1
|
Li J, Li X, Zuo R, Yang L, Xu Y, Yu S, Wang J, Yang J. Exploring the microbe-mediated biological processes of BTEX and toxic metal(loid)s in aging petrochemical landfills. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 285:117103. [PMID: 39326354 DOI: 10.1016/j.ecoenv.2024.117103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 09/19/2024] [Accepted: 09/22/2024] [Indexed: 09/28/2024]
Abstract
Aging petrochemical landfills serve as reservoirs of inorganic and organic contaminants, posing potential risks of contamination to the surrounding environment. Identifying the pollution characteristics and elucidating the translocation/ transformation processes of typical contaminants in aging petrochemical landfills are crucial yet challenging endeavors. In this study, we employed a combination of chemical analysis and microbial metagenomic technologies to investigate the pollution characteristics of benzene, toluene, ethylbenzene, and xylene (BTEX) as well as metal(loid)s in a representative aging landfill, surrounding soils, and underlying groundwater. Furthermore, we aimed to explore their transformations driven by microbial activity. Our findings revealed widespread distribution of metal(loid)s, including Cd, Ni, Cu, As, Mn, Pb, and Zn, in these environmental media, surpassing soil background values and posing potential ecological risks. Additionally, microbial processes were observed to contribute significantly to the degradation of BTEX compounds and the transformation of metal(loid)s in landfills and surrounding soils, with identified microbial communities and functions playing key roles. Notably, co-occurrence network analysis unveiled the coexistence of functional genes associated with BTEX degradation and metal(loid) transformation, driven primarily by As, Ni, and Cd. These results shed light on the co-selection of resistance traits against BTEX and metal(loid) contaminants in soil microbial consortia under co-contamination scenarios, supporting microbial adaptive evolution in aging petrochemical landfills. The insights gained from this study enhance our understanding of characteristic pollutants and microbial transformation processes in aging landfills, thereby facilitating improved landfill management and contamination remediation strategies.
Collapse
Affiliation(s)
- Jian Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Xiaofei Li
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Rui Zuo
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Ying Xu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Shihang Yu
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jinsheng Wang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Jie Yang
- Engineering Research Center of Groundwater Pollution Control and Remediation, Ministry of Education, College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| |
Collapse
|
2
|
Zhu F, Wei Y, Wang F, Xia Z, Gou M, Tang Y. Enrichment of microbial consortia for MEOR in crude oil phase of reservoir-produced liquid and their response to environmental disturbance. Int Microbiol 2024; 27:1049-1062. [PMID: 38010566 DOI: 10.1007/s10123-023-00458-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Developing microbial consortiums is necessary for microbial enhanced oil recovery (MEOR) in heavy crude oil production. The aqueous phase of produced fluid has long been considered an ideal source of microorganisms for MEOR. However, it is recently found that rich microorganisms (including hydrocarbon-degrading bacteria) are present in the crude oil phase, which is completely different from the aqueous phase of produced fluid. So, in this study, the microbial consortia from the crude oil phase of produced fluids derived from four wells were enriched, respectively. The microbial community structure during passage was dynamically tracked, and the response of enriched consortia to successive disturbance of environmental factors was investigated. The results showed the crude oil phase had high microbial diversity, and the original microbial community structure from four wells was significantly different. After ten generations of consecutive enrichment, different genera were observed in the four enriched microbial consortia, namely, Geobacillus, Bacillus, Brevibacillus, Chelativorans, Ureibacillus, and Ornithinicoccus. In addition, two enriched consortia (eG1614 and eP30) exhibited robustness to temperature and oxygen perturbations. These results further suggested that the crude oil phase of produced fluids can serve as a potential microbial source for MEOR.
Collapse
Affiliation(s)
- Fangfang Zhu
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Yanfeng Wei
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Fangzhou Wang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Ziyuan Xia
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China.
| | - Yueqin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan Province, China
| |
Collapse
|
3
|
Zavala-Meneses SG, Firrincieli A, Chalova P, Pajer P, Checcucci A, Skultety L, Cappelletti M. Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source. Microorganisms 2024; 12:753. [PMID: 38674697 PMCID: PMC11052242 DOI: 10.3390/microorganisms12040753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.
Collapse
Affiliation(s)
- Sofía G. Zavala-Meneses
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Faculty of Science, Charles University, Vinicna 5, 12844 Prague, Czech Republic
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
| | - Petra Chalova
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
- Faculty of Pharmacy, Comenius University, Odbojarov 10, 832 32 Bratislava, Slovakia
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, U Vojenske Nemocnice 1200, 16902 Prague, Czech Republic;
| | - Alice Checcucci
- Department of Agriculture, Food, Environment and Forestry, University of Florence, 50100 Firenze, Italy;
| | - Ludovit Skultety
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
- Biomedical Research Center, Slovak Academy of Sciences, Dubravska c. 9, 845 05 Bratislava, Slovakia;
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy or (A.F.); (M.C.)
