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Wu X, Lin Y, Wang Y, Dai M, Wu S, Li X, Yang C. Chemical structure of hydrocarbons significantly affects removal performance and microbial responses in gas biotrickling filters. BIORESOURCE TECHNOLOGY 2024; 398:130480. [PMID: 38395235 DOI: 10.1016/j.biortech.2024.130480] [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: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
The control of emissions of short-chain hydrocarbons with different structures is critical for the petrochemical industry. Herein, three two-carbon-containing (C2) hydrocarbons, ethane, ethylene, and acetylene, were chosen as pollutants to study the effects of chemical structure of hydrocarbons on removal performance and microbial responses in biotrickling filters. Results showed that the removal efficiency (RE) of C2 hydrocarbons followed the sequence of acetylene > ethane > ethylene. When the inlet loading rate was 30 g/(m3·h) and the empty bed residence time was 60 s, the RE of ethane, ethylene, and acetylene was 57 ± 4.0 %, 49 ± 1.0 %, and 84 ± 2.7 %, respectively. The high water solubility resulted in the high removal of C2 hydrocarbons, while a low surface tension enhanced the removal of C2 hydrocarbons. Additionally, the microbial community, enzyme activity, and extracellular properties of microorganisms also contributed to the difference in C2 hydrocarbon removal. These results could be referred for the effective control of light hydrocarbon emissions.
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Affiliation(s)
- Xin Wu
- Academy of Environmental and Resource Sciences, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China; College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yan Lin
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Yongyi Wang
- Qingdao Gold Hisun Environment Protection Equipment Co., Ltd., Qingdao, Shandong 266000, China
| | - Mei Dai
- Academy of Environmental and Resource Sciences, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China; College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Shaohua Wu
- Academy of Environmental and Resource Sciences, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Xiang Li
- Academy of Environmental and Resource Sciences, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China
| | - Chunping Yang
- Academy of Environmental and Resource Sciences, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China; College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China; Key Laboratory of Jiangxi Province for Persistent Pollutants Control and Resources Recycle, Nanchang Hangkong University, Nanchang, Jiangxi 330063, China.
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Kho CJY, Lau MML, Chung HH, Chew IYY, Gan HM. Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides. Curr Microbiol 2023; 80:255. [PMID: 37356021 DOI: 10.1007/s00284-023-03354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/28/2023] [Indexed: 06/27/2023]
Abstract
Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.
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Affiliation(s)
- Cindy Jia Yung Kho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Melinda Mei Lin Lau
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Ivy Yee Yen Chew
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Han Ming Gan
- Department of Biological Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Malaysia
- Patriot Biotech Sdn. Bhd., 47500, Bandar Sunway, Selangor, Malaysia
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Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP. In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas parafulva OS-1. Front Microbiol 2023; 14:1140249. [PMID: 37408640 PMCID: PMC10318148 DOI: 10.3389/fmicb.2023.1140249] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023] Open
Abstract
A metal-resistant bacterium Pseudomonas parafulva OS-1 was isolated from waste-contaminated soil in Ranchi City, India. The isolated strain OS-1 showed its growth at 25-45°C, pH 5.0-9.0, and in the presence of ZnSO4 (upto 5 mM). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain OS-1 belonged to the genus Pseudomonas and was most closely related to parafulva species. To unravel the genomic features, we sequenced the complete genome of P. parafulva OS-1 using Illumina HiSeq 4,000 sequencing platform. The results of average nucleotide identity (ANI) analysis indicated the closest similarity of OS-1 to P. parafulva PRS09-11288 and P. parafulva DTSP2. The metabolic potential of P. parafulva OS-1 based on Clusters of Othologous Genes (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated a high number of genes related to stress protection, metal resistance, and multiple drug-efflux, etc., which is relatively rare in P. parafulva strains. Compared with other parafulva strains, P. parafulva OS-1 was found to have the unique β-lactam resistance and type VI secretion system (T6SS) gene. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain OS-1 have strong biomass degradation potential. The presence of genomic complexity in the OS-1 genome indicates that horizontal gene transfer (HGT) might happen during evolution. Therefore, genomic and comparative genome analysis of parafulva strains is valuable for further understanding the mechanism of resistance to metal stress and opens a perspective to exploit a newly isolated bacterium for biotechnological applications.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Vaishnavi Rawat
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
| | - Afreen Shadan
- Department of Microbiology, Dr. Shyama Prasad Mukerjee University, Ranchi, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Sushanta Deb
- Department of Veterinary Microbiology and Pathology, Washington State University (WSU), Pullman, WA, United States
| | - Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Ranchi, Jharkhand, India
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Ameen F, Al-Homaidan AA. Oily bilge water treatment using indigenous soil bacteria: Implications for recycling the treated sludge in vegetable farming. CHEMOSPHERE 2023:139040. [PMID: 37244558 DOI: 10.1016/j.chemosphere.2023.139040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/06/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Hydrocarbon contamination from motorized vessels operating on seas threaten marine ecosystems and need to treated efficiently. A bilge wastewater treatment using indigenous bacteria isolated from oil contaminated soil was studied. Five bacterial isolates (Acinetobacter baumanni, Klebsiella aerogenes, Pseudomonas fluorescence, Bacillus subtilis and Brevibacterium linens) were isolated from port soil and used in the bilge water treatment. Their crude oil degradation abilities were first confirmed experimentally. The single species and the consortia of each two species were compared in an experiment where the conditions were first optimized. The optimized conditions were 40 °C, carbon source glucose, nitrogen source ammonium chloride, pH 8, and salinity 25%. Each of the species and each combination was able to degrade oil. K. aerogenes and P. fluorescence were the most efficient in reducing the crude oil concentration. The crude oil concentration was reduced from 290 mg/L to 23 mg/L and 21 mg/L, respectively. The respective values for the loss in turbidity were from 320 NTU to 29 mg/L and 27 NTU and for BOD loss from 210 mg/L to 18 mg/L and 16 mg/L. Mn was reduced from 25.4 mg/L to 1.2 mg/L and 1.0 mg/L, Cu from 26.8 mg/L to 2.9 mg/L and 2.4 mg/L, and Pb from 29.8 mg/L to 1.5 mg/L and 1.8 mg/L. The consortium of K. aerogenes and P. fluorescence in the bilge wastewater treatment reduced the crude oil concentration to 11 mg/L. After the treatment, the water was removed and the sludge was composted with palm molasses and cow dung. After 60 days of composting and inoculation with different bacterial consortia, the final product was used as a seedbed for vegetables. The compost with the consortium K. aerogenes and P. fluorescence promoted vegetable plant growth most and could be used in farming.
