1
|
Zhang M, Chen Q, Gong Z. Microbial remediation of petroleum-contaminated soil focused on the mechanism and microbial response: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:33325-33346. [PMID: 38709405 DOI: 10.1007/s11356-024-33474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
The environmental pollution caused by petroleum hydrocarbons has received considerable attention in recent years. Microbial remediation has emerged as the preferred method for the degradation of petroleum hydrocarbons, which is experiencing rapid development driven by advancements in molecular biology. Herein, the capacity of different microorganisms used for crude oil bioremediation was reviewed. Moreover, factors influencing the effectiveness of microbial remediation were discussed. Microbial remediation methods, such as bioaugmentation, biostimulation, and bioventilation, are summarized in this review. Aerobic and anaerobic degradation mechanisms were reviewed to elucidate the metabolic pathways involved. The impacts of petroleum hydrocarbons on microorganisms and the environment were also revealed. A brief overview of synthetic biology and a unique perspective of technique combinations were presented to provide insight into research trends. The challenges and future outlook were also presented to stimulate contemplation of the mechanisms involved and the development of innovative techniques.
Collapse
Affiliation(s)
- Mingjian Zhang
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Qing Chen
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Zheng Gong
- School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China.
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, 116081, People's Republic of China.
| |
Collapse
|
2
|
Lenchi N, Ahmedi WNEH, Llirós M. Simultaneous removal of crude oil and heavy metals by highly adapted bacterial strain Cutibacterium sp. NL2 isolated from Algerian oilfield. Int Microbiol 2024; 27:615-630. [PMID: 37582845 DOI: 10.1007/s10123-023-00419-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/24/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023]
Abstract
Investigating the ability of bacteria to simultaneously enhance hydrocarbon removal and reduce heavy metals' toxicity is necessary to design more effective bioremediation strategies. A bacterium (NL2 strain) isolated from an Algerian oilfield was cultivated on crude oil as sole carbon and energy sources. Molecular analyses of the 16S rRNA gene sequence placed the strain within the Cutibacterium genera. This isolate was able to tolerate up to 60% of crude oil as sole carbon source. Chemical analyses (GC-MS) evidenced that strain NL2 was able to degrade 92.22% of crude oil (at optimal growing conditions: pH 10, 44 °C, 50 g L-1 NaCl, and 20% of crude oil (v/v) as sole carbon source) in only 7 days. NL2 isolate was also able to produce biosurfactants with reduction of surface tension of growing media (29.4 mN m-1). On the other hand, NL2 strain was able to tolerate high lead (Pb) and copper (Cu) concentrations (up to 60 mM). In fact, NL2 cultivated in the presence of 20% of crude oil, and 0.48 mM of Pb was able to reduce Pb concentration by a 41.36%. In turn, when cultivated on high Pb concentration (15 mM), the strain was able to remove 35.19% of it and 86.25% of crude oil, both in a time frame of 7 days. Our findings suggest that Cutibacterium strain NL2 is able to efficiently use and remove a wide range of crude oil substrates in presence of high Pb concentration. Accordingly, NL2 strain is of extreme interest from a biotechnological standpoint.
Collapse
Affiliation(s)
- Nesrine Lenchi
- Department of Natural and Life Sciences, Faculty of Sciences, University Algiers 1 BenYoucef Benkhedda, Algiers, Algeria.
- Bioinformatics, Applied Microbiology and Biomolecules Laboratory, Faculty of Sciences, University of M'Hamed Bougara of Boumerdès, Boumerdes, Algeria.
| | - Wissam Nour El Houda Ahmedi
- Department of Natural and Life Sciences, Faculty of Sciences, University Algiers 1 BenYoucef Benkhedda, Algiers, Algeria
| | - Marc Llirós
- Bioinformatics and Bioimaging (BI-SQUARED) Research Group, Faculty of Sciences, Technology and Engineering, Universitat de Vic - Universitat Central de Catalunya, Vic, Catalunya, Spain
| |
Collapse
|
3
|
Tedesco P, Balzano S, Coppola D, Esposito FP, de Pascale D, Denaro R. Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth. MARINE POLLUTION BULLETIN 2024; 200:116157. [PMID: 38364643 DOI: 10.1016/j.marpolbul.2024.116157] [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: 12/22/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024]
Abstract
The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.
Collapse
Affiliation(s)
- Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Sergio Balzano
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Acton, 55, 80133 Naples, Italy; Institute of Biochemistry and Cellular Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Renata Denaro
- Water Research Institute (IRSA), National Research Council (CNR), 00010 Montelibretti Rome, Italy.
| |
Collapse
|
4
|
Chunyan X, Qaria MA, Qi X, Daochen Z. The role of microorganisms in petroleum degradation: Current development and prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161112. [PMID: 36586680 DOI: 10.1016/j.scitotenv.2022.161112] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/04/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.
Collapse
Affiliation(s)
- Xu Chunyan
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Majjid A Qaria
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Xu Qi
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Zhu Daochen
- Biofuels Institute, School of Emergency Management, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| |
Collapse
|
5
|
Somee MR, Amoozegar MA, Dastgheib SMM, Shavandi M, Maman LG, Bertilsson S, Mehrshad M. Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea. BMC Genomics 2022; 23:690. [PMID: 36203131 PMCID: PMC9535955 DOI: 10.1186/s12864-022-08906-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. Results Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria. Conclusion Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08906-w.
Collapse
Affiliation(s)
- Maryam Rezaei Somee
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Ali Amoozegar
- Extremophile Laboratory, Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | | | - Mahmoud Shavandi
- Biotechnology Research Group, Research Institute of Petroleum Industry, Tehran, Iran
| | - Leila Ghanbari Maman
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences (SLU), Box 7050, 75007, Uppsala, Sweden.
| |
Collapse
|
6
|
Hidangmayum A, Debnath A, Guru A, Singh BN, Upadhyay SK, Dwivedi P. Mechanistic and recent updates in nano-bioremediation for developing green technology to alleviate agricultural contaminants. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2022; 20:1-26. [PMID: 36196301 PMCID: PMC9521565 DOI: 10.1007/s13762-022-04560-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/29/2022] [Accepted: 09/17/2022] [Indexed: 05/09/2023]
Abstract
The rise in environmental pollutant levels in recent years is mostly attributable to anthropogenic activities such as industrial, agricultural and other activities. Additionally, these activities may produce excessive levels of dangerous toxicants such as heavy metals, organic pollutants including pesticide and herbicide chemicals, and sewage discharges from residential and commercial sources. With a focus on environmentally friendly, sustainable technology, new technologies such as combined process of nanotechnology and bioremediation are urgently needed to accelerate the cost-effective remediation process to alleviate toxic contaminants than the conventional remediation methods. Numerous studies have shown that nanoparticles possess special qualities including improved catalysis and adsorption as well as increased reactivity. Currently, microorganisms and their extracts are being used as promising, environmentally friendly catalysts for engineered nanomaterial. In the long term, this combination of both technologies called nano-bioremediation may significantly alter the field of environmental remediation since it is more intelligent, safe, environmentally friendly, economical and green. This review provides an overview of soil and water remediation techniques as well as the use of nano-bioremediation, which is made from various living organisms. Additionally, current developments related to the mechanism, model and kinetic studies for remediation of agricultural contaminants have been discussed.
