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Romero-González LE, Montelongo-Martínez LF, González-Valdez A, Quiroz-Morales SE, Cocotl-Yañez M, Franco-Cendejas R, Soberón-Chávez G, Pardo-López L, Bustamante VH. Pseudomonas aeruginosa Isolates from Water Samples of the Gulf of Mexico Show Similar Virulence Properties but Different Antibiotic Susceptibility Profiles than Clinical Isolates. Int J Microbiol 2024; 2024:6959403. [PMID: 38784405 PMCID: PMC11115996 DOI: 10.1155/2024/6959403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/14/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen found in a wide variety of environments, including soil, water, and habitats associated with animals, humans, and plants. From a One Health perspective, which recognizes the interconnectedness of human, animal, and environmental health, it is important to study the virulence characteristics and antibiotic susceptibility of environmental bacteria. In this study, we compared the virulence properties and the antibiotic resistance profiles of seven isolates collected from the Gulf of Mexico with those of seven clinical strains of P. aeruginosa. Our results indicate that the marine and clinical isolates tested exhibit similar virulence properties; they expressed different virulence factors and were able to kill Galleria mellonella larvae, an animal model commonly used to analyze the pathogenicity of many bacteria, including P. aeruginosa. In contrast, the clinical strains showed higher antibiotic resistance than the marine isolates. Consistently, the clinical strains exhibited a higher prevalence of class 1 integron, an indicator of anthropogenic impact, compared with the marine isolates. Thus, our results indicate that the P. aeruginosa marine strains analyzed in this study, isolated from the Gulf of Mexico, have similar virulence properties, but lower antibiotic resistance, than those from hospitals.
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Affiliation(s)
- Luis E. Romero-González
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Luis F. Montelongo-Martínez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Sara E. Quiroz-Morales
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Miguel Cocotl-Yañez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Rafael Franco-Cendejas
- Instituto Nacional de Rehabilitación “Luis Guillermo Ibarra Ibarra,” Ciudad de México, Mexico
| | - Gloria Soberón-Chávez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Coyoacán, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Víctor H. Bustamante
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Zhou Z, Zhuo L, Fu X, Zou Q. Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs. Brief Bioinform 2023; 25:bbad483. [PMID: 38171927 PMCID: PMC10764208 DOI: 10.1093/bib/bbad483] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/25/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Exploring microbial stress responses to drugs is crucial for the advancement of new therapeutic methods. While current artificial intelligence methodologies have expedited our understanding of potential microbial responses to drugs, the models are constrained by the imprecise representation of microbes and drugs. To this end, we combine deep autoencoder and subgraph augmentation technology for the first time to propose a model called JDASA-MRD, which can identify the potential indistinguishable responses of microbes to drugs. In the JDASA-MRD model, we begin by feeding the established similarity matrices of microbe and drug into the deep autoencoder, enabling to extract robust initial features of both microbes and drugs. Subsequently, we employ the MinHash and HyperLogLog algorithms to account intersections and cardinality data between microbe and drug subgraphs, thus deeply extracting the multi-hop neighborhood information of nodes. Finally, by integrating the initial node features with subgraph topological information, we leverage graph neural network technology to predict the microbes' responses to drugs, offering a more effective solution to the 'over-smoothing' challenge. Comparative analyses on multiple public datasets confirm that the JDASA-MRD model's performance surpasses that of current state-of-the-art models. This research aims to offer a more profound insight into the adaptability of microbes to drugs and to furnish pivotal guidance for drug treatment strategies. Our data and code are publicly available at: https://github.com/ZZCrazy00/JDASA-MRD.
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Affiliation(s)
- Zhecheng Zhou
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, 325000, Wenzhou, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, 325000, Wenzhou, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, 410012, Changsha, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, 611730, Chengdu, China
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Ley Y, Cheng XY, Ying ZY, Zhou NY, Xu Y. Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions. Microbiol Spectr 2023; 11:e0442422. [PMID: 37042774 PMCID: PMC10269927 DOI: 10.1128/spectrum.04424-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 04/13/2023] Open
Abstract
Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.