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Affiliation(s)
- Fuad Ameen
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Ali A Al-Homaidan
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Li X, Zheng S, Li Y, Ding J, Qin W. Effectively facilitating the degradation of chloramphenicol by the synergism of Shewanella oneidensis MR-1 and the metal-organic framework. JOURNAL OF HAZARDOUS MATERIALS 2023; 454:131545. [PMID: 37148794 DOI: 10.1016/j.jhazmat.2023.131545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/14/2023] [Accepted: 04/29/2023] [Indexed: 05/08/2023]
Abstract
Electroactive bacteria (EAB) and metal oxides are capable of synergistically removing chloramphenicol (CAP). However, the effects of redox-active metal-organic frameworks (MOFs) on CAP degradation with EAB are not yet known. This study investigated the synergism of iron-based MOFs (Fe-MIL-101) and Shewanella oneidensis MR-1 on CAP degradation. 0.5 g/L Fe-MIL-101 with more possible active sites led to a three-fold higher CAP removal rate in the synergistic system with MR-1 (initial bacterial concentration of 0.2 at OD600), and showed a superior catalytic effect than exogenously added Fe(III)/Fe(II) or magnetite. Mass spectrometry revealed that CAP was transformed into smaller molecular weight and less toxic metabolites in cultures. Transcriptomic analysis showed that Fe-MIL-101 enhanced the expression of genes related to nitro and chlorinated contaminants degradation. Additionally, genes encoding hydrogenases and c-type cytochromes associated with extracellular electron transfer were significantly upregulated, which may contribute to the simultaneous bioreduction of CAP both intracellularly and extracellularly. These results indicated that Fe-MIL-101 can be used as a catalyst to synergize with EAB to effectively facilitate CAP degradation, which might shed new light on the application in the in situ bioremediation of antibiotic-contaminated environments.
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Affiliation(s)
- Xin Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Shiling Zheng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, PR China.
| | - Yinhao Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jiawang Ding
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China.
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong 266071, PR China
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Sui X, Wang X, Yu L, Ji H. Genomics for the characterization of the mechanisms of microbial strains in degrading petroleum pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:21608-21618. [PMID: 36271069 DOI: 10.1007/s11356-022-23685-3] [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: 04/06/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Four petroleum-tolerant bacteria, namely, Pseudomonas hibiscicola, Enterobacter hormaechei, Rhizobium pusense and Pseudomonas japonica were isolated. These strains showed excellent performance in the remediation of petroleum contamination with degradation percentages of 26.13%, 26.47%, 32.27%, and 18.74% for petroleum hydrocarbons, 29.63%, 70.11%, 88.38%, and 67.03% for n-docosane, and 61.00%, 96.36%, 98.00%, and 67.01% for fluorene. Accordingly, the strain of Rhizobium pusense was used to further study its underlying degradation mechanism. N-docosane could be metabolised through the pathway of subterminal oxidation by Rhizobium pusense, while the main pathway for fluorene metabolism is the meta-cleavage. R. pusense contains 10 genes that are involved in the synthetic of biosurfactants and 71 genes that are involved in the metabolism of petroleum hydrocarbons and organic pollutants, such as hydrocarbons, toluene, xylene, ethylbenzene and naphthalene. This study was the first to determine that concerning the metabolism ability and metabolic genes of R. pusense for petroleum pollutant degradation, which is important for understanding the bioremediation mechanism of petroleum pollution.
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Affiliation(s)
- Xin Sui
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Xuemei Wang
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Ling Yu
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China
| | - Hongbing Ji
- Beijing Key Laboratory of Resource-Oriented Treatment of Industrial Pollution, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Xueyuan Road No. 30, Haidian District, Beijing, 100083, China.
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Gao Y, Cai M, Shi K, Sun R, Liu S, Li Q, Wang X, Hua W, Qiao Y, Xue J, Xiao X. Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2023; 87:228-238. [PMID: 36640034 DOI: 10.2166/wst.2022.406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.
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Affiliation(s)
- Yu Gao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Mengmeng Cai
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Ke Shi
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Rui Sun
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Affiliated Hospital of Jining Medical University, Jining 272007, China
| | - Suxiang Liu
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Qintong Li
- Department of Applied Biosciences, Faculty of Life Sciences, Toyo University, Gunma 3740193, Japan
| | - Xiaoyan Wang
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Wenxin Hua
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail:
| | - Yanlu Qiao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Jianliang Xue
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
| | - Xinfeng Xiao
- College of Safety and Environment Engineering, Shandong University of Science and Technology, Qingdao 266510, China E-mail: ; Institute of Yellow River Delta Earth Surface Processes and Ecological Integrity, Shandong University of Science and Technology, Qingdao 266510, China
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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Medić AB, Karadžić IM. Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation. World J Microbiol Biotechnol 2022; 38:165. [PMID: 35861883 DOI: 10.1007/s11274-022-03349-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/26/2022] [Indexed: 10/17/2022]
Abstract
Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.