Collapse
Affiliation(s)
- A. Hidangmayum
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - A. Debnath
- Department of Civil Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - A. Guru
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - B. N. Singh
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - S. K. Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - P. Dwivedi
- Department of Plant Physiology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| |
Collapse
|
7
|
Stanley M, Palace V, Grosshans R, Levin DB. Floating treatment wetlands for the bioremediation of oil spills: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 317:115416. [PMID: 35653839 DOI: 10.1016/j.jenvman.2022.115416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Conventional oil spill recovery may cause significant damage to shoreline habitats during the removal of oiled material and from human and equipment interaction. In addition, these methods are costly and can leave a significant amount of residual oil in the environment. Biological remediation strategies may be a less invasive option for recovering oil from sensitive regions, with potential to increase recovery. Floating treatment wetlands are a growing area of interest for biodegradation of oil facilitated by plant-bacterial partnerships. Plants are able to stimulate microbial colonization in the rhizosphere, creating greater opportunity for contaminant interaction and degradation. A literature review analysis revealed thirteen articles researching this topic, and found that floating treatment wetlands have high potential to degrade oil contaminants. In some instances, plants and inoculated bacteria exhibited the highest degradation potential, however, plants alone had higher degradation potential than bacteria alone. Research is needed to explore how floating treatment wetlands perform in field-based trials and under variable environmental conditions.
Collapse
Affiliation(s)
- Madeline Stanley
- Department of Biosystems Engineering, University of Manitoba, E2-376 EITC, Winnipeg, MB, R3T 5V6, Canada.
| | - Vince Palace
- International Institute for Sustainable Development Experimental Lakes Area, 325-111 Lombard Ave, Winnipeg, MB, R3B 0T4, Canada.
| | - Richard Grosshans
- International Institute for Sustainable Development, 325-111 Lombard Ave, Winnipeg, MB, R3B 0T4, Canada.
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, E2-376 EITC, Winnipeg, MB, R3T 5V6, Canada.
| |
Collapse
|
8
|
Daâssi D, Qabil Almaghribi F. Petroleum-contaminated soil: environmental occurrence and remediation strategies. 3 Biotech 2022; 12:139. [PMID: 35646506 DOI: 10.1007/s13205-022-03198-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/04/2022] [Indexed: 11/24/2022] Open
Abstract
Soil is an environmental matrix that carries life for all living things. With the rise of human activities and the acceleration of population, the soil has been exposed in part to pollution by the discharge of various xenobiotics and persistent pollutants into it. The disposal of toxic substances such as polycyclic aromatic hydrocarbons (PAHs) alters soil properties, affects microbial biodiversity, and damages objects. Considering the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and clean-up of PAH-polluted sites represents an important technological and environmental challenge for sustainable growth and development. Though several treatment methods to remediate PAH-polluted soils exist, interesting bacteria, fungi, and their enzymes receive considerable attention. The aim of the present review is to discuss PAHs' impact on soil properties. Also, this review illustrates physicochemical and biological remediation strategies for treating PAH-contaminated soil. The degradation pathways and contributing factors of microbial PAH-degradation are elucidated. This review also assesses the use of conventional microbial remediation compared to the application of genetically engineered microorganisms (GEM) that can provide a cost-effective and eco-friendly PAH-bioremediation strategy.
Collapse
Affiliation(s)
- Dalel Daâssi
- Department of Biology, College of Sciences and Arts, Khulais, University of Jeddah, Jeddah, Saudi Arabia
| | - Fatimah Qabil Almaghribi
- Department of Biology, College of Sciences and Arts, Khulais, University of Jeddah, Jeddah, Saudi Arabia
| |
Collapse
|
9
|
Isolation and Characterization of Diesel-Degrading Bacteria from Hydrocarbon-Contaminated Sites, Flower Farms, and Soda Lakes. Int J Microbiol 2022; 2022:5655767. [PMID: 35096070 PMCID: PMC8799363 DOI: 10.1155/2022/5655767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/20/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022] Open
Abstract
Hydrocarbon-derived pollutants are becoming one of the most concerning ecological issues. Thus, there is a need to investigate and develop innovative, low-cost, eco-friendly, and fast techniques to reduce and/or eliminate pollutants using biological agents. The study was conducted to isolate, characterize, and identify potential diesel-degrading bacteria. Samples were collected from flower farms, lakeshores, old aged garages, asphalt, and bitumen soils and spread on selective medium (Bushnell Haas mineral salt agar) containing diesel as the growth substrate. The isolates were characterized based on their growth patterns using optical density measurement, biochemical tests, and gravimetric analysis and identified using the Biolog database and 16S rRNA gene sequencing techniques. Subsequently, six diesel degraders were identified and belong to Pseudomonas, Providencia, Roseomonas, Stenotrophomonas, Achromobacter, and Bacillus. Among these, based on gravimetric analysis, the three potent isolates AAUW23, AAUG11, and AAUG36 achieved 84%, 83.4%, and 83% diesel degradation efficiency, respectively, in 15 days. Consequently, the partial 16S rRNA gene sequences revealed that the two most potent bacterial strains (AAUW23 and AAUG11) were Pseudomonas aeruginosa, while AAUG36 was Bacillus subtilis. This study demonstrated that bacterial species isolated from hydrocarbon-contaminated and/or uncontaminated environments could be optimized to be used as potential bioremediation agents for diesel removal.
Collapse
|
10
|
Exploring the Diversity and Biotechnological Potential of Cultured and Uncultured Coral-Associated Bacteria. Microorganisms 2021; 9:microorganisms9112235. [PMID: 34835361 PMCID: PMC8622030 DOI: 10.3390/microorganisms9112235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
Coral-associated microbes are crucial for the biology of their hosts, contributing to nutrient cycling, adaptation, mitigation of toxic compounds, and biological control of pathogens. Natural products from coral-associated micro-organisms (CAM) may possess unique traits. Despite this, the use of CAM for biotechnological purposes has not yet been adequately explored. Here, we investigated the production of commercially important enzymes by 37 strains of bacteria isolated from the coral species Mussismilia braziliensis, Millepora alcicornis, and Porites astreoides. In-vitro enzymatic assays showed that up to 56% of the isolates produced at least one of the seven enzymes screened (lipase, caseinase, keratinase, cellulase, chitinase, amylase, and gelatinase); one strain, identified as Bacillus amyloliquefaciens produced all these enzymes. Additionally, coral species-specific cultured and uncultured microbial communities were identified. The phylum Firmicutes predominated among the isolates, including the genera Exiguobacterium, Bacillus, and Halomonas, among others. Next-generation sequencing and bacteria culturing produced similar but also complementary data, with certain genera detected only by one or the other method. Our results demonstrate the importance of exploring different coral species as sources of specific micro-organisms of biotechnological and industrial interest, at the same time reinforcing the economic and ecological importance of coral reefs as reservoirs of such diversity.
