 159 kilobase (kb) to 527 kb in length, were found to encode the pmoC gene, an enzymatically critical subunit of the particulate methane monooxygenase, the predominant methane oxidation catalyst in nature. The phage-associated PmoC sequences show high similarity to (>90%), and affiliate phylogenetically with, those of coexisting bacterial methanotrophs, including members of Methyloparacoccus, Methylocystis and Methylobacter spp. In addition, pmoC-phage abundance patterns correlate with those of the coexisting bacterial methanotrophs, supporting host-phage relationships. Future work is needed to determine whether phage-associated PmoC has similar functions to additional copies of PmoC encoded in bacterial genomes, thus contributing to growth on methane. Transcriptomics data from Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in situ and, of interest, that the most rapidly growing methanotroph was infected by three pmoC-phages. Thus, augmentation of bacterial methane oxidation by pmoC-phages during infection could modulate the efflux of this potent greenhouse gas into the environment.
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Affiliation(s)
- Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Raphaël Méheust
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | | | - Katherine D McMahon
- Departments of Civil and Environmental Engineering, and Bacteriology, University of Wisconsin, Madison, WI, USA
| | | | - Gregory F Slater
- School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Lesley A Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada.,School of Geography and Earth Science, McMaster University, Hamilton, Ontario, Canada
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA. .,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. .,Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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20
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Kim E, Yulisa A, Kim S, Hwang S. Monitoring microbial community structure and variations in a full-scale petroleum refinery wastewater treatment plant. BIORESOURCE TECHNOLOGY 2020; 306:123178. [PMID: 32203902 DOI: 10.1016/j.biortech.2020.123178] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Abstract
This research investigated the process efficiency and microbial communities and their diversity in a full-scale wastewater treatment plant (WWTP) fed with petroleum refining wastewater (PRW) that contained toxic hydrocarbon contaminants and carcinogens. Process parameters and bacterial community structures were monitored for six months to create a link between microbial dynamics and influent characteristics of petrochemical wastewater. The WWTP showed a stable process with efficiencies >70% for both soluble chemical oxygen demand (SCOD) and benzene removal. More than 30 genera were identified by metagenomic analysis, and the bacterial populations changed significantly during the operation period. Among them, genera Sulfuritalea (11.9 ± 3.5%), Ottowia (4.3 ± 2.2%), Thauera (3.1 ± 7.2%) and Hyphomicrobium (1.3 ± 0.7%) were dominant and important bacterial genera that may have been responsible for the degradation of aromatic compounds such as benzene and phenol.
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Affiliation(s)
- Eunji Kim
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Arma Yulisa
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Sangmin Kim
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, South Korea.
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21
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Ribera-Pi J, Badia-Fabregat M, Arias D, Gómez V, Taberna E, Sanz J, Martínez-Lladó X, Jubany I. Coagulation-flocculation and moving bed biofilm reactor as pre-treatment for water recycling in the petrochemical industry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136800. [PMID: 32007876 DOI: 10.1016/j.scitotenv.2020.136800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Water recycling and reuse is of important value in water-using sectors like petrochemical industry. The aim of this research was to optimise the pre-treatment of petrochemical wastewater to undergo a further membrane treatment, with the final objective of water recycling within the same industry. Laboratory coagulation-flocculation tests prior to biological treatment were performed using Actiflo® Veolia commercial technology and an optimal coagulant dose of 30 mg/L ferric chloride was obtained. A bench-scale Moving Bed Biofilm Reactor (MBBR) system with two sequential reactors with working volumes of 5 L was filled with Z-carriers at 35% of their working volume. Organic loading rate (OLR) was varied from 0.2 to 3.25 kg/(m3 d) and the hydraulic retention time (HRT) ranged from 23.4 h to 4.5 h. High soluble chemical oxygen demand (sCOD) removals were obtained in stationary states (80-90%) and the calculated maximum sCOD that the system could degrade was 4.96 ± 0.01 kg/(m3 d) at 23 ± 2 °C. Changes in feed composition did not decrease sCOD removals showing that MBBR is a robust technology and the coagulation-flocculation step could be by-passed. Further removal of total suspended solids (TSS) and turbidity from the MBBR effluent would be required before a reverse osmosis (RO) step could be performed. A biofilm-forming genus, Haliscomenobacter spp., and an oil degrading genus Flavobacterium spp. were found in all the attached biomass samples. Acinetobacter spp. was the major bacterial genera found in suspended biomass. Proteobacteria and Bacteroidetes were the major phyla detected in the carrier samples while Proteobacteria the main one detected in the suspended biomass. The lack of fungal annotated sequences in databases led to a major proportion of fungal sequences being categorized as unclassified Fungi. The results obtained indicate that MBBR is an appropriate technology for hydrocarbon-degrading microorganism growth and, thus, for petrochemical wastewater pre-treatment for water regeneration.