| |
Collapse
|
4
|
Saborimanesh N, Xin Q, Ridenour C, Farooqi H. Response of microbial communities in North Saskatchewan River to diluted bitumen and conventional crude under freeze-thaw-refreeze cycle. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121256. [PMID: 36787815 DOI: 10.1016/j.envpol.2023.121256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms are the first responder to oil spills and their response provides insight into the ecological effects of oils on aquatic ecosystems. Limited information is available about the impact of oil spills on freshwater ecosystems under seasonal river-ice regimes. This study aimed to investigate the microbial response of North Saskatchewan River water to diluted bitumen (DB) and conventional crude (CC) during the freeze-thaw-refreeze cycle. In two separate experiments, equivalent to 2 L of fresh DB and CC were spilled on the ice-covered river water within a mesoscale spill tank. The microbial response (changes in abundance and diversity) to oils under the freeze, thaw, and refreeze cycles were assessed for 10 days using 16S rRNA gene sequencing. The results showed that microbial communities exhibited different responses to the DB and CC oils. The effect of oils was more pronounced than that of the freeze or thaw cycles. The river microbial community rapidly responded to both spills, which coincided with a steady increase in the organic content of water throughout the freeze-thaw-refreeze cycle. Microbial diversity increased after the DB spill, but remain unchanged after the CC spill, regardless of the cycles. A higher number of new taxa emerged during the ice-covered period, while more microbial enrichment (increase in abundance) was observed during the thaw cycle. Flavobacterium (37 ± 5%) and Pseudomonas (36 ± 4%) remained the most predominant genera post-DB and CC spill, respectively. The results of this study suggest that ice coverage of 5 cm did not prevent the microbial communities from the effects of oils. Thus, a quick clean-up response to an oil spill on ice-covered water is equally critical to avoid the effects of oils on the underlying freshwater ecosystems.
Collapse
Affiliation(s)
- Nayereh Saborimanesh
- Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada.
| | - Qin Xin
- Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - Christine Ridenour
- Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| | - Hena Farooqi
- Natural Resources Canada, CanmetENERGY Devon, 1 Oil Patch Drive, Devon, AB T9G 1A8, Canada
| |
Collapse
|
5
|
Dell'Anno F, Joaquim van Zyl L, Trindade M, Buschi E, Cannavacciuolo A, Pepi M, Sansone C, Brunet C, Ianora A, de Pascale D, Golyshin PN, Dell'Anno A, Rastelli E. Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120772. [PMID: 36455775 DOI: 10.1016/j.envpol.2022.120772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.
Collapse
Affiliation(s)
- Filippo Dell'Anno
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Leonardo Joaquim van Zyl
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, 7535, Cape Town, South Africa.
| | - Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Antonio Cannavacciuolo
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Milva Pepi
- Department of Integrative Marine Ecology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| | - Clementina Sansone
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Christophe Brunet
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Adrianna Ianora
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Donatella de Pascale
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Villa Comunale, 80121, Naples, Italy.
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Gwynedd LL57 2UW, UK.
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica Delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Eugenio Rastelli
- Department of Marine Biotechnology, Stazione Zoologica "Anton Dohrn", Fano Marine Centre, Viale Adriatico 1-N, 61032, Fano, Italy.
| |
Collapse
|
6
|
Pseudomonas veronii strain 7-41 degrading medium-chain n-alkanes and polycyclic aromatic hydrocarbons. Sci Rep 2022; 12:20527. [PMID: 36443410 PMCID: PMC9705281 DOI: 10.1038/s41598-022-25191-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Pollution of the environment by crude oil and oil products (represented by various types of compounds, mainly aliphatic, mono- and polyaromatic hydrocarbons) poses a global problem. The strain Pseudomonas veronii 7-41 can grow on medium-chain n-alkanes (C8-C12) and polycyclic aromatic hydrocarbons such as naphthalene. We performed a genetic analysis and physiological/biochemical characterization of strain 7-41 cultivated in a mineral medium with decane, naphthalene or a mixture of the hydrocarbons. The genes responsible for the degradation of alkanes and PAHs are on the IncP-7 conjugative plasmid and are organized into the alk and nah operons typical of pseudomonads. A natural plasmid carrying functional operons for the degradation of two different classes of hydrocarbons was first described. In monosubstrate systems, 28.4% and 68.8% of decane and naphthalene, respectively, were biodegraded by the late stationary growth phase. In a bisubstrate system, these parameters were 25.4% and 20.8% by the end of the exponential growth phase. Then the biodegradation stopped, and the bacterial culture started dying due to the accumulation of salicylate (naphthalene-degradation metabolite), which is toxic in high concentrations. The activity of the salicylate oxidation enzymes was below the detection limit. These results indicate that the presence of decane and a high concentration of salicylate lead to impairment of hydrocarbon degradation by the strain.
