1
|
Yessentayeva K, Reinhard A, Berzhanova R, Mukasheva T, Urich T, Mikolasch A. Bacterial crude oil and polyaromatic hydrocarbon degraders from Kazakh oil fields as barley growth support. Appl Microbiol Biotechnol 2024; 108:189. [PMID: 38305872 PMCID: PMC10837267 DOI: 10.1007/s00253-024-13010-y] [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: 10/27/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Bacterial strains of the genera Arthrobacter, Bacillus, Dietzia, Kocuria, and Micrococcus were isolated from oil-contaminated soils of the Balgimbaev, Dossor, and Zaburunye oil fields in Kazakhstan. They were selected from 1376 isolated strains based on their unique ability to use crude oil and polyaromatic hydrocarbons (PAHs) as sole source of carbon and energy in growth experiments. The isolated strains degraded a wide range of aliphatic and aromatic components from crude oil to generate a total of 170 acid metabolites. Eight metabolites were detected during the degradation of anthracene and of phenanthrene, two of which led to the description of a new degradation pathway. The selected bacterial strains Arthrobacter bussei/agilis SBUG 2290, Bacillus atrophaeus SBUG 2291, Bacillus subtilis SBUG 2285, Dietzia kunjamensis SBUG 2289, Kocuria rosea SBUG 2287, Kocuria polaris SBUG 2288, and Micrococcus luteus SBUG 2286 promoted the growth of barley shoots and roots in oil-contaminated soil, demonstrating the enormous potential of isolatable and cultivable soil bacteria in soil remediation. KEY POINTS: • Special powerful bacterial strains as potential crude oil and PAH degraders. • Growth on crude oil or PAHs as sole source of carbon and energy. • Bacterial support of barley growth as resource for soil remediation.
Collapse
Affiliation(s)
- Kuralay Yessentayeva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Anne Reinhard
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Ramza Berzhanova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave 71, 050040, Almaty, Kazakhstan
| | - Tim Urich
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany
| | - Annett Mikolasch
- Institute of Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17487, Greifswald, Germany.
| |
Collapse
|
2
|
Chen Q, Li Z, Chen Y, Liu M, Yang Q, Zhu B, Mu J, Feng L, Chen Z. Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments. MARINE POLLUTION BULLETIN 2024; 199:115925. [PMID: 38113802 DOI: 10.1016/j.marpolbul.2023.115925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.
Collapse
Affiliation(s)
- Qingguo Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhenzhen Li
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Yu Chen
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mei Liu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Qiao Yang
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Baikang Zhu
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Jun Mu
- College of Ecology and Environment, Hainan Tropical Ocean University, Sanya 572022, PR China.
| | - Lijuan Feng
- Zhejiang Key Laboratory of Petrochemical Environmental Pollution, Zhejiang Ocean University, Zhoushan 316022, PR China; National & local Joint Engineering Research Center of Harbor Oil & Gas Storage and Transportation Technology, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Zhi Chen
- Department of Building, Civil and Environmental Engineering, Faculty of Engineering & Computer Sciences, Concordia University, Montreal, Quebec H3G1M8, Canada
| |
Collapse
|
3
|
Wu Y, Xi B, Fang F, Kou B, Gang C, Tang J, Tan W, Yuan Y, Yu T. Insights into relationships between polycyclic aromatic hydrocarbon concentration, bacterial communities and organic matter composition in coal gangue site. ENVIRONMENTAL RESEARCH 2023; 236:116502. [PMID: 37406721 DOI: 10.1016/j.envres.2023.116502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023]
Abstract
Coal mining usually brought polycyclic aromatic hydrocarbons (PAHs) contamination. Relationships between the concentration of PAHs, bacterial communities and soil environmental factors were important for bioremediation of PAHs in soil. Total 4 kinds of soil samples with different concentrations of PAHs were selected from 7 typical coal gangue(CG) sites in Huainan, Anhui Province. The relationships between microorganisms, dissolved organic matter (DOM) composition and PAHs concentration were systematically analyzed in this work. Total 11 kinds of PAHs were enriched in the soil surface layer. That was attributed to the strong binding of soil organic matter (SOM) to PAHs. PAHs contamination reduced the diversity of soil microbial. The abundance of PAHs-degrading genera such as Arthrobacter decreased with the increasing concentration of PAHs. Mycobacterium increased with the increasing concentration of PAHs in all samples. The microbial activities decreased with increasing concentration of PAHs. The increasing contents of LWM-PAHs and DOM were beneficial to improve the activities of soil microbial. The increasing DOM aromaticity was beneficial to improve the bioavailability of PAHs according to the correlation analysis between PAHs content and DOM structural parameters. The obtained results provide a basis for better understanding the contamination characteristics and microbial communities of coal gangue PAH-contaminated sites.
Collapse
Affiliation(s)
- Yuman Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fei Fang
- Technical Centre for Soil, Agriculture and Rural Ecology and Environment, Ministry of Ecology and Environment, Beijing 100012, PR China
| | - Bing Kou
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Chen Gang
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an 710065, China
| | - Jun Tang
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Ying Yuan
- State Key Laboratory of Environmental Criteria and Risk Assessment, And State Environmental Protection Key Laboratory of Simulation and Control of Groundwater, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Tingqiao Yu
- International Education College, Beijing Vocational College of Agriculture, Beijing 102442, China
| |
Collapse
|
4
|
Huang Y, Li L, Yin X, Zhang T. Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach. ENVIRONMENTAL MICROBIOME 2023; 18:39. [PMID: 37122013 PMCID: PMC10150532 DOI: 10.1186/s40793-023-00497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear. RESULTS Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway. CONCLUSIONS Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.