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Affiliation(s)
- Yvette Ley
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yu Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Yue Ying
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Jiang J, Zhao J, Zhao G, Liu L, Song H, Liao S. Recognition, possible source, and risk assessment of organic pollutants in surface water from the Yongding River Basin by non-target and target screening. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023:121895. [PMID: 37236593 DOI: 10.1016/j.envpol.2023.121895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
Organic pollutants in aquatic environment could have important implications on pollution stress on aquatic organisms and even on the risk of human exposure. Thus, revealing their occurrence in aquatic environment is essential for water quality monitoring and ecological risk purposes. In this study, a comprehensive two-dimensional gas chromatography connected with time-of-flight mass spectrometry (GC × GC-TOF-MS) was applied, to enable non-target and target analysis of pollutants in the Yongding River Basin. Based on the isotopic patterns, accurate masses and standard substances, certain environmental contaminants were tentatively identified which including polycyclic aromatic hydrocarbon (PAHs), organochlorine pesticides (OCPs), phenols, amines, etc. The compounds with the highest concentration were naphthalene (109.0 ng/L), 2,3-benzofuran (51.5 ng/L) and 1,4-dichlorobenzene (35.9 ng/L) in Guishui River. Wastewater treatment plants (WWTPs) discharges were a main source of pollutants in Yongding River Basin, as the types of compounds screened in the downstream river were relatively similar to those from WWTPs. According to the target analysis, a number of pollutants were selected due to the acute toxicity and cumulative discharge from WWTPs and downstream rivers. Three PAHs (naphthalene, Benzo(b)fluoranthene and pyrene) homologues showed moderate risk to fish and H. Azteca in Yongding River Basin, while the rest of the measured chemicals showed low ecological impact across the entire study area based on the risk assessment. The results are helpful for understanding the necessity of high-throughput screening analysis for assessing water quality of rivers and the discharge emissions of pollutants from WWTPs to the river environment.
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Affiliation(s)
- Jingqiu Jiang
- Department of Environmental Science & Engineering, North China Electric Power University, Baoding, 071000, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, No.12 South Zhongguancun Ave., Haidian District, Beijing, 100081, China
| | - Jian Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Gaofeng Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, No.12 South Zhongguancun Ave., Haidian District, Beijing, 100081, China.
| | - Lin Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, No.12 South Zhongguancun Ave., Haidian District, Beijing, 100081, China
| | - Huarong Song
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, No.12 South Zhongguancun Ave., Haidian District, Beijing, 100081, China; Qingdao Engineering Research Center for Rural Environment, College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Siyuan Liao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, No.12 South Zhongguancun Ave., Haidian District, Beijing, 100081, China
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Nathani NM, Mootapally C, Sharma P, Solomon S, Kumar R, Fulke AB, Kumar M. Microbial machinery dealing diverse aromatic compounds: Decoded from pelagic sediment ecogenomics in the gulfs of Kathiawar Peninsula and Arabian Sea. ENVIRONMENTAL RESEARCH 2023; 225:115603. [PMID: 36863652 DOI: 10.1016/j.envres.2023.115603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/16/2023] [Accepted: 02/28/2023] [Indexed: 05/25/2023]
Abstract
Aromatic hydrocarbons are persistent pollutants in aquatic systems as endocrine disruptors, significantly impacting natural ecosystems and human health. Microbes perform as natural bioremediators to remove and regulate aromatic hydrocarbons in the marine ecosystem. The present study focuses upon the comparative diversity and abundance of various hydrocarbon-degrading enzymes and their pathways from deep sediments along the Gulf of Kathiawar Peninsula and Arabian Sea, India. The elucidation of large number of degradation pathways in the study area under the presence of a wide range of pollutants whose fate needs to be addressed. Sediment core samples were collected, and the whole microbiome was sequenced. Analysis of the predicted ORFs (open reading frames) against the AromaDeg database revealed 2946 aromatic hydrocarbon-degrading enzyme sequences. Statistical analysis portrayed that the Gulfs were more diverse in degradation pathways compared to the open sea, with the Gulf of Kutch being more prosperous and more diverse than the Gulf of Cambay. The vast majority of the annotated ORFs belonged to groups of dioxygenases that included catechol, gentisate, and benzene dioxygenases, along with Rieske (2Fe-2S) and vicinal oxygen chelate (VOC) family proteins. From the sampling sites, only 960 of the total predicted genes were given taxonomic annotations, which mention the presence of many under-explored marine microorganism-derived hydrocarbon degrading genes and pathways. Through the present study, we tried to unveil the array of catabolic pathways of aromatic hydrocarbon degradation and genes from a marine ecosystem that upholds economic and ecological significance in India. Thus, this study provides vast opportunities and strategies for microbial resource recovery in marine ecosystems, which can be investigated to explore aromatic hydrocarbon degradation and their potential mechanisms under various oxic or anoxic environments. Future studies should focus on aromatic hydrocarbon degradation by considering degradation pathways, biochemical analysis, enzymatic, metabolic, and genetic systems, and regulations.