Collapse
|
7
|
Haque S, Srivastava N, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Naidu R, Gupta VK. Functional microbiome strategies for the bioremediation of petroleum-hydrocarbon and heavy metal contaminated soils: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155222. [PMID: 35421499 DOI: 10.1016/j.scitotenv.2022.155222] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 05/21/2023]
Abstract
Petroleum hydrocarbons and heavy metals are the two major soil contaminants that are released into the environment in the forms of industrial effluents. These contaminants exert serious impacts on human health and the sustainability of the environment. In this context, remediation of these pollutants via a biological approach can be effective, low-cost, and eco-friendly approach. The implementation of microorganisms and metagenomics are regarded as the advanced solution for remediating such pollutants. Further, microbiomes can overcome this issue via adopting specific structural, functional and metabolic pathways involved in the microbial community to degrade these pollutants. Genomic sequencing and library can effectively channelize the degradation of these pollutants via microbiomes. Nevertheless, more advanced technology and reliable strategies are required to develop. The present review provides insights into the role of microbiomes to effectively remediate/degrade petroleum hydrocarbons and heavy metals in contaminated soil. The possible degradation mechanisms of these pollutants have also been discussed in detail along with their existing limitations. Finally, prospects of the bioremediation strategies using microbiomes are discussed.
Collapse
Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Y Areeshi
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan-45142, Saudi Arabia; Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK; Center for Safe and Improved Food, SRUC, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK.
| |
Collapse
|
8
|
Kalia A, Sharma S, Semor N, Babele PK, Sagar S, Bhatia RK, Walia A. Recent advancements in hydrocarbon bioremediation and future challenges: a review. 3 Biotech 2022; 12:135. [PMID: 35620568 PMCID: PMC9127022 DOI: 10.1007/s13205-022-03199-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/04/2022] [Indexed: 11/01/2022] Open
Abstract
Petrochemicals are important hydrocarbons, which are one of the major concerns when accidently escaped into the environment. On one hand, these cause soil and fresh water pollution on land due to their seepage and leakage from automobile and petrochemical industries. On the other hand, oil spills occur during the transport of crude oil or refined petroleum products in the oceans around the world. These hydrocarbon and petrochemical spills have not only posed a hazard to the environment and marine life, but also linked to numerous ailments like cancers and neural disorders. Therefore, it is very important to remove or degrade these pollutants before their hazardous effects deteriorate the environment. There are varieties of mechanical and chemical methods for removing hydrocarbons from polluted areas, but they are all ineffective and expensive. Bioremediation techniques provide an economical and eco-friendly mechanism for removing petrochemical and hydrocarbon residues from the affected sites. Bioremediation refers to the complete mineralization or transformation of complex organic pollutants into the simplest compounds by biological agents such as bacteria, fungi, etc. Many indigenous microbes present in nature are capable of detoxification of various hydrocarbons and their contaminants. This review presents an updated overview of recent advancements in various technologies used in the degradation and bioremediation of petroleum hydrocarbons, providing useful insights to manage such problems in an eco-friendly manner.
Collapse
Affiliation(s)
- Arun Kalia
- Center for Environmental Science and Technology, Central University of Punjab, Bhatinda, 151001 India
| | - Samriti Sharma
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, India
| | - Nisha Semor
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005 India
| | - Piyoosh Kumar Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, 284003 Uttar Pradesh India
| | - Shweta Sagar
- Department of Microbiology, College of Basic Sciences, CSKHPKV, Palampur, 176062 Himachal Pradesh India
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, 171005 India
| | - Abhishek Walia
- Department of Microbiology, College of Basic Sciences, CSKHPKV, Palampur, 176062 Himachal Pradesh India
| |
Collapse
|
9
|
Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas. Folia Microbiol (Praha) 2022; 67:591-604. [PMID: 35318574 DOI: 10.1007/s12223-022-00966-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/15/2022] [Indexed: 11/04/2022]
Abstract
One of the most frequently used methods for elimination of oil pollution is the use of biological preparations based on oil-degrading microorganisms. Such microorganisms often relate to bacteria of the genus Pseudomonas. Pseudomonads are ubiquitous microorganisms that often have the ability to oxidize various pollutants, including oil hydrocarbons. To date, individual biochemical pathways of hydrocarbon degradation and the organization of the corresponding genes have been studied in detail. Almost all studies of this kind have been performed on degraders of individual hydrocarbons belonging to a single particular class. Microorganisms capable of simultaneous degradation of aliphatic and aromatic hydrocarbons are very poorly studied. Most of the works on such objects have been devoted only to phenotype characteristic and some to genetic studies. To identify the patterns of interaction of several metabolic systems depending on the growth conditions, the most promising are such approaches as transcriptomics and proteomics, which make it possible to obtain a comprehensive assessment of changes in the expression of hundreds of genes and proteins at the same time. This review summarizes the existing data on bacteria of the genus Pseudomonas capable of the simultaneous oxidation of hydrocarbons of different classes (alkanes, monoaromatics, and polyaromatics) and presents the most important results obtained in the studies on the biodegradation of hydrocarbons by representatives of this genus using methods of transcriptomic and proteomic analyses.