Collapse
Affiliation(s)
- Yue Huang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Liguan Li
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Xiaole Yin
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| |
Collapse
|
5
|
García Rea VS, Egerland Bueno B, Muñoz Sierra JD, Nair A, Lopez Prieto IJ, Cerqueda-García D, van Lier JB, Spanjers H. Chemical characterization and anaerobic treatment of bitumen fume condensate using a membrane bioreactor. JOURNAL OF HAZARDOUS MATERIALS 2023; 447:130709. [PMID: 36680897 DOI: 10.1016/j.jhazmat.2022.130709] [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: 09/06/2022] [Revised: 12/02/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Bitumen fume condensate (BFC) is a hazardous wastewater generated at asphalt reclamation and production sites. BFC contains a wide variety of potentially toxic organic pollutants that negatively affect anaerobic processes. In this study, we chemically characterized BFC produced at an industrial site and evaluated its degradation under anaerobic conditions. Analyses identified about 900 compounds including acetate, polycyclic aromatic hydrocarbons, phenolic compounds, and metal ions. We estimated the half maximal inhibitory concentrations (IC50) of methanogenesis of 120, 224, and 990 mgCOD·L-1 for three types of anaerobic biomass, which indicated the enrichment and adaptation potentials of methanogenic biomass to the wastewater constituents. We operated an AnMBR (7.0 L, 35 °C) for 188 days with a mixture of BFC, phenol, acetate, and nutrients. The reactor showed a maximum average COD removal efficiency of 87.7 ± 7.0 %, that corresponded to an organic conversion rate of 286 ± 71 mgCOD-1·L-1d-1. The microbial characterization of the reactor's biomass showed the acetoclastic methanogen Methanosaeta as the most abundant microorganism (43 %), whereas the aromatic and phenol degrader Syntrophorhabdus was continuously present with abundances up to 11.5 %. The obtained results offer the possibility for the application of AnMBRs for the treatment of BFC or other petrochemical wastewater.
Collapse
Affiliation(s)
- Víctor S García Rea
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands; Econvert Water & Energy, Venus 35, 8448 CE, Heerenveen, the Netherlands.
| | - Beatriz Egerland Bueno
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands; Laboratory of Environmental Biotechnology, Department of Food Engineering, University of Sao Paulo, 225, Duque de Caxias Norte, Pirassununga, Sao Paulo, 13635-900, Brazil
| | - Julian D Muñoz Sierra
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands; KWR Water Research Institute, Groningenhaven 7, 3430 BB, Nieuwegein, the Netherlands
| | - Athira Nair
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands
| | - Israel J Lopez Prieto
- University of Arizona, Department of Chemical & Environmental Engineering, 1133 E. James E Rogers Way, Harshbarger 108, Tucson, AZ 85721-0011, United States; Facultad de Ciencias Químicas, Universidad Veracruzana campus Coatzacoalcos, Av. Universidad Veracruzana km 7.5, Col. Santa Isabel, C.P. 96535, Coatzacoalcos, Veracruz, Mexico
| | - Daniel Cerqueda-García
- Red de Manejo Biorracional de Plagas y Vectores, Instituto de Ecología, A. C.- INECOL, Xalapa 91073, Veracruz, Mexico
| | - Jules B van Lier
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands
| | - Henri Spanjers
- Sanitary Engineering Section, Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, the Netherlands
| |
Collapse
|
6
|
Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
Collapse
|
7
|
Soloveva O, Tikhonova E, Barabashin T, Eremina E. Hydrocarbons in the water and bottom sediments of Sivash Bay (the Azov Sea) during its salinization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:21186-21198. [PMID: 36264475 DOI: 10.1007/s11356-022-23579-4] [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: 02/22/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Sivash Bay is a unique hypersaline lagoon located in the northern part of the Crimean Peninsula. In 2014, due to political events in connection with the closure of the North Crimean Canal, the inflow of fresh water to Sivash Bay has been significantly reduced. As a result, there has been a steady increase in salinity since 2014 to the present. The main purpose of this work was to determine the spatial distribution and qualitative composition of hydrocarbons (aliphatic hydrocarbons, n-alkanes, polycyclic aromatic hydrocarbons) in the water and bottom sediments of the hypersaline Sivash Bay under increasing water salinity. The analysis of the physico-chemical parameters of Sivash Bay in 2020 showed the continued salinization and change of physico-chemical conditions of the lagoon. At the same time, spatially, the change in salinity affected only the total content and qualitative composition of hydrocarbons in the water. The content of the studied classes of hydrocarbons in the bottom sediments did not demonstrate a reliable correlation with the concentration of salts. There was also no statistically significant dependence of Eh and pH of bottom sediments on salinity. In accordance with the composition of n-alkanes and polyaromatic hydrocarbons, as well as on the basis of PCA analysis, it is possible to make a conclusion on natural, mainly autochthonous, sources of this class of substances and low toxicity of bottom sediments of the bay. Low concentrations and composition of hydrocarbons indicate an insignificant input of pollutants of anthropogenic origin in Sivash Bay during its salinization.