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Affiliation(s)
- Neelam M Nathani
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Life Sciences, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Chandrashekar Mootapally
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India; Department of Marine Science, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, 364001, Gujarat, India
| | - Parth Sharma
- School of Applied Sciences & Technology (SAST-GTU), Gujarat Technological University, Ahmedabad, 382424, Gujarat, India
| | - Solly Solomon
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science & Technology, Kochi, 682022, Kerala, India; Cochin Base of Fishery Survey of India, Post Box 853 Kochangady, Cochin, 682005, Kerala, India
| | - Rakesh Kumar
- School of Ecology and Environment Studies, Nalanda University, Rajgir, 803116, Bihar, India
| | - Abhay B Fulke
- Microbiology Division, CSIR - National Institute of Oceanography (CSIR-NIO), Regional Centre, Andheri (West), Maharashtra, 400053, India
| | - Manish Kumar
- Sustainability Cluster, University of Petroleum & Energy Studies, Dehradun, Uttarakhand, 248007, India; Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Campus Monterey, Monterrey, 64849, Nuevo Leon, Mexico.
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Han Z, Lin Q, Zhang S, Zhou X, Li S, Sun F, Shen C, Su X. High PCBs mineralization capability of a resuscitated strain Bacillus sp. LS1 and its survival in PCB-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159224. [PMID: 36206912 DOI: 10.1016/j.scitotenv.2022.159224] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Polychlorinated biphenyl (PCB)-degrading strains resuscitated by resuscitation promoting factor (Rpf) enlarged pure degraders to screen effective bio-inoculants for soil bioaugmentation. In this study, whole-genome analysis and PCB-degrading performance of a resuscitated strain LS1 were investigated. Importantly, the persistence and the physiological response of soil-inoculated LS1 were checked. The results indicate that the Bacillus sp. strain LS1 possessed the potential to degrade polycyclic aromatic compounds. LS1 exhibited better performance in degrading PCBs 18 and 52, but lower PCB 77 degradation capability. At PCBs concentration of 10 mg/L, the degradation efficiencies of PCBs 18, 52 and 77 within 96 h were 62.8 %, 59.6 % and 39.8 %, respectively. Combined the bph genes and metabolites detected, as well as the genes found in the genome, the abilities of LS1 for oxidative dehalogenation and mineralization of PCBs via HOPDA-benzoate-protocatechuate-β-ketoadipate pathway were determined. Notably, LS1 can still maintain survival and culturable state after inoculation into PCB-contaminated soil for 70 days. This is the first report to demonstrate the fate of resuscitated strain when used as soil bio-inoculant, which revealed the necessity and feasibility of using resuscitated strains to enhance bioremediation of PCB-contaminated soils.
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Affiliation(s)
- Zhen Han
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Qihua Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou 325500, China
| | - Xinru Zhou
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Si Li
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua 321004, China.