Collapse
|
10
|
Rojas-Gätjens D, Fuentes-Schweizer P, Rojas-Jiménez K, Pérez-Pantoja D, Avendaño R, Alpízar R, Coronado-Ruíz C, Chavarría M. Methylotrophs and Hydrocarbon-Degrading Bacteria Are Key Players in the Microbial Community of an Abandoned Century-Old Oil Exploration Well. MICROBIAL ECOLOGY 2022; 83:83-99. [PMID: 33864491 DOI: 10.1007/s00248-021-01748-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
In this work, we studied the microbial community and the physicochemical conditions prevailing in an exploratory oil well, abandoned a century ago, located in the Cahuita National Park (Costa Rica). According to our analysis, Cahuita well is characterized by a continuous efflux of methane and the presence of a mixture of hydrocarbons including phenanthrene/anthracene, fluoranthene, pyrene, dibenzothiophene, tricyclic terpanes, pyrene, sesquiterpenes, sterane, and n-alkanes. Based on the analysis of 16S rRNA gene amplicons, we detected a significant abundance of methylotrophic bacteria such as Methylobacillus (6.3-26.0% of total reads) and Methylococcus (4.1-30.6%) and the presence of common genera associated with hydrocarbon degradation, such as Comamonas (0.8-4.6%), Hydrogenophaga (1.5-3.3%) Rhodobacter (1.0-4.9%), and Flavobacterium (1.1-6.5%). The importance of C1 metabolism in this niche was confirmed by amplifying the methane monooxygenase (MMO)-encoding gene (pmo) from environmental DNA and the isolation of two strains closely related to Methylorubrum rhodesianum and Paracoccus communis with the ability to growth using methanol and formate as sole carbon source respectively. In addition, we were able to isolated 20 bacterial strains from the genera Pseudomonas, Acinetobacter, and Microbacterium which showed the capability to grow using the hydrocarbons detected in the oil well as sole carbon source. This work describes the physicochemical properties and microbiota of an environment exposed to hydrocarbons for 100 years, and it not only represents a contribution to the understanding of microbial communities in environments with permanently high concentrations of these compounds but also has biotechnological implications for bioremediation of petroleum-polluted sites.
Collapse
Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Paola Fuentes-Schweizer
- Centro de Investigación en Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica
| | - Keilor Rojas-Jiménez
- Escuela de Biología, Universidad de Costa Rica, San José, 11501-2060, Costa Rica
| | - Danilo Pérez-Pantoja
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación (PIDi), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Randall Alpízar
- Hidroambiente Consultores, 45, Goicoechea, San José, Costa Rica
| | - Carolina Coronado-Ruíz
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, 1174-1200, Costa Rica.
- Escuela de Química, Universidad de Costa Rica, Sede Central, San Pedro de Montes de Oca, San José, 11501-2060, Costa Rica.
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.
| |
Collapse
|
11
|
Ambust S, Das AJ, Kumar R. Bioremediation of petroleum contaminated soil through biosurfactant and Pseudomonas sp. SA3 amended design treatments. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100031. [PMID: 34841322 PMCID: PMC8610309 DOI: 10.1016/j.crmicr.2021.100031] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/19/2021] [Accepted: 03/31/2021] [Indexed: 01/05/2023] Open
Abstract
Potent PGP strain Pseudomonas sp SA3 was isolated from oil contaminated zone. PGPR strain SA3 produce biosurfactant under petroleum stress. Biosurfactant and strain SA3 amended treatments were developed. Amended treatments effects the plant growth and pigments. Treatment are efficient in reclamation of petroleum contaminated soil.
Toxicity of agricultural soil due to petroleum contamination has become a serious issue in recent times. Petrol oil exhibits toxic effects in agricultural crops due to the presence of various hazardous hydrocarbons. The degradation of petroleum hydrocarbon has been widely studied by the researchers that signify the requirement of effective treatments for the detoxification of petroleum contaminated soil and their reuse for growing crops. Hence, with this intention in the present study secondary metabolites “biosurfactant” (natural surfactant) along with the potent plant growth promoting (PGP) bacterial strain Pseudomonas sp. SA3 was used in the designed treatments for growing agricultural crop. The biosurfactant produced by the strain has the emulsification capacity of 43% and surface tension reduction ability to 34.5 mN/m whereas the plant growth promoting traits demonstrates 93.46 µg/mL phosphate solubilisation ability, siderophores (iron chelating compound) production upto 69.41% units and 81.41 µg/mL indole acetic acid (IAA) production ability. Further, the results of the design treatments signifies that treatments amended with the strain SA3 and biosurfactant is effective in the management of petroleum contaminated soil indicating treatment EX 5 (1 kg soil + 1 L water + Pseudomonas sp. SA3 + 300 mL crude biosurfactant), as an efficient treatment in increment of phytochemical constituents and 10–15% enhancement in growth parameters as compared to negative control. Hence, the developed treatments can be efficaciously used for the management of petroleum contaminated soil for agronomy.