Collapse
|
11
|
Rahmeh R, Akbar A, Kumar V, Al-Mansour H, Kishk M, Ahmed N, Al-Shamali M, Boota A, Al-Ballam Z, Shajan A, Al-Okla N. Insights into Bacterial Community Involved in Bioremediation of Aged Oil-Contaminated Soil in Arid Environment. Evol Bioinform Online 2021; 17:11769343211016887. [PMID: 34163126 PMCID: PMC8191072 DOI: 10.1177/11769343211016887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/16/2021] [Indexed: 11/15/2022] Open
Abstract
Soil contamination by hydrocarbons due to oil spills has become a global concern and it has more implications in oil producing regions. Biostimulation is considered as one of the promising remediation techniques that can be adopted to enhance the rate of degradation of crude oil. The soil microbial consortia play a critical role in governing the biodegradation of total petroleum hydrocarbons (TPHs), in particular polycyclic aromatic hydrocarbons (PAHs). In this study, the degradation pattern of TPHs and PAHs of Kuwait soil biopiles was measured at three-month intervals. Then, the microbial consortium associated with oil degradation at each interval was revealed through 16S rRNA based next generation sequencing. Rapid degradation of TPHs and most of the PAHs was noticed at the first 3 months of biostimulation with a degradation rate of pyrene significantly higher compared to other PAHs counterparts. The taxonomic profiling of individual stages of remediation revealed that, biostimulation of the investigated soil favored the growth of Proteobacteria, Alphaprotobacteria, Chloroflexi, Chlorobi, and Acidobacteria groups. These findings provide a key step towards the restoration of oil-contaminated lands in the arid environment.
Collapse
Affiliation(s)
- Rita Rahmeh
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Abrar Akbar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Vinod Kumar
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Hamad Al-Mansour
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mohamed Kishk
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Nisar Ahmed
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Mustafa Al-Shamali
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anwar Boota
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Zainab Al-Ballam
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Anisha Shajan
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Naser Al-Okla
- Biotechnology Program, Environment & Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| |
Collapse
|
12
|
Rajbongshi A, Gogoi SB. A review on anaerobic microorganisms isolated from oil reservoirs. World J Microbiol Biotechnol 2021; 37:111. [PMID: 34076736 DOI: 10.1007/s11274-021-03080-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/26/2021] [Indexed: 11/25/2022]
Abstract
The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H2S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.
Collapse
Affiliation(s)
- Amarjit Rajbongshi
- Brahmaputra Valley Fertilizer Corporation Limited, Namrup, Assam, India.
| | | |
Collapse
|
13
|
Atsavapranee B, Stark CD, Sunden F, Thompson S, Fordyce PM. Fundamentals to function: Quantitative and scalable approaches for measuring protein stability. Cell Syst 2021; 12:547-560. [PMID: 34139165 DOI: 10.1016/j.cels.2021.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/16/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.
Collapse
Affiliation(s)
| | - Catherine D Stark
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Samuel Thompson
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
| |
Collapse
|
14
|
Vaishnavi J, Devanesan S, AlSalhi MS, Rajasekar A, Selvi A, Srinivasan P, Govarthanan M. Biosurfactant mediated bioelectrokinetic remediation of diesel contaminated environment. CHEMOSPHERE 2021; 264:128377. [PMID: 33017706 DOI: 10.1016/j.chemosphere.2020.128377] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/06/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The present study integrated the electrokinetic (EK) with bioremediation (Bioelectrokinetic -BEK) of diesel hydrocarbon by Staphylococcus epidermidis EVR4. It was identified as efficient biosurfactant producing bacteria and growth parameters was optimized using response surface methodology. Upon degradation, there is a complete disappearance of peaks from nonane (C9) to tricosane (C23) and 85%, 47% of degradation of pentacosane and octacosane respectively. Marine bacterial strain, EVR4 was found to be potential to degrade the diesel with a maximum degradation efficiency of 96% within 4 d, which was due to its synergistic role of biosurfactant and catabolic enzymes (dehydrogenase, catalase and cytochrome C). The application of integrated BEK was an effective insitu method for the remediation of diesel contaminated soil by BEK (84%) than EK (67%). EVR4 as an effective strain can be employed for BIO-EK method to clean the diesel hydrocarbon polluted environment.
Collapse
Affiliation(s)
- Jeevanandam Vaishnavi
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India
| | - Sandhanasamy Devanesan
- Research Chair in Laser Diagnosis of Cancers, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh KSA, P.O. Box -2455, Riyadh, 11451, Saudi Arabia
| | - Mohamad S AlSalhi
- Research Chair in Laser Diagnosis of Cancers, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh KSA, P.O. Box -2455, Riyadh, 11451, Saudi Arabia.
| | - Aruliah Rajasekar
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India.
| | - Adikesavan Selvi
- Environmental Molecular Microbiology Research Laboratory, Department of Biotechnology, Thiruvalluvar University, Serkadu, Vellore, 632115, Tamilnadu, India
| | - Palanisamy Srinivasan
- PG & Research Department of Biotechnology, Mahendra Arts and Science College, Kalipatti, 637501, Tamil Nadu, India
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea.
| |
Collapse
|
15
|
Laczi K, Erdeiné Kis Á, Szilágyi Á, Bounedjoum N, Bodor A, Vincze GE, Kovács T, Rákhely G, Perei K. New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era. Front Microbiol 2020; 11:590049. [PMID: 33304336 PMCID: PMC7701123 DOI: 10.3389/fmicb.2020.590049] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022] Open
Abstract
The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.
Collapse
Affiliation(s)
- Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Ágnes Erdeiné Kis
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Árpád Szilágyi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Naila Bounedjoum
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Attila Bodor
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | | | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Biophysics, Biological Research Centre, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| | - Katalin Perei
- Department of Biotechnology, University of Szeged, Szeged, Hungary.,Institute of Environmental and Technological Sciences, University of Szeged, Szeged, Hungary
| |
Collapse
|
16
|
Peroxidase from waste cabbage (Brassica oleracea capitata L.) exhibits the potential to biodegrade phenol and synthetic dyes from wastewater. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
|
17
|
Functional Gene Diversity of Selected Indigenous Hydrocarbon-Degrading Bacteria in Aged Crude Oil. Int J Microbiol 2020; 2020:2141209. [PMID: 32802067 PMCID: PMC7414327 DOI: 10.1155/2020/2141209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 06/02/2020] [Indexed: 12/05/2022] Open
Abstract
Crude oil pollution has consistently deteriorated all environmental compartments through the cycle of activities of the oil and gas industries. However, there is a growing need to identify microbes with catabolic potentials to degrade these pollutants. This research was conducted to identify bacteria with functional degradative genes. A crude oil-polluted soil sample was obtained from an aged spill site at Imo River, Ebubu, Komkom community, Nigeria. Bacteria isolates were obtained and screened for hydrocarbon degradation potential by turbidometry assay. Plasmid and chromosomal DNA of the potential degraders were further screened for the presence of selected catabolic genes (C230, Alma, Alkb, nahAC, and PAHRHD(GP)) and identified by molecular typing. Sixteen (16) out of the fifty (50) isolates obtained showed biodegradation activity in a liquid broth medium at varying levels. Bacillus cereus showed highest potential for this assay with an optical density of 2.450 @ 600 nm wavelength. Diverse catabolic genes resident in plasmids and chromosomes of the isolates and, in some cases, both plasmid and chromosomes of the same organism were observed. The C230 gene was resident in >50% of the microbial population tested, while other genes occurred in lower proportions with the least observed in nahAC and PAHRHD. These organisms can serve as potential bioremediation agents.