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Sandhu M, Paul AT, Proćków J, de la Lastra JMP, Jha PN. PCB-77 biodegradation potential of biosurfactant producing bacterial isolates recovered from contaminated soil. Front Microbiol 2022; 13:952374. [PMID: 36225351 PMCID: PMC9549355 DOI: 10.3389/fmicb.2022.952374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants widely distributed in the environment and possess deleterious health effects. The main objective of the study was to obtain bacterial isolates from PCB-contaminated soil for enhanced biodegradation of PCB-77. Selective enrichment resulted in the isolation of 33 strains of PCB-contaminated soil nearby Bhilai steel plant, Chhattisgarh, India. Based on the prominent growth using biphenyl as the sole carbon source and the confirmation of its degradation by GC-MS/MS analysis, four isolates were selected for further study. The isolates identified by 16S rRNA gene sequencing were Pseudomonas aeruginosa MAPB-2, Pseudomonas plecoglossicida MAPB-6, Brucella anthropi MAPB-9, and Priestia megaterium MAPB-27. The isolate MAPB-9 showed a degradation of 66.15% biphenyl, while MAPB-2, MAPB-6, and MAPB-27 showed a degradation of 62.06, 57.02, and 56.55%, respectively in 48 h. Additionally, the degradation ability of these strains was enhanced with addition of co-metabolite glucose (0.2%) in the culture medium. Addition of glucose showed 100% degradation of biphenyl by MAPB-9, in 48 h, while MAPB-6, MAPB-2, and MAPB-27 showed 97.1, 67.5, and 53.3% degradation, respectively as analyzed by GC-MS/MS. Furthermore, in the presence of inducer, PCB-77 was found to be 59.89, 30.49, 27.19, and 4.43% degraded by MAPB-6, MAPB-9, MAPB-2, and MAPB-27, respectively in 7 d. The production of biosurfactants that aid in biodegradation process were observed in all the isolates. This was confirmed by ATR-FTIR analysis that showed the presence of major functional groups (CH2, CH3, CH, = CH2, C–O–C, C-O) of the biosurfactant. The biosurfactants were further identified by HPTLC and GC-MS/MS analysis. Present study is the first to report PCB-77 degradation potential of Pseudomonas aeruginosa, B. anthropi, Pseudomonas plecoglossicida, and Priestia megaterium. Similarly, this is the first report on Pseudomonas plecoglossicida and Priestia megaterium for PCB biodegradation. Our results suggest that the above isolates can be used for the biodegradation of biphenyl and PCB-77 in PCB-contaminated soil.
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Affiliation(s)
- Monika Sandhu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Atish T. Paul
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - José Manuel Pérez de la Lastra
- Biotecnología de Macromoléculas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
- José Manuel Pérez de la Lastra,
| | - Prabhat N. Jha
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
- *Correspondence: Prabhat N. Jha,
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Ullah R, Zhu B, Kakar KU, Nawaz Z, Mushtaq M, Durrani TS, Islam ZU, Nawaz F. Micro-synteny conservation analysis revealed the evolutionary history of bacterial biphenyl degradation pathway. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:494-505. [PMID: 35560986 DOI: 10.1111/1758-2229.13081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Phenolic compounds have been enlisted by the United States Environmental Protection Agency (USEPA) and the European Union (EU) as pollutants of priority concern. The biphenyl degradation pathway plays an essential role in prokaryote polychlorinated biphenyls degradation. Our understanding of prokaryotic pathways and their evolution has dramatically increased in recent years with the advancements in prokaryotic genome sequencing and analysis tools. In this work, we applied bioinformatics tools to study the evolution of the biphenyl degradation pathway focusing on the phylogeny and initiation of four representative species (Burkholderia xenovorans LB400, Polaromonas naphthalenivorans CJ2, Pseudomonas putida F1 and Rhodococcus jostii RHA1). These species contained partial or full concatenated genes from bph gene cluster (i.e. bphRbphA1A2A3A4BCKHJID). The aim was to establish this pathway's origin and development mode in the prokaryotic world. Genomic screening revealed that many bacterial species possess genes for the biphenyl degradation pathway. However, the micro-synteny conservation analysis indicated that massive gene recruitment events might have occurred during the evolution of the biphenyl degradation pathway. Combining with the phylogenetic positions, this work points to the evolutionary process of acquiring the biphenyl degradation pathway by different fragments through horizontal gene transfer in these bacterial groups. This study reports the first-ever evidence of the birth of this pathway in the represented species.