Collapse
|
12
|
Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities. Microorganisms 2021; 9:microorganisms9102088. [PMID: 34683409 PMCID: PMC8540654 DOI: 10.3390/microorganisms9102088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ambient air pollution exerts deleterious effects on our environment. Continuously exposed to the atmosphere, diverse communities of microorganisms thrive on leaf surfaces, the phylloplane. The composition of these communities is dynamic, responding to many environmental factors including ambient air pollution. In this field study, over a 2 year period, we sampled Hedera helix (ivy) leaves at six locations exposed to different ambient air pollution conditions. Daily, we monitored ambient black carbon (BC), PM2.5, PM10, nitrogen dioxide, and ozone concentrations and found that ambient air pollution led to a 2–7-fold BC increase on leaves, the phylloplane BC load. Our results further indicated that the phylloplane BC load correlates with the diversity of bacterial and fungal leaf communities, impacting diversity more than seasonal effects. The bacterial genera Novosphingobium, Hymenobacter, and Methylorubrum, and the fungal genus Ampelomyces were indicators for communities exposed to the highest phylloplane BC load. Parallel to this, we present one fungal and two bacterial phylloplane strains isolated from an air-polluted environment able to degrade benzene, toluene, and/or xylene, including a genomics-based description of the degradation pathways involved. The findings of this study suggest that ambient air pollution shapes microbial leaf communities, by affecting diversity and supporting members able to degrade airborne pollutants.
Collapse
|
13
|
Abstract
Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.
Collapse
|
14
|
Korshunova TY, Bakaeva MD, Kuzina EV, Rafikova GF, Chetverikov SP, Chetverikova DV, Loginov ON. Role of Bacteria of the Genus Pseudomonas in the Sustainable Development of Agricultural Systems and Environmental Protection (Review). APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s000368382103008x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Epichloë gansuensis Increases the Tolerance of Achnatherum inebrians to Low-P Stress by Modulating Amino Acids Metabolism and Phosphorus Utilization Efficiency. J Fungi (Basel) 2021; 7:jof7050390. [PMID: 34067720 PMCID: PMC8156409 DOI: 10.3390/jof7050390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023] Open
Abstract
In the long-term evolutionary process, Achnatherum inebrians and seed-borne endophytic fungi, Epichloë gansuensis, formed a mutually beneficial symbiosis relationship, and Epichloë gansuensis has an important biological role in improving the tolerance of host grasses to abiotic stress. In this work, we first assessed the effects of Epichloë gansuensis on dry weight, the content of C, N, P and metal ions, and metabolic pathway of amino acids, and phosphorus utilization efficiency (PUE) of Achnatherum inebrians at low P stress. Our results showed that the dry weights, the content of alanine, arginine, aspartic acid, glycine, glutamine, glutamic acid, L-asparagine, lysine, phenylalanine, proline, serine, threonine, and tryptophan were higher in leaves of Epichloë gansuensis-infected (E+) Achnatherum inebrians than Epichloë gansuensis-uninfected (E−) Achnatherum inebrians at low P stress. Further, Epichloë gansuensis increased C content of roots compared to the root of E− plant at 0.01 mM P and 0.5 mM P; Epichloëgansuensis increased K content of leaves compared to the leaf of E− plant at 0.01 mM P and 0.5 mM P. Epichloëgansuensis reduced Ca content of roots compared to the root of E− plant at 0.01 mM P and 0.5 mM P; Epichloë gansuensis reduced the content of Mg and Fe in leaves compared to the leaf of E− plant at 0.01 mM P and 0.5 mM P. In addition, at low P stress, Epichloë gansuensis most probably influenced aspartate and glutamate metabolism; valine, leucine, and isoleucine biosynthesis in leaves; and arginine and proline metabolism; alanine, aspartate, and glutamate metabolism in roots. Epichloë gansuensis also affected the content of organic acid and stress-related metabolites at low P stress. In conclusion, Epichloë gansuensis improves Achnatherum inebrians growth at low P stress by regulating the metabolic pathway of amino acids, amino acids content, organic acid content, and increasing PUE.