Collapse
|
18
|
Zhang Y, Lin DF, Hao J, Zhao ZH, Zhang YJ. The crucial role of bacterial laccases in the bioremediation of petroleum hydrocarbons. World J Microbiol Biotechnol 2020; 36:116. [PMID: 32661601 DOI: 10.1007/s11274-020-02888-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
Laccases (EC 1.10.3.2) are a class of metallo-oxidases found in a variety of fungi, plants, and bacteria as well as in certain insects. They can oxidize a wide variety of organic compounds and can be widely applied in many fields, especially in the field of biodegradation and detoxification of environmental pollutants. The practical efficacy of laccases depends on their ability to capture the target substance as well as their catalytic activity, which is related to their catalytic center, substrate selectivity, and substrate tolerance. Over the past few decades, many laccases have been identified in plants and fungi. Concurrently, bacterial laccases have received increasing attention because of their high thermostability and high tolerance to organic compounds. The aim of this review is to summarize the role of bacterial laccases in the bioremediation of petroleum hydrocarbons and to outline the correlation between the molecular structure of the mononuclear T1 Cu center of bacterial laccases and their substrate preference.
Collapse
Affiliation(s)
- Yan Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China
| | - Dong-Fa Lin
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China
| | - Jun Hao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China
| | - Zhi-Hao Zhao
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China
| | - Ying-Jiu Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130012, People's Republic of China. .,School of Life Science, Jilin University, Changchun, 130012, People's Republic of China.
| |
Collapse
|
19
|
Abstract
Contaminants, organic or inorganic, represent a threat for the environment and human health and in recent years their presence and persistence has increased rapidly. For this reason, several technologies including bioremediation in combination with nanotechnology have been explored to identify more systemic approaches for their removal from environmental matrices. Understanding the interaction between the contaminant, the microorganism, and the nanomaterials (NMs) is of crucial importance since positive and negative effects may be produced. For example, some nanomaterials are stimulants for microorganisms, while others are toxic. Thus, proper selection is of paramount importance. The main objective of this review was to analyze the principles of bioremediation assisted by nanomaterials, nanoparticles (NPs) included, and their interaction with environmental matrices. It also analyzed the response of living organisms employed to remediate the contaminants in the presence of nanomaterials. Besides, we discuss the international regulatory frame applicable to these technologies and how they might contribute to sustainability.
Collapse
|
20
|
Pinto ÉSM, Dorn M, Feltes BC. The tale of a versatile enzyme: Alpha-amylase evolution, structure, and potential biotechnological applications for the bioremediation of n-alkanes. CHEMOSPHERE 2020; 250:126202. [PMID: 32092569 DOI: 10.1016/j.chemosphere.2020.126202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/10/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
As the primary source of a wide range of industrial products, the study of petroleum-derived compounds is of pivotal importance. However, the process of oil extraction and refinement is among the most environmentally hazardous practices, impacting almost all levels of the ecological chain. So far, the most appropriate strategy to overcome such an issue is through bioremediation, which revolves around the employment of different microorganisms to degrade hazardous compounds, generating less environmental impact and lower monetary costs. In this sense, a myriad of organisms and enzymes are considered possible candidates for the bioremediation process. Amidst the potential candidates is α-amylase, an evolutionary conserved starch-degrading enzyme. Notably, α-amylase was not only seen to degrade n-alkanes, a subclass of alkanes considered the most abundant petroleum-derived compounds but also low-density polyethylene, a dangerous pollutant produced from petroleum. Thus, due to its high conservation in both eukaryotic and prokaryotic lineages, in addition to the capability to degrade different types of hazardous compounds, the study of α-amylase becomes a rising interest. Nevertheless, there are no studies that review all biotechnological applications of α-amylase for bioremediation. In this work, we critically review the potential biotechnological applications of α-amylase, focusing on the biodegradation of petroleum-derived compounds. Evolutionary aspects are discussed, as well for all structural information and all features that could impact on the employment of this protein in the biotechnological industry, such as pH, temperature, and medium conditions. New perspectives and critical assessments are conducted regarding the application of α-amylase in the bioremediation of n-alkanes.
Collapse
Affiliation(s)
- Éderson Sales Moreira Pinto
- Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Márcio Dorn
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil; Laboratory of Structural Bioinformatics and Computational Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Brazil
| | - Bruno César Feltes
- Laboratory of Structural Bioinformatics and Computational Biology, Institute of Informatics, Federal University of Rio Grande do Sul, Brazil.
| |
Collapse
|
21
|
Davoodi SM, Miri S, Taheran M, Brar SK, Galvez-Cloutier R, Martel R. Bioremediation of Unconventional Oil Contaminated Ecosystems under Natural and Assisted Conditions: A Review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2054-2067. [PMID: 31904944 DOI: 10.1021/acs.est.9b00906] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It is a general understanding that unconventional oil is petroleum-extracted and processed into petroleum products using unconventional means. The recent growth in the United States shale oil production and the lack of refineries in Canada built for heavy crude processes have resulted in a significant increase in U.S imports of unconventional oil since 2018. This has increased the risk of incidents and catastrophic emergencies during the transportation of unconventional oils using transmission pipelines and train rails. A great deal of effort has been made to address the remediation of contaminated soil/sediment following the traditional oil spills. However, spill response and cleanup techniques (e.g., oil recuperation, soil-sediment-water treatments) showed slow and inefficient performance when it came to unconventional oil, bringing larger associated environmental impacts in need of investigation. To the best of our knowledge, there is no coherent review available on the biodegradability of unconventional oil, including Dilbit and Bakken oil. Hence, in view of the insufficient information and contrasting results obtained on the remediation of petroleum, this review is an attempt to fill the gap by presenting the collective understanding and critical analysis of the literature on bioremediation of products from the oil sand and shale (e.g., Dilbit and Bakken oil). This can help evaluate the different aspects of hydrocarbon biodegradation and identify the knowledge gaps in the literature.