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Affiliation(s)
- Ana B Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
| | - Ivanka M Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
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10
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Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.
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11
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Delegan Y, Petrikov K, Frantsuzova E, Rudenko N, Solomentsev V, Suzina N, Travkin V, Solyanikova IP. Complete Genome Analysis of Rhodococcus opacus S8 Capable of Degrading Alkanes and Producing Biosurfactant Reveals Its Genetic Adaptation for Crude Oil Decomposition. Microorganisms 2022; 10:microorganisms10061172. [PMID: 35744693 PMCID: PMC9229178 DOI: 10.3390/microorganisms10061172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 02/05/2023] Open
Abstract
Microorganisms capable of decomposing hydrophobic substrates in cold climates are of considerable interest both in terms of studying adaptive reactions to low temperatures and in terms of their application in biotechnologies for cleaning up oil spills in a crude-oil polluted soil. The aim of this work was to investigate the genome of Rhodococcus opacus S8 and explore behavior traits of this strain grown in the presence of hexadecane. The genome size of strain S8 is 8.78 Mb, of which the chromosome size is 7.75 Mb. The S8 strain contains 2 circular plasmids of 135 kb and 105 kb and a linear plasmid with a size of 788 kb. The analysis of the genome revealed the presence of genes responsible for the degradation of alkanes and synthesis of biosurfactants. The peculiarities of morphology of microbial cells when interacting with a hydrophobic substrate were revealed. An adaptive mechanism responsible in the absence of oxygen for maintaining the process of degradation of hexadecane is discussed. The data obtained show that the strain S8 has great potential to be used in biotechnologies.
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Affiliation(s)
- Yanina Delegan
- Laboratory of Physiology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia;
| | - Kirill Petrikov
- Laboratory of Plasmid Biology, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Ekaterina Frantsuzova
- Laboratory of Physiology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (Y.D.); (E.F.)
- The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, 142290 Pushchino, Moscow Region, Russia
| | - Natalia Rudenko
- Institute of Basic Biological Problems of Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Viktor Solomentsev
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia;
| | - Nataliya Suzina
- Laboratory of Cytology of Microorganisms, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia;
| | - Vasili Travkin
- Regional Microbiological Center, Belgorod National Research University, 308015 Belgorod, Belgorod Region, Russia;
| | - Inna P. Solyanikova
- The Federal State Budget Educational Institution of Higher Education Pushchino State Institute of Natural Science, 142290 Pushchino, Moscow Region, Russia
- Regional Microbiological Center, Belgorod National Research University, 308015 Belgorod, Belgorod Region, Russia;
- Laboratory of Microbial Enzymology, Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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12
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Taxonomic and functional trait-based approaches suggest that aerobic and anaerobic soil microorganisms allow the natural attenuation of oil from natural seeps. Sci Rep 2022; 12:7245. [PMID: 35508504 PMCID: PMC9068923 DOI: 10.1038/s41598-022-10850-4] [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: 11/16/2021] [Accepted: 03/31/2022] [Indexed: 12/02/2022] Open
Abstract
Natural attenuation, involving microbial adaptation, helps mitigating the effect of oil contamination of surface soils. We hypothesized that in soils under fluctuating conditions and receiving oil from seeps, aerobic and anaerobic bacteria as well as fungi could coexist to efficiently degrade hydrocarbons and prevent the spread of pollution. Microbial community diversity was studied in soil longitudinal and depth gradients contaminated with petroleum seeps for at least a century. Hydrocarbon contamination was high just next to the petroleum seeps but this level drastically lowered from 2 m distance and beyond. Fungal abundance and alpha-diversity indices were constant along the gradients. Bacterial abundance was constant but alpha-diversity indices were lower next to the oil seeps. Hydrocarbon contamination was the main driver of microbial community assemblage. 281 bacterial OTUs were identified as indicator taxa, tolerant to hydrocarbon, potentially involved in hydrocarbon-degradation or benefiting from the degradation by-products. These taxa belonging to lineages of aerobic and anaerobic bacteria, have specific functional traits indicating the development of a complex community adapted to the biodegradation of petroleum hydrocarbons and to fluctuating conditions. Fungi are less impacted by oil contamination but few taxa should contribute to the metabolic complementary within the microbial consortia forming an efficient barrier against petroleum dissemination.
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13
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Reclamation of actual automobile wash wastewater combined with energy recovery in 3D- microbial fuel cell packed with acid-activated multi walled carbon nanotubes coated anode. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.120455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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Xiao L, Liu F, Kumar PS, Wei Y, Liu J, Han D, Shan S, Wang X, Dang R, Yu J. Rapid removal of chloramphenicol via the synergy of Geobacter and metal oxide nanoparticles. CHEMOSPHERE 2022; 286:131943. [PMID: 34426266 DOI: 10.1016/j.chemosphere.2021.131943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/31/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
The wide use of chloramphenicol and its residues in the environments are an increasing threat to human beings. Electroactive microorganisms were proven with the ability of biodegradation of chloramphenicol, but the removal rate and efficiency need to be improved. In this study, a model electricigens, Geobacter metallireducens, was supplied with and Fe3O4 and MnO2 nanoparticles. Five times higher chloramphenicol removal rate (0.71 d-1) and two times higher chloramphenicol removal efficiency (100%) was achieved. Fe3O4 and MnO2 nanoparticles highly increased the current density and NADH-quinone oxidoreductase expression. Fe3O4 nanoparticles enhanced the expression of alcohol dehydrogenase and c-type cytochrome, while MnO2 nanoparticles increased the transcription of pyruvate dehydrogenase and Type IV pili assembly genes. Chloramphenicol was reduced to a type of dichlorination reducing product named CPD3 which is a benzene ring containing compound. Collectively, Fe3O4 and MnO2 nanoparticles increased the chloramphenicol removal capacity in MFCs by enhancing electron transfer efficiency. This study provides new enhancing strategies for the bioremediation of chloramphenicol in the environments.