Collapse
Affiliation(s)
- Olga Soloveva
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 2 Nakhimov Avenue, 299011, Sevastopol, Russian Federation
| | - Elena Tikhonova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 2 Nakhimov Avenue, 299011, Sevastopol, Russian Federation.
| | - Timofey Barabashin
- Azov-Black Sea Branch of "VNIRO" ("AzNIIRKH"), 21v Beregovaya Str, 344002, Rostov-on-Don, Russian Federation
| | - Ekaterina Eremina
- Marine Hydrophysical Institute of RAS, 2 Kapitanskaya St, 299011, Sevastopol, Russian Federation
| |
Collapse
|
8
|
Castro AR, Martins G, Salvador AF, Cavaleiro AJ. Iron Compounds in Anaerobic Degradation of Petroleum Hydrocarbons: A Review. Microorganisms 2022; 10:2142. [PMID: 36363734 PMCID: PMC9695802 DOI: 10.3390/microorganisms10112142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 09/22/2023] Open
Abstract
Waste and wastewater containing hydrocarbons are produced worldwide by various oil-based industries, whose activities also contribute to the occurrence of oil spills throughout the globe, causing severe environmental contamination. Anaerobic microorganisms with the ability to biodegrade petroleum hydrocarbons are important in the treatment of contaminated matrices, both in situ in deep subsurfaces, or ex situ in bioreactors. In the latter, part of the energetic value of these compounds can be recovered in the form of biogas. Anaerobic degradation of petroleum hydrocarbons can be improved by various iron compounds, but different iron species exert distinct effects. For example, Fe(III) can be used as an electron acceptor in microbial hydrocarbon degradation, zero-valent iron can donate electrons for enhanced methanogenesis, and conductive iron oxides may facilitate electron transfers in methanogenic processes. Iron compounds can also act as hydrocarbon adsorbents, or be involved in secondary abiotic reactions, overall promoting hydrocarbon biodegradation. These multiple roles of iron are comprehensively reviewed in this paper and linked to key functional microorganisms involved in these processes, to the underlying mechanisms, and to the main influential factors. Recent research progress, future perspectives, and remaining challenges on the application of iron-assisted anaerobic hydrocarbon degradation are highlighted.
Collapse
Affiliation(s)
- Ana R. Castro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Gilberto Martins
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Andreia F. Salvador
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| | - Ana J. Cavaleiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
- LABBELS—Associate Laboratory, 4704-553 Braga/Guimarães, Portugal
| |
Collapse
|
9
|
Hauptfeld E, Pelkmans J, Huisman TT, Anocic A, Snoek BL, von Meijenfeldt FAB, Gerritse J, van Leeuwen J, Leurink G, van Lit A, van Uffelen R, Koster MC, Dutilh BE. A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater. WATER RESEARCH 2022; 221:118767. [PMID: 35777321 DOI: 10.1016/j.watres.2022.118767] [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: 03/15/2022] [Revised: 05/18/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.
Collapse
Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Jordi Pelkmans
- Department of Molecular Microbiology, Science for Life, Utrecht University, the Netherlands
| | - Terry T Huisman
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Armin Anocic
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | | | | | | | | | | | | | - Margot C Koster
- Department of Molecular Microbiology, Science for Life, Utrecht University, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands; Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Germany.
| |
Collapse
|
10
|
Su Q, Albani G, Sundberg J, Andersen HR, Nielsen TG, Thamdrup B, Jensen MM. Microbial bioremediation of produced water under different redox conditions in marine sediments. WATER RESEARCH 2022; 218:118428. [PMID: 35461099 DOI: 10.1016/j.watres.2022.118428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The discharge of produced water from offshore oil platforms is an emerging concern due to its potential adverse effects on marine ecosystems. In this study, we investigated the feasibility and capability of using marine sediments for the bioremediation of produced water. We utilized a combination of porewater and solid phase analysis in a series of sediment batch incubations amended with produced water and synthetic produced water to determine the biodegradation of hydrocarbons under different redox conditions. Significant removal of benzene, toluene, ethylbenzene and xylene (BTEX) compounds was observed under different redox conditions, with biodegradation efficiencies of 93-97% in oxic incubations and 45-93% in anoxic incubations with nitrate, iron oxide or sulfate as the electron acceptor. Higher biodegradation rates of BTEX were obtained by incubations dominated by nitrate reduction (104-149 nmolC/cm3/d) and oxygen respiration (52-57 nmolC/cm3/d), followed by sulfate reduction (14-76 nmolC/cm3/d) and iron reduction (29-39 nmolC/cm3/d). Chemical fingerprint analysis showed that hydrocarbons were biodegraded to smaller alcohols/acids under oxic conditions compared to anoxic conditions with nitrate, indicating that the presence of oxygen facilitated a more complete biodegradation process. Toxicity of treated produced water to the marine copepod Acartia tonsa was reduced by half after sediment incubations with oxygen and nitrate. Our study emphasizes the possibility to use marine sediment as a biofilter for treating produced water at sea without extending the oil and gas platform or implementing a large-scale construction.
Collapse
Affiliation(s)
- Qingxian Su
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, Denmark.
| | - Giovanna Albani
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby 2800, Denmark
| | - Jonas Sundberg
- Danish Offshore Technology Center, Technical University of Denmark, Lyngby 2800, Denmark
| | - Henrik Rasmus Andersen
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, Denmark
| | - Torkel Gissel Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Lyngby 2800, Denmark
| | - Bo Thamdrup
- Nordic Center for Earth Evolution and Institute of Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Marlene Mark Jensen
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, Denmark.
| |
Collapse
|
11
|
Dhar K, Panneerselvan L, Subashchandrabose SR, Venkateswarlu K, Megharaj M. Anaerobic Degradation of Naphthalene and Pyrene by Sulfate-Reducing Cultures Enriched from Former Manufactured Gas Plant Soil. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02042-4. [PMID: 35610382 DOI: 10.1007/s00248-022-02042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of polycyclic aromatic hydrocarbons (PAHs) under completely anaerobic sulfate-reducing conditions is an energetically challenging process. To date, anaerobic degradations of only two-ringed naphthalene and three-ringed phenanthrene by sediment-free and enriched sulfate-reducing bacteria have been reported. In this study, sulfate-reducing enrichment cultures capable of degrading naphthalene and four-ringed PAH, pyrene, were enriched from a contaminated former gas plant site soil. Bacterial community composition analysis revealed that a naphthalene-degrading enrichment culture, MMNap, was dominated (84.90%) by a Gram-positive endospore-forming member of the genus Desulfotomaculum with minor contribution (8.60%) from a member of Clostridium. The pyrene-degrading enrichment, MMPyr, was dominated (97.40%) by a species of Desulfotomaculum. The sequences representing the Desulfotomaculum phylotypes shared 98.80% similarity to each other. After 150 days of incubation, MMNap degraded 195 µM naphthalene with simultaneous reduction of sulfate and accumulation of sulfide. Similarly, MMPyr degraded 114 µM pyrene during 180 days of incubation with nearly stochiometric sulfate consumption and sulfide accumulation. In both cases, the addition of sulfate reduction inhibitor, molybdate (20 mM), resulted in complete cessation of the substrate utilization and sulfate reduction that clearly indicated the major role of the sulfate-reducing Desulfotomaculum in biodegradation of the two PAHs. This study is the first report on anaerobic pyrene degradation by a matrix-free, strictly anaerobic, and sulfate-reducing enrichment culture.