Collapse
Affiliation(s)
- Seyyed Mohammadreza Davoodi
- INRS-ETE , Université du Québec , 490, Rue de la Couronne , Québec City , Québec , Canada G1K 9A9
- Department of Civil Engineering, Lassonde School of Engineering , York University, North York , Toronto , Ontario Canada M3J 1P3
| | - Saba Miri
- INRS-ETE , Université du Québec , 490, Rue de la Couronne , Québec City , Québec , Canada G1K 9A9
- Department of Civil Engineering, Lassonde School of Engineering , York University, North York , Toronto , Ontario Canada M3J 1P3
| | - Mehrdad Taheran
- INRS-ETE , Université du Québec , 490, Rue de la Couronne , Québec City , Québec , Canada G1K 9A9
| | - Satinder Kaur Brar
- INRS-ETE , Université du Québec , 490, Rue de la Couronne , Québec City , Québec , Canada G1K 9A9
- Department of Civil Engineering, Lassonde School of Engineering , York University, North York , Toronto , Ontario Canada M3J 1P3
| | | | - Richard Martel
- INRS-ETE , Université du Québec , 490, Rue de la Couronne , Québec City , Québec , Canada G1K 9A9
| |
Collapse
|
22
|
Machado LF, de Assis Leite DC, da Costa Rachid CTC, Paes JE, Martins EF, Peixoto RS, Rosado AS. Tracking Mangrove Oil Bioremediation Approaches and Bacterial Diversity at Different Depths in an in situ Mesocosms System. Front Microbiol 2019; 10:2107. [PMID: 31572322 PMCID: PMC6753392 DOI: 10.3389/fmicb.2019.02107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022] Open
Abstract
In this study, oil spills were simulated in field-based mangrove mesocosms to compare the efficiency of bioremediation strategies and to characterize the presence of the alkB, ndo, assA, and bssA genes and the ecological structures of microbial communities in mangrove sediments at two different depths, (D1) 1–10 cm and (D2) 25–35 cm. The results indicated that the hydrocarbon degradation efficiency was higher in superficial sediment layers, although no differences in the hydrocarbon degradation rates or in the abundances of the alkB and ndo genes were detected among the tested bioremediation strategies at this depth. Samples from the deeper layer exhibited higher abundances of the analyzed genes, except for assA and bssA, which were not detected in our samples. For all of the treatments and depths, the most abundant phyla were Proteobacteria, Firmicutes and Bacteroidetes, with Gammaproteobacteria, Flavobacteriales and Clostridiales being the most common classes. The indicator species analysis (ISA) results showed strong distinctions among microbial taxa in response to different treatments and in the two collection depths. Our results indicated a high efficiency of the monitored natural attenuation (MNA) for oil consumption in the tested mangrove sediments, revealing the potential of this strategy for environmental decontamination and suggesting that environmental and ecological factors may select for specific bacterial populations in distinct niches.
Collapse
Affiliation(s)
- Laís Feitosa Machado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Jorge Eduardo Paes
- Research Center Leopoldo Américo Miguez de Mello, Rio de Janeiro, Brazil
| | - Edir Ferreira Martins
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| | - Alexandre Soares Rosado
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, Brazil
| |
Collapse
|
23
|
Zhang L, Zhang Y, Gamal El-Din M. Integrated mild ozonation with biofiltration can effectively enhance the removal of naphthenic acids from hydrocarbon-contaminated water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 678:197-206. [PMID: 31075586 DOI: 10.1016/j.scitotenv.2019.04.302] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/30/2019] [Accepted: 04/20/2019] [Indexed: 06/09/2023]
Abstract
An innovative biofiltration-ozonation-biofiltration process was established and applied for the treatment of oil sands process water (OSPW). With an equivalent hydraulic retention time (HRT) of 8 h, the biofiltration pretreatment removed 24.4% of classical naphthenic acids (NAs) and 3.3% of oxidized NAs from raw OSPW with removal rate of 0.4 mg/L/h and 0.1 mg/L. Oxidized NAs showed higher resistance to the biofiltration process than classical NAs. The mild ozonation process (with utilized ozone dose of 30 mg/L) removed 84.8% of classical NAs and 11.5% of oxidized NAs from the biofiltrated OSPW with a degradation efficiency of 0.3 mg classical NAs/mg O3 and 0.1 mg oxidized NAs/mg O3. However, by using the same utilized ozone dose, the degradation of classical NAs and oxidized NAs from raw OSPW was 32.1% and 3.9% with ozonation efficiency of 0.1 mg classical NAs/mg O3 and 0.0 mg oxidized NAs/mg O3, respectively. Compared with the biofiltration pretreatment, the post biofiltration process (with HRT of 8 h) showed higher degradation effect on oxidized NAs with removal ratio of 22.9% and removal rate of 0.4 mg/L/h, but showed lower degradation effect on classical NAs with removal ratio of 6.7% and removal rate of 0.0 mg/L/h. After biofiltration-ozonation-biofiltration treatment, the microbial community structure in the biofilter was investigated by next generation sequencing. Proteobacteria and Rhodococcus were dominant bacterial phyla and genus in the biofilter, the abundance of which were 47.21% and 9.50% which were different from those in raw OSPW (62.88% and 0.72%). The change of microbial community structure could be resulted from the interaction between microbial community and the circulating OSPW. The ozonation integrated biodegradation process removed 89.3% and 34.0% of classical and oxidized NAs from OSPW which shows high potential to be applied by the oil and gas industry.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Yanyan Zhang
- Department of Civil Engineering, New Mexico State University, Las Cruces, NM 88003, United States
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada.
| |
Collapse
|
24
|
Crude Oil Biodegradation by Newly Isolated Bacterial Strains and Their Consortium Under Soil Microcosm Experiment. Appl Biochem Biotechnol 2019; 189:1223-1244. [DOI: 10.1007/s12010-019-03058-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/22/2019] [Indexed: 12/12/2022]
|
25
|
Muñoz-García A, Mestanza O, Isaza JP, Figueroa-Galvis I, Vanegas J. Influence of salinity on the degradation of xenobiotic compounds in rhizospheric mangrove soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 249:750-757. [PMID: 30933772 DOI: 10.1016/j.envpol.2019.03.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/25/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Mangroves are highly productive tropical ecosystems influenced by seasonal and daily salinity changes, often exposed to sewage contamination, oil spills and heavy metals, among others. There is limited knowledge of the influence of salinity on the ability of microorganisms to degrade xenobiotic compounds. The aim of this study were to determine the salinity influence on the degradation of xenobiotic compounds in a semi-arid mangrove in La Guajira-Colombia and establish the more abundant genes and degradation pathways. In this study, rhizospheric soil of Avicennia germinans was collected in three points with contrasting salinity (4H, 2 M and 3 L). Total DNA extraction was performed and shotgun sequenced using the Illumina HiSeq technology. We annotated 507,343 reads associated with 21 pathways and detected 193 genes associated with the degradation of xenobiotics using orthologous genes from the KEGG Orthology (KO) database, of which 16 pathways and 113 genes were influenced by salinity. The highest abundances were found in high salinity. The degradation of benzoate showed the highest abundance, followed by the metabolism of the drugs and the degradation of chloroalkane and chloroalkene. The majority of genes were associated with phase I degradation of xenobiotics. The most abundant genes were acetyl-CoA C-acetyltransferase (atoB), catalase-peroxidase (katG) and GMP synthase (glutamine-hydrolysing) (guaA). In conclusion, the metagenomic analysis detected all the degradation pathways of xenobiotics of KEGG and 59% of the genes associated with these pathways were influenced by salinity.