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Affiliation(s)
- Leilei Xiao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
| | - Fanghua Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China; Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| | - Yunwei Wei
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, PR China.
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, PR China.
| | - Dianfeng Han
- Shandong Marine Resource and Environment Research Institute, Yantai, 264006, PR China.
| | | | - Xingyu Wang
- Yantai University, Yantai, 264005, PR China.
| | - Run Dang
- Yantai University, Yantai, 264005, PR China.
| | - Jiafeng Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, PR China.
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15
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Saeed M, Ilyas N, Bibi F, Jayachandran K, Dattamudi S, Elgorban AM. Biodegradation of PAHs by Bacillus marsiflavi, genome analysis and its plant growth promoting potential. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118343. [PMID: 34662593 DOI: 10.1016/j.envpol.2021.118343] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
The biodegradation of hazardous petroleum hydrocarbons has recently received a lot of attention because of its many possible applications. Bacillus marsiflavi strain was isolated from oil contaminated soil of Rawalpindi, Pakistan. Initial sequencing was done by 16s rRNA sequencing technique. Bac 144 had shown 78% emulsification index and 72% hydrophobicity content. Further, the strain displayed production of 15.5 mg/L phosphate sloubilization and 30.25 μg/ml indole acetic acid (IAA) in vitro assay. The strain showed 65% biodegradation of crude oil within 5 days by using Gas Chromatography-Mass Spectrometry (GC-MS) analysis. Whole Genome analysis of Bac 144 was performed by PacBio sequencing and results indicated that Bacillus marsiflavi Bac144 strain consisted of size of 4,417,505bp with closest neighbor Bacillus cereus ATCC 14579. The number of the coding sequence was 4662 and number of RNAs was 141. The GC content comprised 48.1%. Various genes were detected in genome responsible for hydrocarbon degradation and plant defense mechanism. The toxic effect of petroleum hydrocarbons in soil and its mitigation with Bac 144 was tested by soil experiment with three levels of oil contamination (5%, 10% and 15%). Soil enzymatic activity such as dehydrogenase and fluorescein diacetate (FDA) increased up to 49% and 40% with inoculation of Bac 144, which was considered to be correlated with hydrocarbon degradation recorded as 46%. An increase of 20%, 14% and 9% in shoot length of plant at 5%, 10% and 15% level of oil was recorded treated with Bac 144 as compared to untreated plants. A percent increase of 14.89%, 16.85%, and 13.87% in chlorophyll, carotenoid, and proline content of plant was observed by inoculation with Bac 144 under oil stress. Significant reduction of 14% and 18%, 21% was recorded in the malondialdehyde content of plant due to inoculation of Bac 144. A considerable increase of 21.33%, 19.5%, and 24.5% in super oxide dismutase, catalase, and peroxidase dismutase activity was also observed in plants inoculated with strain Bac 144. These findings suggested that Bac-144 can be considered as efficient candidate for bioremediation of hydrocarbons.
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Affiliation(s)
- Maimona Saeed
- Department of Botany, PMAS-Arid Agriculture University Rawalpindi, 46300, Rawalpindi, Pakistan
| | - Noshin Ilyas
- Department of Botany, PMAS-Arid Agriculture University Rawalpindi, 46300, Rawalpindi, Pakistan.
| | - Fatima Bibi
- Department of Botany, PMAS-Arid Agriculture University Rawalpindi, 46300, Rawalpindi, Pakistan
| | | | - Sanku Dattamudi
- Earth and Environment Department, Florida International University, USA
| | - Abdallah M Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh, 11451, Saudi Arabia
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16
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Chlebek D, Płociniczak T, Gobetti S, Kumor A, Hupert-Kocurek K, Pacwa-Płociniczak M. Analysis of the Genome of the Heavy Metal Resistant and Hydrocarbon-Degrading Rhizospheric Pseudomonas qingdaonensis ZCR6 Strain and Assessment of Its Plant-Growth-Promoting Traits. Int J Mol Sci 2021; 23:ijms23010214. [PMID: 35008639 PMCID: PMC8745256 DOI: 10.3390/ijms23010214] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
The Pseudomonas qingdaonensis ZCR6 strain, isolated from the rhizosphere of Zea mays growing in soil co-contaminated with hydrocarbons and heavy metals, was investigated for its plant growth promotion, hydrocarbon degradation, and heavy metal resistance. In vitro bioassays confirmed all of the abovementioned properties. ZCR6 was able to produce indole acetic acid (IAA), siderophores, and ammonia, solubilized Ca3(PO4)2, and showed surface active properties and activity of cellulase and very high activity of 1-aminocyclopropane-1-carboxylic acid deaminase (297 nmol α-ketobutyrate mg−1 h−1). The strain degraded petroleum hydrocarbons (76.52% of the initial hydrocarbon content was degraded) and was resistant to Cd, Zn, and Cu (minimal inhibitory concentrations reached 5, 15, and 10 mM metal, respectively). The genome of the ZCR6 strain consisted of 5,507,067 bp, and a total of 5055 genes were annotated, of which 4943 were protein-coding sequences. Annotation revealed the presence of genes associated with nitrogen fixation, phosphate solubilization, sulfur metabolism, siderophore biosynthesis and uptake, synthesis of IAA, ethylene modulation, heavy metal resistance, exopolysaccharide biosynthesis, and organic compound degradation. Complete characteristics of the ZCR6 strain showed its potential multiway properties for enhancing the phytoremediation of co-contaminated soils. To our knowledge, this is the first analysis of the biotechnological potential of the species P. qingdaonensis.