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Affiliation(s)
- Raqeeb Ullah
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Kaleem U Kakar
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Zarqa Nawaz
- Department of Botany, University of Central Punjab, Rawalpindi, Pakistan
| | - Muhammd Mushtaq
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Taimoor Shah Durrani
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
| | - Zia Ul Islam
- Department of Civil and Environmental Engineering, The University of Toledo, Toledo, OH, USA
| | - Faheem Nawaz
- Department of Environmental Science, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, 87300, Pakistan
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Cai X, Luo X, Yuan Y, Li J, Yu Z, Zhou S. Stimulation of phenanthrene and biphenyl degradation by biochar-conducted long distance electron transfer in soil bioelectrochemical systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 797:149124. [PMID: 34303229 DOI: 10.1016/j.scitotenv.2021.149124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
The bioelectrochemical degradation of organic pollutants has attracted considerable attention owing to its remarkable sustainability and low cost. However, the application of bioelectrochemical system (BES) for the degradation of pollutants in soils is hindered by limitations in the effective distance in the soil matrix. In this study, a biochar-amended BES was constructed to evaluate the degradation of organic pollutants. This system was expected to extend the electron transfer distance via conductive biochar in soils. The results showed that biochar pyrolyzed at 900 °C facilitated the degradation of phenanthrene (PHE) and biphenyl (BP) in the soil BES (SBES), reaching 86.4%-95.1% and 88.8%-95.3% in 27 days, respectively. The effective distance of SBESs was estimated to be 154-271 cm away from the electrode, which increased 1.9-3 fold after the addition of biochar. Microbial community and functional gene analysis confirmed that biochar enriched functional degrading bacteria. These findings demonstrate that the promotion of long-distance electron transfer and the formation of soil conductive networks can be achieved by biochar amendment. Thus, this study provides a basis for the effective degradation of for persistent organic pollutants in petroleum-contaminated soils using bioelectrochemical strategy.
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Affiliation(s)
- Xixi Cai
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiaoshan Luo
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Yong Yuan
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Zhen Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Muriel-Millán LF, Millán-López S, Pardo-López L. Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics. Appl Microbiol Biotechnol 2021; 105:7171-7185. [PMID: 34515846 DOI: 10.1007/s00253-021-11569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/25/2022]
Abstract
Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
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Affiliation(s)
- Luis Felipe Muriel-Millán
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Ciudad Universitaria, CDMX, Mexico.
| | - Sofía Millán-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Liliana Pardo-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
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11
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Li J, Chen W, Zhou W, Wang Y, Deng M, Zhou S. Synergistic degradation of pyrene by Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 with sodium citrate as the co-metabolic carbon source. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1487-1498. [PMID: 32844301 DOI: 10.1007/s10646-020-02268-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Two pyrene-degrading strains, Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 were co-incubated in equal proportions as a microbiological consortium and could enhance the degradation of pyrene. The enzymatic activities of the catechol 1,2-dioxygenase (C12O) and 2,3-dioxygenase activities (C23O) were produced complementary expression by P. aeruginosa PA06 and Achromobacter sp. AC15, respectively. Meanwhile, results showed that pyrene degradation was sufficiently promoted in the presence of sodium citrate as a co-metabolic carbon source, likely a result of enhanced biomass and biosurfactant production. The optimized dosage and ideal initial pHs were 1.4 g L-1 and 5.5, respectively. We also analyzed the rate constant of pyrene degradation, cell growth, and enzyme activity. Results show that P. aeruginosa PA06 had a better effect than Achromobacter sp. AC15 in bacterial growth. However, the C23O or C12O activity produced by Achromobacter sp. AC15 continued at a similar or even faster than that of P. aeruginosa PA06. The mixed bacteria had a better effect than any single bacteria, suggesting the strains worked synergistically to enhance the degradation efficiency. In the co-metabolism system of 600 mg/L pyrene and 1.4 g/L sodium citrate, pyrene degradation reached 74.6%, was 1.57 times, 2.06 times, and 3.89 times that of the mix-culture strains, single PA06 and single AC15 without sodium citrate, respectively. Overall, these findings are valuable as a potential tool for the bioremediation of high-molecular-weight PAHs.