Collapse
|
16
|
Portillo‐Estrada M, Van Moorleghem C, Janssenswillen S, Cooper RJ, Birkemeyer C, Roelants K, Van Damme R. Proton‐transfer‐reaction time‐of‐flight mass spectrometry (PTR‐TOF‐MS) as a tool for studying animal volatile organic compound (VOC) emissions. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miguel Portillo‐Estrada
- Research Group Pleco (Plants and Ecosystems) Department of Biology University of Antwerp Wilrijk Belgium
| | - Charlotte Van Moorleghem
- Laboratory for Functional Morphology Department of Biology University of Antwerp Wilrijk Belgium
| | - Sunita Janssenswillen
- Amphibian Evolution Lab Biology Department Vrije Universiteit Brussel Brussels Belgium
| | - Richard Joseph Cooper
- Amphibian Evolution Lab Biology Department Vrije Universiteit Brussel Brussels Belgium
| | | | - Kim Roelants
- Amphibian Evolution Lab Biology Department Vrije Universiteit Brussel Brussels Belgium
| | - Raoul Van Damme
- Laboratory for Functional Morphology Department of Biology University of Antwerp Wilrijk Belgium
| |
Collapse
|
17
|
Oyewusi HA, Wahab RA, Huyop F. Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria. Mol Biol Rep 2021; 48:2687-2701. [PMID: 33650078 DOI: 10.1007/s11033-021-06239-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
An integral approach to decoding both culturable and uncultured microorganisms' metabolic activity involves the whole genome sequencing (WGS) of individual/complex microbial communities. WGS of culturable microbes, amplicon sequencing, metagenomics, and single-cell genome analysis are selective techniques integrating genetic information and biochemical mechanisms. These approaches transform microbial biotechnology into a quick and high-throughput culture-independent evaluation and exploit pollutant-degrading microbes. They are windows into enzyme regulatory bioremediation pathways (i.e., dehalogenase) and the complete bioremediation process of organohalide pollutants. While the genome sequencing technique is gaining the scientific community's interest, it is still in its infancy in the field of pollutant bioremediation. The techniques are becoming increasingly helpful in unraveling and predicting the enzyme structure and explore metabolic and biodegradation capabilities.
Collapse
Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB 5351, Ado Ekiti, Ekiti State, Nigeria.
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
| |
Collapse
|
18
|
Galitskaya P, Biktasheva L, Kuryntseva P, Selivanovskaya S. Response of soil bacterial communities to high petroleum content in the absence of remediation procedures. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:9610-9627. [PMID: 33155112 DOI: 10.1007/s11356-020-11290-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
Oil spills are events that frequently lead to petroleum pollution. This pollution may cause stress to microbial communities, which require long adaption periods. Soil petroleum pollution is currently considered one of the most serious environmental problems. In the present work, processes occurring in the bacterial communities of three soil samples with different physicochemical characteristics, artificially polluted with 12% of crude oil, were investigated in 120-day laboratory experiment. It was found that the total petroleum hydrocarbon content did not decrease during this time; however, the proportion of petroleum fractions was altered. Petroleum pollution led to a short-term decrease in the bacterial 16S rRNA gene copy number. On the basis of amplicon sequencing analysis, it was concluded that bacterial community successions were similar in the three soils investigated. Thus, the phyla Actinobacteria and Proteobacteria and candidate TM7 phylum (Saccaribacteria) were predominant with relative abundances ranging from 35 to 58%, 25 to 30%, and 15 to 35% in different samples, respectively. The predominant operational taxonomic units (OTUs) after pollution belonged to the genera Rhodococcus and Mycobacterium, families Nocardioidaceae and Sinobacteraceae, and candidate class ТМ7-3. Genes from the alkIII group encoding monoxygenases were the most abundant compared with other catabolic genes from the alkI, alkII, GN-PAH, and GP-PAH groups, and their copy number significantly increased after pollution. The copy numbers of expressed genes involved in the horizontal transfer of catabolic genes, FlgC, TraG, and OmpF, also increased after pollution by 11-33, 16-63, and 11-71 times, respectively. The bacterial community structure after a high level of petroleum pollution changed because of proliferation of the cells that initially were able to decompose hydrocarbons, and in the second place, because proliferation of the cells that received these catabolic genes through horizontal transfer.
Collapse
Affiliation(s)
- Polina Galitskaya
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008
| | - Liliya Biktasheva
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008.
| | - Polina Kuryntseva
- Institute of Environmental Sciences, Kazan Federal University, Kazan, Russia, 420008
| | | |
Collapse
|
19
|
Garbisu C, Alkorta I, Kidd P, Epelde L, Mench M. Keep and promote biodiversity at polluted sites under phytomanagement. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:44820-44834. [PMID: 32975751 DOI: 10.1007/s11356-020-10854-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
The phytomanagement concept combines a sustainable reduction of pollutant linkages at risk-assessed contaminated sites with the generation of both valuable biomass for the (bio)economy and ecosystem services. One of the potential benefits of phytomanagement is the possibility to increase biodiversity in polluted sites. However, the unique biodiversity present in some polluted sites can be severely impacted by the implementation of phytomanagement practices, even resulting in the local extinction of endemic ecotypes or species of great conservation value. Here, we highlight the importance of promoting measures to minimise the potential adverse impact of phytomanagement on biodiversity at polluted sites, as well as recommend practices to increase biodiversity at phytomanaged sites without compromising its effectiveness in terms of reduction of pollutant linkages and the generation of valuable biomass and ecosystem services.