Collapse
Affiliation(s)
- Andrea Muñoz-García
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
| | - Orson Mestanza
- Universidad Nacional de Colombia, Carrera 45 No. 26-85, Bogotá, Colombia.
| | - Juan Pablo Isaza
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
| | | | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Cra 3 Este No. 47 A 15, Bogotá, Colombia.
| |
Collapse
|
26
|
Villela HDM, Peixoto RS, Soriano AU, Carmo FL. Microbial bioremediation of oil contaminated seawater: A survey of patent deposits and the characterization of the top genera applied. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:743-758. [PMID: 30812008 DOI: 10.1016/j.scitotenv.2019.02.153] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 02/09/2019] [Accepted: 02/10/2019] [Indexed: 05/20/2023]
Abstract
Petroleum has been the world's major source of energy since the middle of the twentieth century, leading to positive changes but also social, political, and environmental problems worldwide. Oil contamination affects all ecosystems, and the remediation of polluted sites using environmentally friendly strategies is crucial. Here, we report an analysis of the patent documents of potential petroleum bioremediation techniques that use microbes to clean seawater. The patent search was performed using Orbit Intelligence®, SciFinder® and the Derwent World Patents Index®. A group of 500 patent documents were validated according to the search objective and carefully studied. Increases in patent deposits coincide with periods following widely reported oil spills, suggesting a relationship between media disclosure and stimulation of innovation activities. China leads the list of countries with patent applications in bioremediation with 152 deposits, followed by Russia with 133 and the US with 48. These three countries have completely different temporal deposit profiles, influenced by their historical, political, and economic scenarios. A total of 368 patents described degradation of the oil compounds exclusively by bacteria, 24 by fungi and yeasts, 1 by Archaea, 1 using a microalgal strain, and 32 by mixed consortia. The leading microbial genera found in the patents are Pseudomonas (114 patents), Bacillus (75), and Rhodococcus (60). In the top-10 list of microbial strains mostly cited/claimed, no genera are obligate hydrocarbonoclastic bacteria. This fact, together with the broad pattern found in the main International Patent Classification (IPC) codes, suggest that most of the documents are general bioremediation approaches and not focused on oil-polluted seawater. This work highlights the importance of stimulating the development of innovative environmentally friendly strategies focused on the degradation of oil hydrocarbons in marine ecosystems.
Collapse
Affiliation(s)
- Helena D M Villela
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Raquel S Peixoto
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil; IMAM-AquaRio - Rio Marine Aquarium Research Center, Praça Muhammad Ali, Gambôa, Rio de Janeiro, RJ 20220-360, Brazil
| | - Adriana U Soriano
- Leopoldo A. Miguez de Mello Research and Development Center, CENPES, PETROBRAS - Petroleo Brasileiro S. A, CENPES, Cidade Universitária, Rio de Janeiro, RJ, 21941-598, Brazil
| | - Flavia L Carmo
- Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS, Bl E, Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil; Innovation Agency UFRJ, Federal University of Rio de Janeiro. R. Hélio de Almeida, s/n - Incubadora de Empresas - Prédio 2 (salas 25 a 29), Cidade Universitária, Rio de Janeiro, RJ 21941-614, Brazil
| |
Collapse
|
27
|
Sun W, Ali I, Liu J, Dai M, Cao W, Jiang M, Saren G, Yu X, Peng C, Naz I. Isolation, identification, and characterization of diesel-oil-degrading bacterial strains indigenous to Changqing oil field, China. J Basic Microbiol 2019; 59:723-734. [PMID: 31081547 DOI: 10.1002/jobm.201800674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/04/2019] [Accepted: 04/25/2019] [Indexed: 11/07/2022]
Abstract
In the present study, 12 indigenous diesel-oil-degrading bacteria were isolated from the petroleum-contaminated soils of the Changqing oil field (Xi'an, China). Measurement of the diesel-oil degradation rates of these strains by the gravimetric method revealed that they ranged from 42% to 66% within 2 weeks. The highest degradation rates were observed from strains CQ8-1 (66%), CQ8-2 (62.6%), and CQ11 (59%), which were identified as Bacillus thuringiensis, Ochrobactrum anthropi, and Bordetella bronchialis, respectively, based on their 16S rDNA sequences. Moreover, the physiological and biochemical properties of these three strains were analyzed by Gram staining, catalase, oxidase, and Voges-Proskauer tests. Transmission electron microscopy showed that all three strains were rod shaped with flagella. Gas chromatography and mass spectrometric analyses indicated that medium- and long-chain n-alkanes in diesel oil (C11-C29) were degraded to different degrees by B. thuringiensis, O. anthropi, and B. bronchialis, and the degradation rates gradually decreased as the carbon numbers increased. Overall, the results of this study indicate strains CQ8-1, CQ8-2, and CQ11 might be useful for environmentally friendly and cost-effective bioremediation of oil-contaminated soils.
Collapse
Affiliation(s)
- Wuyang Sun
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Imran Ali
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Jiwei Liu
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Min Dai
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing, China
| | - Wenrui Cao
- The Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Mingyu Jiang
- The Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Gaowa Saren
- The Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xinke Yu
- The Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Changsheng Peng
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, China
- School of Environmental and Chemical Engineering, Zhaoqing University, Zhaoqing, China
| | - Iffat Naz
- Department of Biology, Qassim University, Buraidah, Kingdom of Saudi Arabia (KSA)
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
28
|
Anyasi RO, Atagana HI, Sutherland R. Identification and characterization of PAH-degrading endophytes isolated from plants growing around a sludge dam. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:672-682. [PMID: 30942084 DOI: 10.1080/15226514.2018.1556585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study involved the isolation of bacteria endophytes with PAH-degrading ability from plants growing around a sludge dam. A total of 19 distinct isolates that were morphologically identified were isolated from 4 species of plant with a follow-up confirmatory identification using the molecular technique. Polymerase chain reaction (PCR) of the 16S rRNA gene with specific primers (16S-27F PCR and 16S-1491R PCR) was carried out. The sequence of the PCR products was carried out, compared with similar nucleotides available in GenBank. Results of the phylogenetic analysis of the isolates indicated their belonging to 4 different clades including Proteobacteria, Actinobacteria, Cyanobacteria, and Firmicutes. These were related to the genera Bacillus, Pseudomonas, Terribacillus, Virgibacillus, Stenotrophomonas, Paenibacillus, Brevibacterium, Geobacillus, Acinetobacter. From the result, Pseudomonas demonstrated a high incidence in the plants sampled. The in-vitro degradation study and the presence of dioxygenase genes indicated that these lists of endophytes are able to use the list of PAHs tested as their source of food and energy leading to their breakdown. This means that the bacterial endophytes contributed to the remediation of petroleum hydrocarbons in planta, a situation that may have been phytotoxic to plant alone. Therefore, these bacteria endophytes could be potential organisms for enhanced phytoremediation of PAHs.