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17
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Genomic characterization of a dehalogenase-producing bacterium (Bacillus megaterium H2) isolated from hypersaline Lake Tuz (Turkey). GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Satti SM, Castro-Aguirre E, Shah AA, Marsh TL, Auras R. Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp. Int J Mol Sci 2021; 22:ijms22147385. [PMID: 34299026 PMCID: PMC8305213 DOI: 10.3390/ijms22147385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.
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Affiliation(s)
- Sadia Mehmood Satti
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- University Institute of Biochemistry and Biotechnology, PMAS Arid Agriculture University, Shamasabad, Muree Road, Rawalpindi 46300, Pakistan
| | - Edgar Castro-Aguirre
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Kraft Heinz Company, Glenview, IL 60025-4312, USA
| | - Aamer Ali Shah
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (S.M.S.); (A.A.S.)
| | - Terence L. Marsh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-1223, USA
- Correspondence: (T.L.M.); (R.A.)
| | - Rafael Auras
- School of Packaging, Michigan State University, East Lansing, MI 48824-1223, USA;
- Correspondence: (T.L.M.); (R.A.)
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19
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Pandit PR, Kumar R, Kumar D, Patel Z, Pandya L, Kumar M, Joshi C. Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112448. [PMID: 33831764 DOI: 10.1016/j.jenvman.2021.112448] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.
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Affiliation(s)
- Priti Raj Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Raghawendra Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Dinesh Kumar
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Labdhi Pandya
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Manish Kumar
- Discipline of Earth Sciences, IIT Gandhinagar, Gujarat, 382355, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India.
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20
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Draft genome sequence and potential identification of a biosurfactant from Brevibacterium casei strain LS14 an isolate from fresh water Loktak Lake. 3 Biotech 2021; 11:326. [PMID: 34194910 DOI: 10.1007/s13205-021-02867-9] [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: 10/24/2020] [Accepted: 05/31/2021] [Indexed: 10/21/2022] Open
Abstract
This study reports the whole-genome sequencing and sequence analysis of a bacterial isolate Brevibacterium casei strain LS14, isolated from Loktak Lake, Imphal, India. The de novo assembled genome reported in this paper featured a size of 3,809,532 bp, has GC content of 68% and contains 3602 genomic features, including 3551 protein-coding genes, 46 tRNA and 5rRNA. A biosurfactant biosynthesis gene cluster in the genome of the isolated strain was identified using AntiSMASH online tool V3.0.5 and KAAS (KEGG Automatic Annotation Server). The presence of biosurfactant was demonstrated by drop collapse, oil displacement and emulsification index. Subsequent chemical characterization using FTIR and LC-MS analyses revealed surfactin and terpene containing biosurfactant moieties. Also, the presence of genes involved in terpenoid synthesis pathway in the genome sequence may account for biosurfactant terpenoid backbone, but genes for later-stage conversion of terpenoid to biosurfactant were not ascertained. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02867-9.
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21
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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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22
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Oyewusi HA, Wahab RA, Huyop F. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Mol Biol Rep 2021; 48:2687-2701. [PMID: 33650078 DOI: 10.1007/s11033-021-06239-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB 5351, Ado Ekiti, Ekiti State, Nigeria.
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
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23
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Singha LP, Pandey P. Rhizosphere assisted bioengineering approaches for the mitigation of petroleum hydrocarbons contamination in soil. Crit Rev Biotechnol 2021; 41:749-766. [PMID: 33626996 DOI: 10.1080/07388551.2021.1888066] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The high demand for petroleum oil has led to hydrocarbon contamination in soil, including agricultural lands, and many other ecosystems across the globe. Physical and chemical treatments are effective strategies for the removal of high contamination levels and are useful for small areas, although with concerns of cost-effectiveness. Alternatively, several bacteria belonging to the Phylum: Proteobacteria, Bacteroidetes, Actinobacteria, Nocardioides, or Firmicutes are used for biodegradation of different hydrocarbons - aliphatic, polyaromatic hydrocarbons (PAH), and asphaltenes in the oil-contaminated soil. The rhizoremediation strategy with plant-microbe interactions has prospects to achieve the desired result in the field conditions. However, adequate biostimulation, and bioaugmentation with the suitable plant-microbe combination, and efficiency under a toxic environment needs to be evaluated. Modifying the microbiomes to achieve better biodegradation of contaminants is an upcoming strategy popularly known as microbiome engineering. In this review, rhizoremediation for the successful removal of the hydrocarbons have been critically discussed, with challenges for making it a feasible technology.HIGHLIGHTSPetroleum hydrocarbon contamination has increased around the globe.Rhizoremediation has the potential for the mitigation of pollutants from the contaminated sites.An accurate and detailed analysis of the physio-chemical and climatic conditions of the contaminated sites must be focused on.The suitable plant and bacteria, with other major considerations, may be employed for in-situ remediation.The appropriate data should be obtained using the omics approach to help toward the success of the rhizoremediation strategy.
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Affiliation(s)
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, India
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Gonçalves T, Vasconcelos U. Colour Me Blue: The History and the Biotechnological Potential of Pyocyanin. Molecules 2021; 26:927. [PMID: 33578646 PMCID: PMC7916356 DOI: 10.3390/molecules26040927] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
Pyocyanin was the first natural phenazine described. The molecule is synthesized by about 95% of the strains of Pseudomonas aeruginosa. From discovery up to now, pyocyanin has been characterised by a very rich and avant-garde history, which includes its use in antimicrobial therapy, even before the discovery of penicillin opened the era of antibiotic therapy, as well as its use in electric current generation. Exhibiting an exuberant blue colour and being easy to obtain, this pigment is the subject of the present review, aiming to narrate its history as well as to unveil its mechanisms and suggest new horizons for applications in different areas of engineering, biology and biotechnology.