Collapse
Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Logeshwaran Panneerselvan
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, 515003, India
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), College of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment (CRC CARE), The University of Newcastle, ATC Building, Callaghan, NSW, 2308, Australia.
| |
Collapse
|
12
|
Shi Y, Fang H, Li YY, Wu H, Liu R, Niu Q. Single and simultaneous effects of naphthalene and salinity on anaerobic digestion: Response surface methodology, microbial community analysis and potential functions prediction. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118188. [PMID: 34547659 DOI: 10.1016/j.envpol.2021.118188] [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: 07/17/2021] [Revised: 08/27/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a persistent and prevalent class of pollutants in petroleum-contaminated saline environment, which pose potential harm to organisms. Researches on anaerobic biodegradation of PAHs are gradually emerging, but the response of anaerobic microorganisms to salinity changes and the co-effects of salinity and PAHs in anaerobic digestion (AD) system have seldom been reported. Thus, we investigated the variations of AD system performance and anaerobic microbial community caused by different concentrations of naphthalene (Nap) or/and NaCl based on Box-Behnken Design (0 mg/L ≤ Nap ≤150 mg/L, 0 g/L ≤ NaCl ≤25 g/L). The promoted efficiencies of acidogenesis and methanogenesis were found in presence of moderate NaCl or Nap, but high salinity (NaCl >4.4 g/L) weakened AD performance. Moreover, the high salinity (NaCl >4.4 g/L) and Nap resulted in reduced microbial Ca2+ Mg2+- ATPase activity, poor EPS secretion and the highest difference of the microbial operational taxonomic units (OTUs), and synergistically inhibited AD process. Microbiological analysis revealed that the relative abundance of Clostridium and acetoclastic Methanosaeta was increased by 2.01 times and 2.17 times in single Nap treated group compared to control. With the simultaneous addition of NaCl and Nap, Proteiniphilum and hydrogenotrophic methanogens (Methanobacterium, Methanofollis, and Methanolinea) occupied the major abundance. Potential functions prediction indicated that high salinity could disrupt the co-metabolism between carbohydrate metabolism and Nap degradation. This study provides basis for anaerobic bioremediation of PAHs-polluted saline environment.
Collapse
Affiliation(s)
- Yongsen Shi
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Hongli Fang
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Hanyang Wu
- Jiangxi Bocent Advanced Ceramic Environmental Technology Co., Ltd, Pingxiang, 337000, Jiangxi Province, China
| | - Rutao Liu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China
| | - Qigui Niu
- School of Environmental Science and Engineering, China-America CRC for Environment & Health, Shandong University, 72#Jimo Binhai Road, Qingdao, Shandong Province, 266237, China.
| |
Collapse
|
13
|
Wang YQ, Wang MX, Chen YY, Li CM, Zhou ZF. Microbial community structure and co-occurrence are essential for methanogenesis and its contribution to phenanthrene degradation in paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126086. [PMID: 34020358 DOI: 10.1016/j.jhazmat.2021.126086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/29/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Although polycyclic aromatic hydrocarbons (PAHs) degradation under methanogenesis is an ideal approach to remediating PAH-polluted soil, the contribution of methanogenesis to soil PAH elimination and the relationships between microbial ecological characteristics and PAH degradation during this process remain unclear. Here, we conducted a short-term (60 days) incubation using a paddy soil amended with phenanthrene and examined the effects of a specific methanogenic inhibitor (2-bromoethanesulfonate, BES) on this process. As treatment assessments, the methane production activity (MPA), phenanthrene degradation rate (PDR), and microbial ecological characteristics were determined. The results indicated that BES significantly inhibited both soil MPA and PDR, and we detected a positive relationship between MPA and PDR. Furthermore, BES significantly altered the soil microbial community structure, and it was the microbial community structure but not α-diversity was significantly correlated with soil MPA and PDR. BES decentralized the co-occurrence of bacterial genera but intensified the co-occurrence of methanogens. Moreover, certain bacterial taxa, including Bacteroidetes-vadinHA17, Gemmatimonas, and Sporomusaceae, were responsible for the MPA and PDR in this paddy soil. Collectively, these findings confirm the role of methanogenesis in PAH elimination from paddy soil, and reveal the importance of microbial co-occurrence characteristics in the determination of soil MPA and pollutant metabolism.