Collapse
Affiliation(s)
- Carlos Garbisu
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia P812, E-48160, Derio, Spain.
| | - Itziar Alkorta
- Department of Biochemistry and Molecular Biology, University of the Basque Country, P. O. Box 644, 48080, Bilbao, Spain
| | - Petra Kidd
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Investigacións Agrobiolóxicas de Galicia (IIAG), 15780, Santiago de Compostela, Spain
| | - Lur Epelde
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia P812, E-48160, Derio, Spain
| | - Michel Mench
- INRAE, BIOGECO, University of Bordeaux, F-33615, Pessac, France
| |
Collapse
|
20
|
Chicca I, Becarelli S, Dartiahl C, La China S, De Kievit T, Petroni G, Di Gregorio S, Levin DB. Degradation of BTEX mixture by a new Pseudomonas putida strain: role of the quorum sensing in the modulation of the upper BTEX oxidative pathway. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:36203-36214. [PMID: 32557076 DOI: 10.1007/s11356-020-09650-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/08/2020] [Indexed: 06/11/2023]
Abstract
A new Pseudomonas putida strain (AQ8) was isolated from a decommissioned oil refinery's soil in Italy and characterized for its ability to degrade BTEX. The draft genome of the new strain was sequenced and annotated for genes that encode enzymes putatively involved in BTEX degradation and quorum sensing. The strain was transformed with a plasmid expressing lactonase, which cleaves the autoinducer quorum sensing signal molecule, the acyl-homoserine lactone, to obtain a quorum sensing minus strain. P. putida AQ8 depleted the 40% on average of all the components of the initial BTEX concentration in 36 h. The quorum sensing minus strain, in the same time interval, depleted only the 10% of the initial BTEX concentration. The role of quorum sensing in regulating the expression of the annotated benzene/toluene dioxygenase gene (benzA) and biphenyl/toluene/benzene dioxygenase (bphA) genes, which are involved in BTEX degradation, was studied by quantitative RT-real-time quantitative (q)PCR analysis. The qPCR data showed decreased levels of expression of the benzA and bphA genes in the quorum sensing minus strain. Our results showed, for the first time, quorum sensing modulation of the level of transcription of dioxygenase genes in the upper BTEX oxidation pathway.
Collapse
Affiliation(s)
- Ilaria Chicca
- Department of Biology, University of Pisa, Pisa, Italy
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Christopher Dartiahl
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Salvatore La China
- Department of Life Sciences, University of Modena and Reggio-Emilia, Modena, Italy
| | - Teresa De Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
21
|
Borinelli JB, Blom J, Portillo-Estrada M, Kara De Maeijer P, Van den bergh W, Vuye C. VOC Emission Analysis of Bitumen Using Proton-Transfer Reaction Time-Of-Flight Mass Spectrometry. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E3659. [PMID: 32825044 PMCID: PMC7504115 DOI: 10.3390/ma13173659] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 01/06/2023]
Abstract
Bitumen is one of the most important materials used in roads. During asphalt pavement construction, workers can be affected by emissions, such as volatile organic compounds (VOCs), when bitumen is heated. Therefore, it is crucial to correctly identify and measure VOCs. This paper presents a novel, promising method to determine VOC emissions. The proposed method offers a way to standardize routine measurements on a lab scale, enabling reliable comparison across bitumen types and their modifications or additives. A proton-transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS) was used to monitor VOC emissions from commercial unmodified bitumen and crumb rubber modified bitumen (CRMB) with heating of up to 180 °C. Results confirmed that the temperature range of 160-180 °C is a highly influential factor for VOC emissions from heated commercial bitumen and particularly CRMB. A significant increase in alkane and aromatic emission was detected when the binders were heated to 180 °C. Sulfur-containing VOCs were almost nonexistent for the base bitumen fumes, while a significant increase was detected in the fumes when two different types of CR were added to the bitumen, even at 120 °C. The additional CR in the bituminous binder contributed to the potentially harmful VOC emission of benzothiazole, which belongs to the class of sulfur-containing compounds. The concentration of benzothiazole was 65%, 38%, and 35% higher for CR1 in comparison to CR2 at 140, 160, and 180 °C, respectively. It is clear from the results that this method allows different bitumen sources or modifications to be quickly analyzed and their VOC emissions cross-compared. If adopted and confirmed further, the method could offer the asphalt industry a viable solution to monitor VOC emissions by analyzing samples in real time at different steps of the production process.
Collapse
Affiliation(s)
- Jaffer Bressan Borinelli
- Road Engineering Research Section (RERS), EMIB, Faculty of Applied Engineering, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (P.K.D.M.); (W.V.d.b.); (C.V.)
| | - Johan Blom
- Road Engineering Research Section (RERS), EMIB, Faculty of Applied Engineering, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (P.K.D.M.); (W.V.d.b.); (C.V.)
| | - Miguel Portillo-Estrada
- Research Group PLECO (Plants and Ecosystems), Faculty of Science, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Patricia Kara De Maeijer
- Road Engineering Research Section (RERS), EMIB, Faculty of Applied Engineering, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (P.K.D.M.); (W.V.d.b.); (C.V.)