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Affiliation(s)
| | - Ulrich Vasconcelos
- Centro de Biotecnologia, Departamento de Biotecnologia, Universidade Federal da Paraíba, R. Ipê Amarelo, s/n, Campus I, João Pessoa PB-CEP 58051-900, Brazil;
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Screening of Bacteria Isolated from Refinery Sludge of Assam for Hydrocarbonoclastic Activities. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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26
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Das D, Mawlong GT, Sarki YN, Singh AK, Chikkaputtaiah C, Boruah HPD. Transcriptome analysis of crude oil degrading Pseudomonas aeruginosa strains for identification of potential genes involved in crude oil degradation. Gene 2020; 755:144909. [PMID: 32569720 DOI: 10.1016/j.gene.2020.144909] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 12/27/2022]
Abstract
In the microbial world, bacteria are the most effective agents in petroleum hydrocarbons (PHs) degradation, utilization/mineralization and they serve as essential degraders of crude oil contaminated environment. Some genes and traits are involved in the hydrocarbon utilization process for which transcriptome analyses are important to identify differentially expressed genes (DEGs) among different conditions, leading to a new understanding of genes or pathways associated with crude oil degradation. In this work, three crude oil utilizing Pseudomonas aeruginosa strains designated as N002, TP16 and J001 subjected to transcriptome analyses revealed a total of 81, 269 and 137 significant DEGs. Among them are 80 up-regulated genes and one downregulated gene of N002, 121 up- regulated and 148 down-regulated genes of TP16, 97 up-regulated and 40 down-regulated genes of J001 which are involved in various metabolic pathways. TP16 strain has shown more number of DEGs upon crude oil treatment in comparison to the other two strains. Through quantitative real time polymerase chain reaction (qRT-PCR), the selected DEGs of each strain from transcriptome data were substantiated. The results have shown that the up- regulated and down-regulated genes observed by qRT-PCR were consistent with transcriptome data. Taken together, our transcriptome results have revealed that TP16 is a potential P. aeruginosa strain for functional analysis of identified potential DEGs involved in crude oil degradation.
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Affiliation(s)
- Dhrubajyoti Das
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Gabriella T Mawlong
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - Yogita N Sarki
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Anil Kumar Singh
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Channakeshavaiah Chikkaputtaiah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India
| | - Hari Prasanna Deka Boruah
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat 785006, Assam, India; Academy of Innovative and Scientific Research (AcSIR), CSIR-NEIST, Jorhat 785006, Assam, India.
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Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
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Noor H, Satti SM, Din SU, Farman M, Hasan F, Khan S, Badshah M, Shah AA. Insight on esterase from Pseudomonas aeruginosa strain S3 that depolymerize poly(lactic acid) (PLA) at ambient temperature. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109096] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Xu A, Wang D, Ding Y, Zheng Y, Wang B, Wei Q, Wang S, Yang L, Ma LZ. Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil. Front Microbiol 2020; 11:519. [PMID: 32300337 PMCID: PMC7145413 DOI: 10.3389/fmicb.2020.00519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/10/2020] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental microorganism that can thrive in diverse ecological niches including plants, animals, water, soil, and crude oil. It also one of the microorganism widely used in tertiary recovery of crude oil and bioremediation. However, the genomic information regarding the mechanisms of survival and adapation of this bacterium in crude oil is still limited. In this study, three Pseudomonads strains (named as IMP66, IMP67, and IMP68) isolated from crude oil were taken for whole-genome sequencing by using a hybridized PacBio and Illumina approach. The phylogeny analysis showed that the three strains were all P. aeruginosa species and clustered in clade 1, the group with PAO1 as a representitive. Subsequent comparative genomic analysis revealed a high degree of individual genomic plasticity, with a probable alkane degradation genomic island, one type I-F CRISPR-Cas system and several prophages integrated into their genomes. Nine genes encoding alkane hydroxylases (AHs) homologs were found in each strain, which might enable these strains to degrade alkane in crude oil. P. aeruginosa can produce rhamnolipids (RLs) biosurfactant to emulsify oil, which enables their survival in crude oil enviroments. Our previous report showed that IMP67 and IMP68 were high RLs producers, while IMP66 produced little RLs. Genomic analysis suggested that their RLs yield was not likely due to differences at genetic level. We then further analyzed the quorum sensing (QS) signal molecules that regulate RLs synthesis. IMP67 and IMP68 produced more N-acyl-homoserine lactones (AHLs) signal molecules than that of PAO1 and IMP66, which could explain their high RLs yield. This study provides evidence for adaptation of P. aeruginosa in crude oil and proposes the potential application of IMP67 and IMP68 in microbial-enhanced oil recovery and bioremediation.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Jurong West, Singapore
| | - Yaqian Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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Elufisan TO, Rodríguez-Luna IC, Oyedara OO, Sánchez-Varela A, Hernández-Mendoza A, Dantán Gonzalez E, Paz-González AD, Muhammad K, Rivera G, Villalobos-Lopez MA, Guo X. The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico. PeerJ 2020; 8:e8102. [PMID: 31934497 PMCID: PMC6951288 DOI: 10.7717/peerj.8102] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/25/2019] [Indexed: 11/20/2022] Open
Abstract
Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.