Collapse
Affiliation(s)
- Yan-Qin Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Ming-Xia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Yong-Yi Chen
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Chun-Ming Li
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhi-Feng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| |
Collapse
|
14
|
Leng Q, Mu J, Yang G. Efficient anaerobic bioremediation of high-concentration benzo[a]pyrene in marine environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117210. [PMID: 33932831 DOI: 10.1016/j.envpol.2021.117210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Benzo[a]pyrene (BaP), a persistent organic pollutant that may accumulate in sea sediments after oil spill or BaP chemical leakage accidents, considerably harms marine ecosystems and human health. Previous studies have been predominantly focused on its degradation at low concentrations, while the remediation of BaP pollution with high concentrations was neglected. Additionally, the metabolic pathways associated with its anaerobic degradation remain unclear. As a first attempt, super-efficient systems for BaP anaerobic degradation were established, and the corresponding metabolic pathways were elucidated in this study. The results showed that the BaP removal rate in BaP-only system with initial concentrations of 200 mg/L reached 3.09 mg/(L·d) within 45 days. Co-solvent, acetone promoted anaerobic BaP degradation (4.252 mg/(L·d)), while dichloromethane showed a newly-discovered co-metabolic effect. In the system with 500 mg/L of BaP and dichloromethane addition, the removal rate increased drastically (14.64 mg/(L·d)) at 400 mg/L turn point of BaP. Additionally, the corresponding microbial community-level metabolic network was firstly proposed.
Collapse
Affiliation(s)
- Qingxue Leng
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
| | - Jun Mu
- School of Ecological & Environment, Hainan Tropical Ocean University, Sanya, Hainan, 572022, China.
| | - Guangfeng Yang
- School of Marine Science & Technology, Zhejiang Ocean University, Zhoushan, Zhejiang, 316022, China
| |
Collapse
|
15
|
C Campbell B, Gong S, Greenfield P, J Midgley D, T Paulsen I, C George S. Aromatic compound-degrading taxa in an anoxic coal seam microbiome from the Surat Basin, Australia. FEMS Microbiol Ecol 2021; 97:6206826. [PMID: 33791788 DOI: 10.1093/femsec/fiab053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Methane is an important energy resource internationally, and a large proportion of this methane is produced by microbial communities living in coal seams. Despite the value of this resource for human energy security, our understanding of the metabolic roles played by specific taxa during the biodegradation of coal to methane in situ is quite limited. In order to develop a greater understanding of microbial catabolism on coal, a community from a coal seam in the Surat Basin, Australia, was incubated on 10 different aromatic organic compounds: coronene, benzo[a]pyrene, pyrene, phenanthrene, naphthalene, ethylbenzene, phenol, benzoate, vanillate and syringate. Each of these aromatic compounds either occurs in coal or is a possible product of the coal biodegradation process. 16S rRNA sequencing revealed substantial changes to each community in response to each aromatic carbon substrate provided. Abundant taxa from these substrate-specific communities were identified and their probable catabolic roles proposed based on literature searches of related taxa. This study is the first to link specific coal seam taxa to aromatic substrates available in coal seam environments. Two conceptual models of the putative degradation pathways and key taxa responsible are proposed.
Collapse
Affiliation(s)
- Bronwyn C Campbell
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia.,Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Se Gong
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Paul Greenfield
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - David J Midgley
- Energy Business Unit, Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| |
Collapse
|
16
|
Zhang Z, Guo H, Sun J, Gong X, Wang C, Wang H. Exploration of the biotransformation processes in the biodegradation of phenanthrene by a facultative anaerobe, strain PheF2, with Fe(III) or O 2 as an electron acceptor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:142245. [PMID: 33182168 DOI: 10.1016/j.scitotenv.2020.142245] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
The study of biodegradation of polycyclic aromatic hydrocarbons (PAHs) with metal ions as electron acceptors is still in its infancy. Here, a pure culture of PheF2 sharing 99.79% 16S rRNA-sequence similarity with Trichococcus alkaliphilus, which was recently reported to degrade PAHs, was isolated and found to degrade PAHs with Fe (III) or O2 reduction. Phenanthrene was selected as a model of PAH to study the biodegradation process by PheF2 with Fe (III) or O2 as an electron acceptor. PheF2 exhibited nearly 100%, 37.1%, and 28.5% anaerobic biodegradation of phenanthrene at initial concentrations of 280.7 μM, 280.6 μM, and 281.3 μM, respectively, within 10 days under anaerobic conditions with XAD-7 as a carrier, heptamethylnonane (HMN) as a solution, and nothing, respectively. PheF2 could degrade nearly 100% of the initial phenanthrene concentration of 283.4 μM under aerobic conditions within three days. The initial step of phenanthrene biodegradation by PheF2 involved carboxylation and dioxygenation under anaerobic and aerobic conditions, respectively. The biotransformation processes of phenanthrene degradation by PheF2 with Fe(III) or O2 as an electron acceptor were explored by metabolite and genome analysis. These findings provide an important theoretical support for evaluation of PAHs fate and for PAHs pollution control or remediation in anaerobic and aerobic environments.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaoqiang Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| |
Collapse
|
17
|
Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 18:ijerph18010262. [PMID: 33396411 PMCID: PMC7795093 DOI: 10.3390/ijerph18010262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 12/24/2022]
Abstract
Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.
Collapse
|
18
|
Zamanpour MK, Kaliappan RS, Rockne KJ. Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 271:110997. [PMID: 32778285 DOI: 10.1016/j.jenvman.2020.110997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/19/2020] [Accepted: 06/21/2020] [Indexed: 06/11/2023]
Abstract
Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C10 alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.