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Affiliation(s)
- Jing Li
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, 510006, People's Republic of China
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, 510300, People's Republic of China
| | - Weixin Chen
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, 510300, People's Republic of China
| | - Wei Zhou
- Guizhou Academy of Sciences, 1 Shanxi Road, Guiyang, 550001, People's Republic of China
| | - Yao Wang
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, 510300, People's Republic of China
| | - Maocheng Deng
- School of Food and Biotechnology, Guangdong Industry Polytechnic, Guangzhou, 510300, People's Republic of China.
| | - Shaoqi Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou, 510006, People's Republic of China.
- Guizhou Academy of Sciences, 1 Shanxi Road, Guiyang, 550001, People's Republic of China.
- State Key Laboratory of Subtropical Building Science, South China University of Technology, Guangzhou, 510641, People's Republic of China.
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12
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Segura A, Udaondo Z, Molina L. PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres. Environ Microbiol 2021; 23:2969-2991. [PMID: 33817928 PMCID: PMC8360164 DOI: 10.1111/1462-2920.15509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 01/23/2023]
Abstract
Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.
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Affiliation(s)
- Ana Segura
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
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Hentati D, Chebbi A, Mahmoudi A, Hadrich F, Cheffi M, Frikha I, Sayadi S, Chamkha M. Biodegradation of hydrocarbons and biosurfactants production by a newly halotolerant Pseudomonas sp. strain isolated from contaminated seawater. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107861] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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14
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Mahto KU, Das S. Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111087. [PMID: 32871516 DOI: 10.1016/j.ecoenv.2020.111087] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Zhu L, Zhou J, Zhang R, Tang X, Wang J, Li Y, Zhang Q, Wang W. Degradation mechanism of biphenyl and 4-4'-dichlorobiphenyl cis-dihydroxylation by non-heme 2,3 dioxygenases BphA: A QM/MM approach. CHEMOSPHERE 2020; 247:125844. [PMID: 32069708 DOI: 10.1016/j.chemosphere.2020.125844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
Biphenyl 2,3-dioxygenase (BphA), a Rieske-type and first enzyme in the aerobic degradation process, plays a key role in the metabolizing process of biphenyl/polychlorinated biphenyl aromatic pollutants in the environment. To understand the catalytic mechanism of biphenyl 2,3-dioxygenase, the conversions leading to the cis-diols are investigated by means of quantum mechanics/molecular mechanics (QM/MM) method. A hydroperoxo-iron (III) species is involved in the enzyme-catalyzed reaction. Herein, we explored the direct reaction mechanism of hydroperoxo-iron (III) species with biphenyl and 4-4'-dichlorobiphenyl. The reaction process involves an epoxide intermediate, it could develop into a carbocation intermediate, and ultimately evolve into a cis-diol product. The important roles of several residues during the dioxygenation process were highlighted. This study may provide theoretical support for further directed mutations and enzymatic engineering of BphA, as well as promote the development of degrading environmentally persistent biphenyl/polychlorinated biphenyl aromatic contaminants.
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Affiliation(s)
- Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Jie Zhou
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Junjie Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao, 266237, PR China
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Steliga T, Wojtowicz K, Kapusta P, Brzeszcz J. Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture. Molecules 2020; 25:E709. [PMID: 32041368 PMCID: PMC7036857 DOI: 10.3390/molecules25030709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 01/31/2023] Open
Abstract
Biodegradation is one of the most effective and profitable methods for the elimination of toxic polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPH) from the environment. In this study, aerobic degradation of the mentioned pollutants by bacterial strains Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN129, and Rhodococcus sp. IN306 and mixed culture M1 developed based on those strains at 1:1:1 ratio was analyzed. The effectiveness of individual strains and of the mixed culture was assessed based on carried out respirometric tests and chromatographic analyses. The Rhodococcus sp. IN306 turned out most effective in terms of 18 PCB congeners biodegradation (54.4%). The biodegradation index was decreasing with an increasing number of chlorine atoms in a molecule. Instead, the Mycolicobacterium frederiksbergense IN53 was the best TPH degrader (37.2%). In a sterile soil, contaminated with PCBs and TPH, the highest biodegradation effectiveness was obtained using inoculation with mixed culture M1, which allowed to reduce both the PCBs (51.8%) and TPH (34.6%) content. The PCBs and TPH biodegradation capacity of the defined mixed culture M1 was verified ex-situ with prism method in a non-sterile soil polluted with aged petroleum hydrocarbons (TPH) and spent transformer oil (PCBs). After inoculation with mixed culture M1, the PCBs were reduced during 6 months by 84.5% and TPH by 70.8% as well as soil toxicity was decreased.