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Affiliation(s)
- Judit Ribera-Pi
- Eurecat, Centre Tecnològic de Catalunya, Sustainability Area, Manresa, Spain.
| | | | - David Arias
- DuPont Water Solutions, Global Water Technology Center, Tarragona, Spain
| | - Verónica Gómez
- DuPont Water Solutions, Global Water Technology Center, Tarragona, Spain
| | | | - Joan Sanz
- Veolia Water Technologies, Sant Cugat del Vallès, Spain
| | | | - Irene Jubany
- Eurecat, Centre Tecnològic de Catalunya, Sustainability Area, Manresa, Spain
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22
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Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME JOURNAL 2019; 14:714-726. [PMID: 31796935 DOI: 10.1038/s41396-019-0561-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022]
Abstract
Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. This study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.
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Yu X, Lee K, Ulrich AC. Model naphthenic acids removal by microalgae and Base Mine Lake cap water microbial inoculum. CHEMOSPHERE 2019; 234:796-805. [PMID: 31247489 DOI: 10.1016/j.chemosphere.2019.06.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/27/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Naphthenic acids (NAs) originate from bitumen and are considered a major contributor to acute toxicity in oil sands process-affected water (OSPW) produced from bitumen extraction processes. To reclaim oil sands tailings and remediate OSPW, in-pit fluid fine tailings can be water-capped as end pit lakes (EPL). Addressing NAs present in OSPW, either through removal, dilution or degradation, is an objective for oil sands reclamation. EPLs can remediate NAs through degradation or dilution or both. To assess and understand degradation potential, Chlorella kessleri and Botryococcus braunii were tested for their tolerance to, and ability to biodegrade, three model NAs (cyclohexanecarboxylic acid, cyclohexaneacetic acid, and cyclohexanebutyric acid). Water sourced from the industry's first EPL, the Base Mine Lake (BML), was used alone as an inoculum or co-cultured with C. kessleri to biodegrade cyclohexanecarboxylic acid and cyclohexanebutyric acid. All cultures metabolized the model compounds via β-oxidation. Biodegradation by the co-culture of C. kessleri and BML inoculum was most effective and rapid: the cyclohexaneacetic acid generated from cyclohexanebutyric acid could be further degraded by the co-culture, while the cyclohexaneacetic acid generated could not be consumed by pure algal cultures or BML inoculum alone. Adding C. kessleri greatly increased the diversity of the microbial community in the BML inoculum; many known hydrocarbon and NA degraders were identified from the 16S rRNA gene sequencing from this co-culture. This more diverse microbial community could have potential for EPL remediation.
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Affiliation(s)
- Xiaoxuan Yu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Korris Lee
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
| | - Ania C Ulrich
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 2W2, Canada.
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Zhao YJ, Sato Y, Inaba T, Aoyagi T, Hori T, Habe H. Activated sludge microbial communities of a chemical plant wastewater treatment facility with high-strength bromide ions and aromatic substances. J GEN APPL MICROBIOL 2019; 65:106-110. [DOI: 10.2323/jgam.2018.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yan-Jie Zhao
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology
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Spatial Pattern of Bacterial Community Diversity Formed in Different Groundwater Field Corresponding to Electron Donors and Acceptors Distributions at a Petroleum-Contaminated Site. WATER 2018. [DOI: 10.3390/w10070842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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