Collapse
Affiliation(s)
| | - Raja Shankar Kaliappan
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Karl John Rockne
- Department of Civil and Materials Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| |
Collapse
|
19
|
Sakshi, Haritash AK. A comprehensive review of metabolic and genomic aspects of PAH-degradation. Arch Microbiol 2020; 202:2033-2058. [DOI: 10.1007/s00203-020-01929-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
|
20
|
Qian Y, Zhang K, Jin H, Lei L, Zhang H, Gan H. Removal of acenaphthene from wastewater by Pseudomonas sp. in anaerobic conditions: the effects of extra and intracellular substances. ENVIRONMENTAL TECHNOLOGY 2020; 41:1298-1306. [PMID: 30284962 DOI: 10.1080/09593330.2018.1531940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Sorption and degradation are considered two primary modes of pollutant removal by microorganisms, and extracellular polymeric substances (EPS) have been shown to play an important role in these biological processes. However, their role in removing refractory organic pollutants the effects of intracellular substances in microorganisms remain unclear. In this study, we investigated both the removal mechanism and intracellular substances involved in removing the pollutant acenaphthene (ACE) from Pseudomonas sp. bacteria in anaerobic conditions. The results indicated that the ACE was mainly adsorbed rather than degraded by bacteria. Moreover, ACE had little impact on EPS secretion at concentrations ranging 0-3 mg/L. Cell walls and membranes accounted for more than 70% of ACE adsorption, whereas intra-cellular substances accounted for about 10-25% and the effect of other components on ACE adsorption was not obvious. A possible mechanism of ACE removal by bacteria is proposed.
Collapse
Affiliation(s)
- Yongxing Qian
- Ningbo Institute of Technology, Zhejiang University, Ningbo, People's Republic of China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou, People's Republic of China
| | - Kefeng Zhang
- Ningbo Institute of Technology, Zhejiang University, Ningbo, People's Republic of China
| | - Huixia Jin
- Ningbo Institute of Technology, Zhejiang University, Ningbo, People's Republic of China
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou, People's Republic of China
| | - Huining Zhang
- Ningbo Institute of Technology, Zhejiang University, Ningbo, People's Republic of China
| | - Huihui Gan
- Ningbo Institute of Technology, Zhejiang University, Ningbo, People's Republic of China
| |
Collapse
|
21
|
Zhang Z, Guo H, Sun J, Wang H. Investigation of anaerobic phenanthrene biodegradation by a highly enriched co-culture, PheN9, with nitrate as an electron acceptor. JOURNAL OF HAZARDOUS MATERIALS 2020; 383:121191. [PMID: 31525689 DOI: 10.1016/j.jhazmat.2019.121191] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/08/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
In this study, we developed a highly enriched phenanthrene-degrading co-culture, PheN9, which uses nitrate as an electron acceptor under anaerobic conditions, and the processes mediating biodegradation were proposed. The dominant bacteria populations included Pseudomonas stutzeri (91.7% relative abundance), which shared 98% 16S rRNA-sequence similarity with the naphthalene-degrading, nitrate-reducing strain NAP-3-1, and Candidatus_Kuenenia (2.3% relative abundance), which is a type of anammox bacteria. Enrichment transformed 54% of the added phenanthrene, reduced nitrate, and generated significant amounts of nitrite. Enrichment also result in partial consumption of the produced nitrite by the anammox bacteria. The key initial steps of anaerobic phenanthrene biodegradation by PheN9 were methylation and carboxylation, which were identified for detection of metabolic products, as well as carboxylase and methyltransferase activities. The methylation product was then oxidized to 2-naphthoic acid and then underwent sequential biodegradation steps. Then, ring-system reducing occurred, and the metabolic products were identified as dihydro-, tetrahydro-, hexahydro-, and octahydro-2-phenanthroic acid. Downstream degradation proceeded via a substituted benzene series and cyclohexane derivatives. This study employed anaerobic phenanthrene-biodegradation processes with nitrate as an electron acceptor. These findings can improve our understanding of anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation processes and guide PAH bioremediation by adding nitrate to anaerobic environments.
Collapse
Affiliation(s)
- Zuotao Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Haijiao Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Jiao Sun
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
| |
Collapse
|
22
|
Dhar K, Subashchandrabose SR, Venkateswarlu K, Krishnan K, Megharaj M. Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 251:25-108. [PMID: 31011832 DOI: 10.1007/398_2019_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.
Collapse
Affiliation(s)
- Kartik Dhar
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
- Department of Microbiology, University of Chittagong, Chittagong, Bangladesh
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, India
| | - Kannan Krishnan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, NSW, Australia.
| |
Collapse
|
23
|
Krepsky N, Bispo MDGS, Fontana LF, da Silva FS, Torres JPM, Malm O, Silva CG, Crapez MAC. Effects of aeration on the suspended matter from a tropical and eutrophic estuary. J Environ Sci (China) 2019; 86:175-186. [PMID: 31787182 DOI: 10.1016/j.jes.2019.05.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 06/10/2023]
Abstract
A comprehensive understanding of the complex biogeochemical interactions between organic matter and persistent contaminants in the suspended matter is vital for eco-efficient estuary recovery. However, little is known regarding aeration effects in suspended particulate aggregates. Therefore, this study aimed to investigate the effects of aeration on the suspended matter from a Tropical and Eutrophic estuarine environment. Anoxic water with 60 g/L of suspended particulate matter (SPM) was collected from Guanabara Bay, Rio de Janeiro, Brazil, transferred to experimental boxes and aerated for 61 days. SPM aggregates monitoring included abiotic variables measurements and, determination of total organic matter (TOM), biopolymers composition, bacterial activity, trace metals, and polycyclic aromatic hydrocarbons (PAHs) concentrations. The aeration enhanced dissolved oxygen (DO) concentration and the redox potential (Eh). However, from days 0 to 61 the predominant bacterial activities were denitrification and fermentation. Electron transport system activity increased after day 10, and aerobic activity was detected after day 19. In summary, aeration increased aerobic bacterial activity, lipids (LIP) and trace metal concentrations, although diminished protein/carbohydrate ratio and PAH concentration. Trace metals concentration (Ni, Pb, Cu, Cr, Mn, and Fe) were the highest on day 19 when the pH was 5.9. Copper presented toxic values (Cu > 20.0 μg/g). The pH showed a strong negative correlation with Eh (r = -0.94; p < 0.001). Acidic environment (pH ≤ 5.9) in marine ecosystems with high loads of toxic trace metals is unsafe for biota. Therefore, managers must be aware of the environmental and biological risks of introducing the aeration technique into a eutrophic marine environment.