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Affiliation(s)
- Teresa Steliga
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Katarzyna Wojtowicz
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
| | - Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
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17
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Liu G, Li X, Ma L, Ma X, Chen H. Enhancement of excess sludge hydrolysis and decomposition by combined lysozyme and rhamnolipid pretreatment. BIORESOURCE TECHNOLOGY 2019; 289:121703. [PMID: 31271912 DOI: 10.1016/j.biortech.2019.121703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/22/2019] [Accepted: 06/25/2019] [Indexed: 06/09/2023]
Abstract
Feasibility of combined lysozyme and rhamolipid (RL) pretreatment on the enhancement of excess sludge (ES) hydrolysis and decomposition was assessed in this study. Results showed lysozyme and RL combined treatment could significantly promote ES hydrolysis and decomposition, an additional 1196.9 mg/L soluble chemical oxygen demand (SCOD), 792.5 mg/L protein and 133.5 mg/L polysaccharide were released compared with the sum of sole RL and sole lysozyme treatment at the optimal RL dosage of 0.3 g/gSS and lysozyme dosage of 0.15 g/gSS after 8 h co-digestion. 45.3% bacteria and 84.5% archaea decomposition degree were gained under the combined treatment at the optimal RL dosage. Class Gammaproteobacteria and genus Methanothrix were the predominant bacteria and archaea with the relative abundance of 72.4% and 60.8%, respectively. After the combined pretreatment, ES was beneficial for volatile fatty acids accumulation and acetic acid dependent methane generating inferred from the results of microbial community composition.
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Affiliation(s)
- Gaige Liu
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiangkun Li
- School of Environment, Harbin Institute of Technology, Harbin 150090, China; School of Civil and Transportation, Hebei University of Technology, Tianjin 300401, China.
| | - Linli Ma
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiaochen Ma
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hongying Chen
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
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18
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Voronina AO, Egorova DO, Korsakova ES, Plotnikova EG. Diversity of the bphA1 Genes in a Microbial Community from Anthropogenically Contaminated Soil and Isolation of New Pseudomonads Degrading Biphenyl/Chlorinated Biphenyls. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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Zeng Z, Liu Y, Zhong H, Xiao R, Zeng G, Liu Z, Cheng M, Lai C, Zhang C, Liu G, Qin L. Mechanisms for rhamnolipids-mediated biodegradation of hydrophobic organic compounds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1-11. [PMID: 29625372 DOI: 10.1016/j.scitotenv.2018.03.349] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
The widespread existence of hydrophobic organic compounds (HOCs) in soil and water poses a potential health hazard to human, such as skin diseases, heart diseases, carcinogenesis, etc. Surfactant-enhanced bioremediation has been regarded as one of the most viable technologies to treat HOCs contaminated soil and groundwater. As a biosurfactant that has been intensively studied, rhamnolipids have shown to enhance biodegradation of HOCs in the environment, however, the underlying mechanisms are not fully disclosed. In this paper, properties and production of rhamnolipids are summarized. Then effects of rhamnolipids on the biodegradation of HOCs, including solubilization, altering cell affinity to HOCs, and facilitating microbial uptake are reviewed in detail. Special attention is paid to how rhamnolipids change the bioavailability of HOCs, which are crucial for understanding the mechanism of rhamnolipids-mediated biodegradation. The biodegradation and toxicity of rhamnolipids are also discussed. Finally, perspectives and future research directions are proposed. This review adds insight to rhamnolipids-enhanced biodegradation process, and helps in application of rhamnolipids in bioremediation.