| | - Wim Van den bergh
- Road Engineering Research Section (RERS), EMIB, Faculty of Applied Engineering, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (P.K.D.M.); (W.V.d.b.); (C.V.)
| | - Cedric Vuye
- Road Engineering Research Section (RERS), EMIB, Faculty of Applied Engineering, University of Antwerp, 2020 Antwerp, Belgium; (J.B.); (P.K.D.M.); (W.V.d.b.); (C.V.)
| |
Collapse
|
22
|
Smułek W, Zdarta A, Grzywaczyk A, Guzik U, Siwińska-Ciesielczyk K, Ciesielczyk F, Strzemiecka B, Jesionowski T, Voelkel A, Kaczorek E. Evaluation of the physico-chemical properties of hydrocarbons-exposed bacterial biomass. Colloids Surf B Biointerfaces 2020; 196:111310. [PMID: 32911293 DOI: 10.1016/j.colsurfb.2020.111310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/14/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
In the efforts for the removal of hazardous materials from the environment biological processes are a valuable tool. Although much attention has been paid to the changes in bacteria at the omics level, another, physical-chemical perspective on the issue is essential, as little is known of microbial response to continuous exposition on harmful substances. This study provides in-depth characterization of the physical-chemical parameters of bacterial biomass after hydrocarbons exposure. To provide comparability of the harmful effects of chlorotoluenes and xylenes non-exposed and 12-months hydrocarbons exposed cells were analyzed, using the advanced spectrometric methods, inverse gas chromatography and low-temperature N2 sorption to evaluate acid-base as well as dispersive properties of the studied biomass. Presented results indicate P. fluorescens B01 cells strategy aimed at protecting the cell, thus lowering its' biodegradation efficiency as a result of metabolic stress. The outcome of the study was that prolonged exposure to pollutants might reduce the bioavailability of hydrocarbons to bacteria cells, and consequently decrease the effectiveness of decontamination of polluted sites by indigenous microorganisms.
Collapse
Affiliation(s)
- Wojciech Smułek
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Agata Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland.
| | - Adam Grzywaczyk
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Urszula Guzik
- University of Silesia in Katowice, Faculty of Biology and Environmental Protection, Department of Biochemistry, Jagiellońska 28, 40-032 Katowice, Poland
| | - Katarzyna Siwińska-Ciesielczyk
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Filip Ciesielczyk
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Beata Strzemiecka
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Adam Voelkel
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| |
Collapse
|
23
|
Trifolium repens-Associated Bacteria as a Potential Tool to Facilitate Phytostabilization of Zinc and Lead Polluted Waste Heaps. PLANTS 2020; 9:plants9081002. [PMID: 32781790 PMCID: PMC7466184 DOI: 10.3390/plants9081002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022]
Abstract
Heavy metals in soil, as selective agents, can change the structure of plant-associated bacterial communities and their metabolic properties, leading to the selection of the most-adapted strains, which might be useful in phytoremediation. Trifolium repens, a heavy metal excluder, naturally occurs on metal mine waste heaps in southern Poland characterized by high total metal concentrations. The purpose of the present study was to assess the effects of toxic metals on the diversity and metabolic properties of the microbial communities in rhizospheric soil and vegetative tissues of T. repens growing on three 70–100-years old Zn–Pb mine waste heaps in comparison to Trifolium-associated bacteria from a non-polluted reference site. In total, 113 cultivable strains were isolated and used for 16S rRNA gene Sanger sequencing in order to determine their genetic affiliation and for in vitro testing of their plant growth promotion traits. Taxa richness and phenotypic diversity in communities of metalliferous origin were significantly lower (p < 0.0001) compared to those from the reference site. Two strains, Bacillus megaterium BolR EW3_A03 and Stenotrophomonas maltophilia BolN EW3_B03, isolated from a Zn–Pb mine waste heap which tested positive for all examined plant growth promoting traits and which showed co-tolerance to Zn, Cu, Cd, and Pb can be considered as potential facilitators of phytostabilization.
Collapse
|
24
|
Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
Collapse
Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| |
Collapse
|
25
|
Special Issue: Genetics of Biodegradation and Bioremediation. Genes (Basel) 2020; 11:genes11040441. [PMID: 32316688 PMCID: PMC7230606 DOI: 10.3390/genes11040441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023] Open
Abstract
Many different biodegradation pathways, both aerobic and anaerobic, have already been characterised, and the phylogenetic relationships among catabolic genes within the different types of pathways have been studied. However, new biodegradation activities and their coding genes are continuously being reported, including those involved in the catabolism of emerging contaminants or those generally regarded as non-biodegradable. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to the bacterial physiological needs. New biodegradation pathways can be assembled in a particular strain or in a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, constitute valuable indicators of the biodegradation potential of a particular environmental niche. This knowledge paves the way to systems metabolic engineering approaches to valorise biowaste for the production of value-added products.
Collapse
|
26
|
Isolation and Characterization of Microbial Strains from Refinery Effluent to Screen their Bioremediation Potential. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|