Collapse
Affiliation(s)
- Natascha Krepsky
- Laboratory of Marine Geology, Fluminense Federal University, Ave. Gen. Milton Tavares de Souza s/n°-Gragoatá, 24210-346 Niterói, RJ, Brazil; Radioisotopes Laboratory Eduardo Penna Franca, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS - Bl. G, 21941-902 Rio de Janeiro, RJ, Brazil; Marine Biology Department, Fluminense Federal University, R. Mario Santos Braga, s/n, Niterói, 24.020-141 Niterói, RJ, Brazil.
| | - Maria das Graças S Bispo
- Marine Biology Department, Fluminense Federal University, R. Mario Santos Braga, s/n, Niterói, 24.020-141 Niterói, RJ, Brazil
| | - Luiz F Fontana
- Laboratory of Marine Geology, Fluminense Federal University, Ave. Gen. Milton Tavares de Souza s/n°-Gragoatá, 24210-346 Niterói, RJ, Brazil; Marine Biology Department, Fluminense Federal University, R. Mario Santos Braga, s/n, Niterói, 24.020-141 Niterói, RJ, Brazil
| | - Frederico S da Silva
- Laboratory of Marine Geology, Fluminense Federal University, Ave. Gen. Milton Tavares de Souza s/n°-Gragoatá, 24210-346 Niterói, RJ, Brazil; Marine Biology Department, Fluminense Federal University, R. Mario Santos Braga, s/n, Niterói, 24.020-141 Niterói, RJ, Brazil
| | - João P M Torres
- Radioisotopes Laboratory Eduardo Penna Franca, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS - Bl. G, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Olaf Malm
- Radioisotopes Laboratory Eduardo Penna Franca, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373 CCS - Bl. G, 21941-902 Rio de Janeiro, RJ, Brazil
| | - Cleverson G Silva
- Laboratory of Marine Geology, Fluminense Federal University, Ave. Gen. Milton Tavares de Souza s/n°-Gragoatá, 24210-346 Niterói, RJ, Brazil
| | - Mirian A C Crapez
- Marine Biology Department, Fluminense Federal University, R. Mario Santos Braga, s/n, Niterói, 24.020-141 Niterói, RJ, Brazil
| |
Collapse
|
24
|
Li L, Shen X, Zhao C, Liu Q, Liu X, Wu Y. Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:50-57. [PMID: 30921696 DOI: 10.1016/j.ecoenv.2019.03.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/16/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C8-C8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C1-DBT, C2-DBT, C3-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.
Collapse
Affiliation(s)
- Lin Li
- State Key Laboratory of Petroleum Pollution Control, Beijing, 102206, PR China; College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China.
| | - Xianwei Shen
- Qingdao Dongjiakou Economic Zone Management Committee, Qingdao, Shandong, 266409, China
| | - Chaocheng Zhao
- College of Chemical Engineering, China University of Petroleum (East China), No. 66, Changjiang West Road, Huangdao District, Qingdao, PR China.
| | - Qiyou Liu
- College of Chemical Engineering, China University of Petroleum (East China), No. 66, Changjiang West Road, Huangdao District, Qingdao, PR China
| | - Xuwei Liu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
| | - Yanan Wu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao, Shandong, 266590, China
| |
Collapse
|
25
|
Montagnolli RN, Lopes PRM, Bidoia ED. Fluorinated waste and firefighting activities: biodegradation of hydrocarbons from petrochemical refinery soil co-contaminated with halogenated foams. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:36002-36013. [PMID: 29484621 DOI: 10.1007/s11356-018-1593-2] [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: 11/16/2017] [Accepted: 02/18/2018] [Indexed: 06/08/2023]
Abstract
Perfluorinated compounds, including fluorotelomers, are important constituents of firefighting foams to extinguish fuel fires in the petrochemical industry, airports, and at fire-training sites. In this study, we monitored the biodegradation process in a co-contamination scenario with monoaromatic hydrocarbons commonly found in fuels (benzene, toluene) and fluorotelomers. The CO2 production rates were evaluated by a factorial design taking into account the effect of seasonality at in situ natural attenuation processes. Headspace analysis by gas chromatography with a thermal conductivity detector (GC-TCD) was applied to detect CO2 production, whereas monoaromatics were analyzed by gas chromatography coupled to mass spectrometry (GC-MS). According to our results, seasonality had a detectable effect during summer, yielding different CO2 production rates. Higher temperatures increased CO2 production rate, while higher concentrations of fluorotelomer inhibited the biodegradation process. On average, benzene and toluene were depleted 17.5 days earlier in control assays without fluorotelomers. Toluene removal efficiency was also notably higher than benzene. The noticeable decrease in degradation rates of monoaromatics was caused by perfluorinated compounds that are possibly linked to metabolic inhibition mechanisms. Fluorotelomer diminished catabolism in all of our batch cultures. In addition to this, an alternative production of by-products could be detected. Thus, we propose that transient components of the benzene and toluene degradation may be differentially formed, causing the benzene, toluene, and perfluorinated co-contaminations to go through switched metabolic stages under the presence of fluoride in a contamination scenario.