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Affiliation(s)
- Temidayo O Elufisan
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico.,Science Policy and Innovation Studies (SPIS), National Center for Technology Management Obafemi Awolowo University campus Ile-Ife, Ile-Ife, Osun, Nigeria
| | - Isabel C Rodríguez-Luna
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Alejandro Sánchez-Varela
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), Cuernavaca, Morelos, Mexico
| | - Edgar Dantán Gonzalez
- Laboratorio de Estudios Ecogenómicos (UAEM), Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Alma D Paz-González
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Kashif Muhammad
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | - Gildardo Rivera
- Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
| | | | - Xianwu Guo
- Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
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Hydrocarbon degradation potential and competitive persistence of hydrocarbonoclastic bacterium Acinetobacter pittii strain ABC. Arch Microbiol 2019; 201:1129-1140. [DOI: 10.1007/s00203-019-01687-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 02/11/2019] [Accepted: 05/21/2019] [Indexed: 12/18/2022]
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32
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Lee TH, Cao WZ, Tsang DCW, Sheu YT, Shia KF, Kao CM. Emulsified polycolloid substrate biobarrier for benzene and petroleum-hydrocarbon plume containment and migration control - A field-scale study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:839-848. [PMID: 30818208 DOI: 10.1016/j.scitotenv.2019.02.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/10/2019] [Accepted: 02/10/2019] [Indexed: 05/06/2023]
Abstract
The objective of this field-scale study was to assess the effectiveness of applying an emulsified polycolloid substrate (EPS; containing cane molasses, soybean oil, and surfactants) biobarrier in the control and remediation of a petroleum-hydrocarbon plume in natural waters. An abandoned petrochemical manufacturing facility site was contaminated by benzene and other petroleum products due to a leakage from a storage tank. Because benzene is a petroleum hydrocarbon with a high migration ability, it was used as the target compound in the field-scale study. Batch partition and sorption experiment results indicated that the EPS to water partition coefficient for benzene was 232 mg/mg at 25 °C. This suggests that benzene had a higher sorption affinity to EPS, which decreased the benzene concentrations in groundwater. The EPS solution was pressure-injected into three remediation wells (RWs; 150 L EPS in 800 L groundwater). Groundwater samples were collected from an upgradient background well, two downgradient monitor wells (MWs), and the three RWs for analyses. EPS injection increased total organic carbon (TOC) concentrations (up to 786 mg/L) in groundwater, which also resulted in the formation of anaerobic conditions. An abrupt drop in benzene concentration (from 6.9 to below 0.04 mg/L) was observed after EPS supplementation in the RWs due to both sorption and biodegradation mechanisms. Results show that the EPS supplement increased total viable bacteria and enhanced bioremediation efficiency, which accounted for the observed decrease in benzene concentration. The first-order decay rate in RW1 increased from 0.003 to 0.023 d-1 after EPS application. Injection of EPS resulted in significant growth of indigenous bacteria, and 23 petroleum-hydrocarbon-degrading bacterial species were detected, which enhanced the in situ benzene biodegradation efficiency. Results demonstrate that the EPS biobarrier can effectively contain a petroleum-hydrocarbon plume and prevent its migration to downgradient areas, which reduces the immediate risk presented to downgradient receptors.
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Affiliation(s)
- T H Lee
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - W Z Cao
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - D C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Y T Sheu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - K F Shia
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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Promoting the treatment of crude oil alkane pollution through the study of enzyme activity. Int J Biol Macromol 2018; 119:708-716. [PMID: 30055278 DOI: 10.1016/j.ijbiomac.2018.07.160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
Microbes appear to play a key role in bioremediation of petroleum hydrocarbons pollution and little attention has been paid to the enzyme activity in the process of alkane bioremediation. Oil field bacterium identified as Pseudomonas synxantha LSH-7' was chosen as the tested strain. Periodically collected samples were analyzed by GC-FID (Gas Chromatography- Flame Ionization Detector) and RT-qPCR (Quantitative-Real-Time-PCR). GC-FID results showed this bacterial strain has great degradation ability on crude oil n-alkanes and RT-qPCR data indicated the differences between the three genes expression including AlkB-, Cytochromes P450-, and almA- related when grown on different-chain alkanes. Meanwhile, enzyme activity like alkane hydroxylase, alcohol dehydrogenase, dehydrogenase, protease, phosphatase, catalase and lipase were measured. Extracellular alkane hydroxylase was induced in a higher degree than intracellular in the early incubation time, alcohol dehydrogenase increased/decreased along with alkane hydroxylase, and the pH of the medium obviously decreased. Other enzymes were also described including dehydrogenase activity that reached a highest point that was slower than alcohol dehydrogenase, protease activity started multiplying after a period of culture while biomass was immediately increased, catalase activity dramatically enhanced in the presence of alkanes, phosphatase activity was closely linked to pH approximately but lipase activity was found to be moderate.
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Characterization of the genome of a Nocardia strain isolated from soils in the Qinghai-Tibetan Plateau that specifically degrades crude oil and of this biodegradation. Genomics 2018; 111:356-366. [PMID: 29474825 DOI: 10.1016/j.ygeno.2018.02.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 02/16/2018] [Indexed: 11/22/2022]
Abstract
A strain of Nocardia isolated from crude oil-contaminated soils in the Qinghai-Tibetan Plateau degrades nearly all components of crude oil. This strain was identified as Nocardia soli Y48, and its growth conditions were determined. Complete genome sequencing showed that N. soli Y48 has a 7.3 Mb genome and many genes responsible for hydrocarbon degradation, biosurfactant synthesis, emulsification and other hydrocarbon degradation-related metabolisms. Analysis of the clusters of orthologous groups (COGs) and genomic islands (GIs) revealed that Y48 has undergone significant gene transfer events to adapt to changing environmental conditions (crude oil contamination). The structural features of the genome might provide a competitive edge for the survival of N. soli Y48 in oil-polluted environments and reflect the adaptation of coexisting bacteria to distinct nutritional niches.