Collapse
Affiliation(s)
- Raymond O Anyasi
- a Department of Environmental Sciences, Institute for Science and Technology Education , University of South Africa , Pretoria , South Africa
| | - Harrison I Atagana
- a Department of Environmental Sciences, Institute for Science and Technology Education , University of South Africa , Pretoria , South Africa
| | - Rene Sutherland
- b Plant Protection Unit , Agricultural Research Council , Pretoria , South Africa
| |
Collapse
|
29
|
Enzymatic Bioremediation: Current Status, Challenges of Obtaining Process, and Applications. MICROORGANISMS FOR SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-7462-3_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
30
|
Whole-Genome Sequence of Pseudomonas sp. Strain 1239, Isolated from Soil in Western France. Microbiol Resour Announc 2018; 7:MRA01097-18. [PMID: 30533625 PMCID: PMC6256603 DOI: 10.1128/mra.01097-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/21/2018] [Indexed: 11/27/2022] Open
Abstract
We report here the draft genome sequence of Pseudomonas sp. strain 1239, a bacterium that is potentially usable as a biostimulant for agriculture or in depollution. We report here the draft genome sequence of Pseudomonas sp. strain 1239, a bacterium that is potentially usable as a biostimulant for agriculture or in depollution. Its genome encodes resistance to mercury, heavy metals, and several antibiotics. It is potentially able to produce marinocine, a broad-spectrum antibiotic.
Collapse
|
31
|
Whole-Genome Sequence of Pseudomonas putida Strain 1312, a Potential Biostimulant Developed for Agriculture. Microbiol Resour Announc 2018; 7:MRA01073-18. [PMID: 30533614 PMCID: PMC6256590 DOI: 10.1128/mra.01073-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/15/2018] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments. We report the draft genome sequence of strain 1312 of Pseudomonas putida, which could be interesting to develop as a biostimulant for agriculture and soil depollution treatments.
Collapse
|
32
|
Li J, Chen Q, Bao B, Liu M, Bao M, Liu J, Mu J. RNA-seq analysis reveals the significant effects of different light conditions on oil degradation by marine Chlorella vulgaris. MARINE POLLUTION BULLETIN 2018; 137:267-276. [PMID: 30503435 DOI: 10.1016/j.marpolbul.2018.10.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/30/2018] [Accepted: 10/08/2018] [Indexed: 06/09/2023]
Abstract
Marine Chlorella vulgaris, an efficient hydrocarbon-degrading organism, is easily affected by light. In this study, we investigated the direct effects of different light conditions on crude oil degradation by C. vulgaris and its crude enzyme. Under 12 h illumination, the crude enzyme improved hydrocarbon removal by 39.36%, whereas the addition of the enzyme and C. vulgaris increased the degradation rate by 121.73%. Conversely, the addition of enzyme under heterotrophic condition was negatively related to oil degradation by C. vulgaris, and the degradation rate decreased from 74.32% to 48.65% and further reduced by 34.54%. The results of RNA sequencing analysis suggested that hydrocarbons removal was attributed to C. vulgaris metabolism in heterotrophic physiological state. While enhanced removal efficiency of hydrocarbons was achieved in mixotrophic physiological state due to the coupling of C. vulgaris metabolism with photocatalytic oxidation. Functional enzymes played key roles in photocatalysis and biodegradation processes.
Collapse
Affiliation(s)
- Jingjing Li
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Qingguo Chen
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China.
| | - Bo Bao
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mei Liu
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, PR China
| | - Junzhi Liu
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jun Mu
- College of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| |
Collapse
|
33
|
Napp AP, Pereira JES, Oliveira JS, Silva-Portela RCB, Agnez-Lima LF, Peralba MCR, Bento FM, Passaglia LMP, Thompson CE, Vainstein MH. Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste. CHEMOSPHERE 2018; 209:7-16. [PMID: 29908430 DOI: 10.1016/j.chemosphere.2018.06.068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/24/2018] [Accepted: 06/10/2018] [Indexed: 06/08/2023]
Abstract
The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds.
Collapse
Affiliation(s)
- Amanda P Napp
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
| | - José Evandro S Pereira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
| | - Jorge S Oliveira
- INESC-ID/IST-Instituto de Engenharia de Sistemas e Computadores/Instituto Superior Técnico, Universidade de Lisboa, Lisboa 1000-029, Portugal; Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Rita C B Silva-Portela
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Lucymara F Agnez-Lima
- Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Maria C R Peralba
- Departamento de Química Inorgânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil.
| | - Fátima M Bento
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 90050-170, Brazil.
| | - Luciane M P Passaglia
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91500-970, Brazil.
| | - Claudia E Thompson
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil; Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.
| | - Marilene H Vainstein
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501-070, Brazil.
| |
Collapse
|
34
|
Alves NJ, Moore M, Johnson BJ, Dean SN, Turner KB, Medintz IL, Walper SA. Environmental Decontamination of a Chemical Warfare Simulant Utilizing a Membrane Vesicle-Encapsulated Phosphotriesterase. ACS APPLIED MATERIALS & INTERFACES 2018; 10:15712-15719. [PMID: 29672020 DOI: 10.1021/acsami.8b02717] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
While technologies for the remediation of chemical contaminants continue to emerge, growing interest in green technologies has led researchers to explore natural catalytic mechanisms derived from microbial species. One such method, enzymatic degradation, offers an alternative to harsh chemical catalysts and resins. Recombinant enzymes, however, are often too labile or show limited activity when challenged with nonideal environmental conditions that may vary in salinity, pH, or other physical properties. Here, we demonstrate how phosphotriesterase encapsulated in a bacterial outer membrane vesicle can be used to degrade the organophosphate chemical warfare agent (CWA) simulant paraoxon in environmental water samples. We also carried out remediation assays on solid surfaces, including glass, painted metal, and fabric, that were selected as representative materials, which could potentially be contaminated with a CWA.