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Affiliation(s)
- Zhuotong Zeng
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, PR China
| | - Yang Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Hua Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China; State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430070, PR China
| | - Rong Xiao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, PR China
| | - Guangming Zeng
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, PR China; College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Zhifeng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Min Cheng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Cui Lai
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Chen Zhang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guansheng Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Lei Qin
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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21
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Tripathi L, Irorere VU, Marchant R, Banat IM. Marine derived biosurfactants: a vast potential future resource. Biotechnol Lett 2018; 40:1441-1457. [PMID: 30145666 PMCID: PMC6223728 DOI: 10.1007/s10529-018-2602-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/21/2018] [Indexed: 01/25/2023]
Abstract
Surfactants and emulsifiers are surface-active compounds (SACs) which play an important role in various industrial processes and products due to their interfacial properties. Many of the chemical surfactants in use today are produced from non-renewable petrochemical feedstocks, while biosurfactants (BS) produced by microorganisms from renewable feedstocks are considered viable alternatives to petroleum based surfactants, due to their biodegradability and eco-friendly nature. However, some well-characterised BS producers are pathogenic and therefore, not appropriate for scaled-up production. Marine-derived BS have been found to be produced by non-pathogenic organisms making them attractive possibilities for exploitation in commercial products. Additionally, BS produced from marine bacteria may show excellent activity at extreme conditions (temperature, pH and salinity). Despite being non-pathogenic, marine-derived BS have not been exploited commercially due to their low yields, insufficient structural elucidation and uncharacterised genes. Therefore, optimization of BS production conditions in marine bacteria, characterization of the compounds produced as well as the genes involved in the biosynthesis are necessary to improve cost-efficiency and realise the industrial demands of SACs.
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Affiliation(s)
- Lakshmi Tripathi
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, BT52 1SA, UK
| | - Victor U Irorere
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, BT52 1SA, UK
| | - Roger Marchant
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, BT52 1SA, UK
| | - Ibrahim M Banat
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Coleraine, BT52 1SA, UK.
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22
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23
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Ma J, Zhu C, Lu J, Wang T, Hu S, Chen T. Photochemical reaction between biphenyl and N(III) in the atmospheric aqueous phase. CHEMOSPHERE 2017; 167:462-468. [PMID: 27750170 DOI: 10.1016/j.chemosphere.2016.10.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 10/02/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
The photochemical reaction between biphenyl (Bp) and N(III) under irradiation at 365 nm UV light was investigated. The results showed that Bp conversion efficiency was strongly influenced by N (III) concentration, Bp initial concentration and pH. Species-specific rate constants determined by reaction of Bp with H2ONO+ (k1), HONO (k2) and NO2- (k3) were k1 = (0.058 ± 0.005 L mol-1 s-1), k2 = (0.12 ± 0.06 L mol-1 s-1) and k3 = (0.0019 ± 0.0003 L mol-1 s-1), respectively. Laser flash photolysis studies confirmed that OH radical deriving from the photolysis of N(III) attacked aromatic ring to form Bp-OH adduct with a rate constant of 9.4 × 109 L mol-1 s-1. The products analysis suggested that Bp-OH adduct could be nitrated by N (III) and NO2 to generate nitro-compounds.
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Affiliation(s)
- Jianzhong Ma
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China; Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, PR China
| | - Chengzhu Zhu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China; Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, PR China.
| | - Jun Lu
- Center of Analysis & Measurement, Hefei University of Technology, Hefei 230009, PR China
| | - Tao Wang
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China; Institute of Atmospheric Environment & Pollution Control, Hefei University of Technology, Hefei 230009, PR China
| | - Shuheng Hu
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China
| | - Tianhu Chen
- School of Resource and Environmental Engineering, Hefei University of Technology, Hefei 230009, PR China
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Evidence of mercury trapping in biofilm-EPS and mer operon-based volatilization of inorganic mercury in a marine bacterium Bacillus cereus BW-201B. Arch Microbiol 2016; 199:445-455. [DOI: 10.1007/s00203-016-1317-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 08/23/2016] [Accepted: 10/25/2016] [Indexed: 01/17/2023]
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Chakraborty J, Das S. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:16883-16903. [PMID: 27234838 DOI: 10.1007/s11356-016-6887-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.
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Affiliation(s)
- Jaya Chakraborty
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769 008, Odisha, India.
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