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Mahmoud GAE, Bagy MMK. Microbial Degradation of Petroleum Hydrocarbons. MICROBIAL ACTION ON HYDROCARBONS 2018:299-320. [DOI: 10.1007/978-981-13-1840-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Satti SM, Shah AA, Auras R, Marsh TL. Isolation and characterization of bacteria capable of degrading poly(lactic acid) at ambient temperature. Polym Degrad Stab 2017. [DOI: 10.1016/j.polymdegradstab.2017.08.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Pal S, Kundu A, Banerjee TD, Mohapatra B, Roy A, Manna R, Sar P, Kazy SK. Genome analysis of crude oil degrading Franconibacter pulveris strain DJ34 revealed its genetic basis for hydrocarbon degradation and survival in oil contaminated environment. Genomics 2017. [DOI: 10.1016/j.ygeno.2017.06.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Draft Genome Sequence of the Type Strain Pseudomonas jessenii DSM 17150. GENOME ANNOUNCEMENTS 2017; 5:5/39/e01035-17. [PMID: 28963214 PMCID: PMC5624760 DOI: 10.1128/genomea.01035-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We present the draft genome sequence of Pseudomonas jessenii type strain DSM 17150. The assembly consists of 13 contigs, contains 6,537,206 bp, and has a GC content of 59.7%.
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Whole genome sequencing and functional features of UMX-103: a new Bacillus strain with biosurfactant producing capability. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas aeruginosa DN1 isolated from petroleum-contaminated soil. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lim MW, Lau EV, Poh PE. A comprehensive guide of remediation technologies for oil contaminated soil - Present works and future directions. MARINE POLLUTION BULLETIN 2016; 109:14-45. [PMID: 27267117 DOI: 10.1016/j.marpolbul.2016.04.023] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED Oil spills result in negative impacts on the environment, economy and society. Due to tidal and waves actions, the oil spillage affects the shorelines by adhering to the soil, making it difficult for immediate cleaning of the soil. As shoreline clean-up is the most costly component of a response operation, there is a need for effective oil remediation technologies. This paper provides a review on the remediation technologies for soil contaminated with various types of oil, including diesel, crude oil, petroleum, lubricating oil, bitumen and bunker oil. The methods discussed include solvent extraction, bioremediation, phytoremediation, chemical oxidation, electrokinetic remediation, thermal technologies, ultrasonication, flotation and integrated remediation technologies. Each of these technologies was discussed, and associated with their advantages, disadvantages, advancements and future work in detail. Nonetheless, it is important to note that no single remediation technology is considered the best solution for the remediation of oil contaminated soil. CAPSULE This review provides a comprehensive literature on the various remediation technologies studied in the removal of different oil types from soil.
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Affiliation(s)
- Mee Wei Lim
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Ee Von Lau
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Phaik Eong Poh
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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Chai LJ, Jiang XW, Zhang F, Zheng BW, Shu FC, Wang ZL, Cui QF, Dong HP, Zhang ZZ, Hou DJ, She YH. Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains. J Zhejiang Univ Sci B 2016; 16:865-74. [PMID: 26465134 DOI: 10.1631/jzus.b1500029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 °C and pH 5.5. We sequenced the genome and found a single chromosome of 4 800 175 bp, with a G+C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified: many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains (M86, 229E, and LMG3301(T)) showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.
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Affiliation(s)
- Lu-jun Chai
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing 100083, China
| | - Xia-wei Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Fan Zhang
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing 100083, China
| | - Bei-wen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Fu-chang Shu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Zheng-liang Wang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
| | - Qing-feng Cui
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China
| | - Han-ping Dong
- Institute of Porous Flow & Fluid Mechanics, Chinese Academy of Sciences, Langfang 065007, China
| | - Zhong-zhi Zhang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 257061, China
| | - Du-jie Hou
- Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, School of Energy Resources, China University of Geosciences, Beijing 100083, China
| | - Yue-hui She
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, China
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Characterization of the transcriptome of Achromobacter sp. HZ01 with the outstanding hydrocarbon-degrading ability. Gene 2016; 584:185-94. [PMID: 26915487 DOI: 10.1016/j.gene.2016.02.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 01/24/2016] [Accepted: 02/20/2016] [Indexed: 12/19/2022]
Abstract
Microbial remediation has become one of the most important strategies for eliminating petroleum pollutants. Revealing the transcript maps of microorganisms with the hydrocarbon-degrading ability contributes to enhance the degradation of hydrocarbons and further improve the effectiveness of bioremediation. In this study, we characterized the transcriptome of hydrocarbon-degrading Achromobacter sp. HZ01 after petroleum treatment for 16h. A total of 38,706,280 and 38,954,413 clean reads were obtained by RNA-seq for the petroleum-treated group and control, respectively. By an effective de novo assembly, 3597 unigenes were obtained, including 3485 annotated transcripts. Petroleum treatment had significantly influenced the transcriptional profile of strain HZ01, involving 742 differentially expressed genes. A part of genes were activated to exert specific physiological functions, whereas more genes were down-regulated including specific genes related to cell motility, genes associated with glycometabolism, and genes coding for ribosomal proteins. Identification of genes related to petroleum degradation revealed that the fatty acid metabolic pathway and a part of monooxygenases and dehydrogenases were activated, whereas the TCA cycle was inactive. Additionally, terminal oxidation might be a major aerobic pathway for the degradation of n-alkanes in strain HZ01. The newly obtained data contribute to better understand the gene expression profiles of hydrocarbon-degrading microorganisms after petroleum treatment, to further investigate the genetic characteristics of strain HZ01 and other related species and to develop cost-effective and eco-friendly strategies for remediation of crude oil-polluted environments.
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