Collapse
Affiliation(s)
- Nathan J Alves
- Department of Emergency Medicine , Indiana University School of Medicine , Indianapolis , Indiana 46202 , United States
| | - Martin Moore
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Brandy J Johnson
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Scott N Dean
- National Research Council Postdoctoral Fellow , Washington , District of Columbia 20001 , United States
| | - Kendrick B Turner
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Igor L Medintz
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| | - Scott A Walper
- Center for Bio/Molecular Science & Engineering , Naval Research Laboratory , Code 6900 Washington , District of Columbia 20375 , United States
| |
Collapse
|
35
|
Vidal-Limon A, García Suárez PC, Arellano-García E, Contreras OE, Aguila SA. Enhanced Degradation of Pesticide Dichlorophen by Laccase Immobilized on Nanoporous Materials: A Cytotoxic and Molecular Simulation Investigation. Bioconjug Chem 2018; 29:1073-1080. [DOI: 10.1021/acs.bioconjchem.7b00739] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abraham Vidal-Limon
- Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autonoma de Mexico, km. 107 Carretera Tijuana-Ensenada, Pedregal Playitas, 22860 Ensenada, Baja California, Mexico
| | - Patricia Concepción García Suárez
- Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autonoma de Mexico, km. 107 Carretera Tijuana-Ensenada, Pedregal Playitas, 22860 Ensenada, Baja California, Mexico
- Facultad de Deportes, Universidad Autónoma de Baja California, Ensenada, Baja California 22890, Mexico
| | - Evarista Arellano-García
- Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California 22800, Mexico
| | - Oscar E. Contreras
- Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autonoma de Mexico, km. 107 Carretera Tijuana-Ensenada, Pedregal Playitas, 22860 Ensenada, Baja California, Mexico
| | - Sergio A. Aguila
- Centro de Nanociencias y Nanotecnologia, Universidad Nacional Autonoma de Mexico, km. 107 Carretera Tijuana-Ensenada, Pedregal Playitas, 22860 Ensenada, Baja California, Mexico
| |
Collapse
|
36
|
|
37
|
Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01704-15. [PMID: 26868394 PMCID: PMC4751318 DOI: 10.1128/genomea.01704-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe here a 5.8-Mb draft genome sequence of Rhodococcus pyridinivorans strain KG-16, which was obtained from the soil samples collected from the oilfields of Krishna-Godavari basin in India. This genomic resource can provide insights into the pathways and mechanisms of hydrocarbon degradation and potentially aid in bioremediation applications.
Collapse
|
38
|
Shahzad A, Siddiqui S, Bano A. Rhizoremediation of petroleum hydrocarbon, prospects and future. RSC Adv 2016. [DOI: 10.1039/c6ra12458e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Oil refineries generate several tones of oily waste which is dumped in an open pit within the vicinity of oil field.
Collapse
Affiliation(s)
- Asim Shahzad
- Mohi-Ud-Din Islamic University
- Pakistan
- Department of Bio Sciences
- University of Wah
- Wah Cannt
| | - Samina Siddiqui
- National Center for Excellence in Geology
- University of Peshawar
- Pakistan
| | - Asghari Bano
- Department of Bio Sciences
- University of Wah
- Wah Cannt
- Pakistan
| |
Collapse
|
39
|
Hassan I, Mohamedelhassan E, Yanful EK, Yuan ZC. A Review Article: Electrokinetic Bioremediation Current Knowledge and New Prospects. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/aim.2016.61006] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
40
|
Rodríguez-Morgado B, Gómez I, Parrado J, García C, Hernández T, Tejada M. Accelerated degradation of PAHs using edaphic biostimulants obtained from sewage sludge and chicken feathers. JOURNAL OF HAZARDOUS MATERIALS 2015; 300:235-242. [PMID: 26188866 DOI: 10.1016/j.jhazmat.2015.05.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/29/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
We studied in the laboratory the bioremediation effects over a 100-day period of three edaphic biostimulants (BS) obtained from sewage sludge (SS) and from two different types of chicken feathers (CF1 and CF2), in a soil polluted with three polycyclic aromatic hydrocarbons (PAH) (phenanthrene, Phe; pyrene, Py; and benzo(a)pyrene, BaP), at a concentration of 100 mg kg(-1) soil. We determined their effects on enzymatic activities and on soil microbial community. Those BS with larger amounts of proteins and a higher proportion of peptides (<300 daltons), exerted a greater stimulation on the soil biochemical properties and microbial community, possibly because low molecular weight proteins can be easily assimilated by soil microorganisms. The soil dehydrogenase, urease, β-glucosidase and phosphatase activities and microbial community decreased in PAH-polluted soil. This decrease was more pronounced in soils contaminated with BaP than with Py and Phe. The application of the BS to PAH-polluted soils decreased the inhibition of the soil biological properties, principally at 7 days into the experiment. This decrease was more pronounced in soils contaminated with BaP than with Py and Phe and was higher in polluted soils amended with CF2, followed by SS and CF1, respectively.
Collapse
Affiliation(s)
- Bruno Rodríguez-Morgado
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, C/ Prof. García González 2, 41012 Sevilla, Spain
| | - Isidoro Gómez
- Grupo de Investigación Edafología Ambiental, Departamento de Cristalografía, Mineralogía y Química Agrícola, E.T.S.I.A. Universidad de Sevilla, Crta de Utrera km. 1, 41013 Sevilla, Spain
| | - Juan Parrado
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla, C/ Prof. García González 2, 41012 Sevilla, Spain
| | - Carlos García
- Departamento de Conservación de Suelos y Agua y Manejo de Residuos Orgánicos, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, P.O. Box 4195, 30080 Murcia, Spain
| | - Teresa Hernández
- Departamento de Conservación de Suelos y Agua y Manejo de Residuos Orgánicos, Centro de Edafología y Biología Aplicada del Segura, CEBAS-CSIC, P.O. Box 4195, 30080 Murcia, Spain
| | - Manuel Tejada
- Grupo de Investigación Edafología Ambiental, Departamento de Cristalografía, Mineralogía y Química Agrícola, E.T.S.I.A. Universidad de Sevilla, Crta de Utrera km. 1, 41013 Sevilla, Spain.
| |
Collapse
|
41
|
Whole-Genome Sequence of Pseudomonas putida Strain UASWS0946, a Highly Ammonia-Tolerant Nitrifying Bacterium Isolated from Sewage Sludge Aerobic Granules. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01153-15. [PMID: 26450728 PMCID: PMC4599087 DOI: 10.1128/genomea.01153-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here the genome of Pseudomonas putida strain UASWS0946, a highly ammonia-tolerant nitrifying strain isolated from sewage sludge aerobic granules, which displays adequate genetic equipment for soil depollution, sludge treatment, and biological fertilization in agriculture.
Collapse
|
42
|
Draft Genome Sequence of Hydrocarbon-Degrading Pseudomonas putida Strain KG-4, Isolated from Soil Samples Collected from Krishna-Godavari Basin in India. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00590-15. [PMID: 26044433 PMCID: PMC4457070 DOI: 10.1128/genomea.00590-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report here the 5.58-Mb draft genome of Pseudomonas putida strain KG-4 obtained from the oil fields of the Krishna-Godavari basin, Andhra Pradesh, India. The genome sequence is expected to facilitate identification and understanding of genes associated with hydrocarbon metabolism, which can help in developing strategies for managing oil spills and bioremediation.
Collapse
|
43
|
Metagenomics of petroleum muck: revealing microbial diversity and depicting microbial syntrophy. Arch Microbiol 2014; 196:531-44. [DOI: 10.1007/s00203-014-0992-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 04/06/2014] [Accepted: 05/08/2014] [Indexed: 10/25/2022]
|
44
|
Gan HM, Hudson AO, Rahman AYA, Chan KG, Savka MA. Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics 2013; 14:431. [PMID: 23809012 PMCID: PMC3704786 DOI: 10.1186/1471-2164-14-431] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/17/2013] [Indexed: 12/03/2022] Open
Abstract
Background Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures. Results The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme. Conclusions The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.
Collapse
Affiliation(s)
- Han Ming Gan
- Science Vision SB, Shah Alam, Selangor, Malaysia
| | | | | | | | | |
Collapse
|