Collapse
Affiliation(s)
- Renato Nallin Montagnolli
- Department of Biochemistry and Microbiology, Biosciences Institute, Sao Paulo State University (UNESP), Rio Claro, São Paulo, Brazil
| | - Paulo Renato Matos Lopes
- College of Agricultural and Technological Sciences, São Paulo State University (UNESP), Dracena, São Paulo, Brazil
| | - Ederio Dino Bidoia
- Department of Biochemistry and Microbiology, Biosciences Institute, Sao Paulo State University (UNESP), Rio Claro, São Paulo, Brazil.
| |
Collapse
|
26
|
Himmelberg AM, Brüls T, Farmani Z, Weyrauch P, Barthel G, Schrader W, Meckenstock RU. Anaerobic degradation of phenanthrene by a sulfate-reducing enrichment culture. Environ Microbiol 2018; 20:3589-3600. [DOI: 10.1111/1462-2920.14335] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Anne M. Himmelberg
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
| | - Thomas Brüls
- CEA, DRF, Institut Jacob, Genoscope; Evry France
- CNRS-UMR8030; Université Paris-Saclay; Evry France
| | - Zahra Farmani
- Biofilm Centre; University of Duisburg-Essen; Essen Germany
- Max-Planck-Institut für Kohlenforschung; Mülheim Germany
| | | | - Gabriele Barthel
- Institute of Groundwater Ecology; Helmholtz Zentrum München; Neuherberg Germany
| | | | | |
Collapse
|
27
|
Nzila A. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons under anaerobic conditions: Overview of studies, proposed pathways and future perspectives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:788-802. [PMID: 29751337 DOI: 10.1016/j.envpol.2018.04.074] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 05/20/2023]
Abstract
The biodegradation of low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) (LWM-PAHs and HMW-PAHs, respectively) has been studied extensively under aerobic conditions. Molecular O2 plays 2 critical roles in this biodegradation process. O2 activates the aromatic rings through hydroxylation prior to ring opening and serves as a terminal electron acceptor (TEA). However, several microorganisms have devised ways of activating aromatic rings, leading to ring opening (and thus biodegradation) when TEAs other than O2 are used (under anoxic conditions). These microorganisms belong to the sulfate-, nitrate-, and metal-ion-reducing bacteria and the methanogens. Although the anaerobic biodegradation of monocyclic aromatic hydrocarbons and LWM-PAH naphthalene have been studied, little information is available about the biodegradation of HMW-PAHs. This manuscript reviews studies of the anaerobic biodegradation of HMW-PAHs and identifies gaps that limit both our understanding and the efficiency of this biodegradation process. Strategies that can be employed to overcome these limitations are also discussed.
Collapse
Affiliation(s)
- Alexis Nzila
- King Fahd University of Petroleum and Minerals, Department of Life Sciences, PO Box 468, Dhahran, 31261, Saudi Arabia.
| |
Collapse
|
28
|
Contaminant concentration versus flow velocity: drivers of biodegradation and microbial growth in groundwater model systems. Biodegradation 2018; 29:211-232. [PMID: 29492777 PMCID: PMC5943387 DOI: 10.1007/s10532-018-9824-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/23/2018] [Indexed: 11/07/2022]
Abstract
Aromatic hydrocarbons belong to the most abundant contaminants in groundwater systems. They can serve as carbon and energy source for a multitude of indigenous microorganisms. Predictions of contaminant biodegradation and microbial growth in contaminated aquifers are often vague because the parameters of microbial activity in the mathematical models used for predictions are typically derived from batch experiments, which don’t represent conditions in the field. In order to improve our understanding of key drivers of natural attenuation and the accuracy of predictive models, we conducted comparative experiments in batch and sediment flow-through systems with varying concentrations of contaminant in the inflow and flow velocities applying the aerobic Pseudomonas putida strain F1 and the denitrifying Aromatoleum aromaticum strain EbN1. We followed toluene degradation and bacterial growth by measuring toluene and oxygen concentrations and by direct cell counts. In the sediment columns, the total amount of toluene degraded by P. putida F1 increased with increasing source concentration and flow velocity, while toluene removal efficiency gradually decreased. Results point at mass transfer limitation being an important process controlling toluene biodegradation that cannot be assessed with batch experiments. We also observed a decrease in the maximum specific growth rate with increasing source concentration and flow velocity. At low toluene concentrations, the efficiencies in carbon assimilation within the flow-through systems exceeded those in the batch systems. In all column experiments the number of attached cells plateaued after an initial growth phase indicating a specific “carrying capacity” depending on contaminant concentration and flow velocity. Moreover, in all cases, cells attached to the sediment dominated over those in suspension, and toluene degradation was performed practically by attached cells only. The observed effects of varying contaminant inflow concentration and flow velocity on biodegradation could be captured by a reactive-transport model. By monitoring both attached and suspended cells we could quantify the release of new-grown cells from the sediments to the mobile aqueous phase. Studying flow velocity and contaminant concentrations as key drivers of contaminant transformation in sediment flow-through microcosms improves our system understanding and eventually the prediction of microbial biodegradation at contaminated sites.
Collapse
|
29
|
Wołejko E, Wydro U, Jabłońska-Trypuć A, Butarewicz A, Łoboda T. The effect of sewage sludge fertilization on the concentration of PAHs in urban soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:347-357. [PMID: 28986083 DOI: 10.1016/j.envpol.2017.08.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
This paper analyses sources of sixteen PAHs - polycyclic aromatic hydrocarbons in urbanized areas by using selected diagnostic ratios. Simultaneously, an attempt was made to determine how sewage sludge changes PAHs content in urbanized areas soils. In the experiment three lawns along the main roads in Bialystok with different traffic intensity, three doses of sewage sludge and two years of study were considered. There was no effect of fertilization with sewage sludge on the sum of 16 PAHs in urban soil samples, nevertheless, the sum of 16 PAHs was reduced from 2.6 in 2011 to 2.3 mg/kg in 2012. Among 16 tested PAHs compounds, benzo[a]pyrene was the most dominant compound in samples collected in both years - about 15% of all PAHs. The results suggest that application of sludge into the soil did not influence the concentration of 2-3-ring, 4-ring and 5-6-ring PAHs. For the objects fertilized with a dose 150.0 Mg/ha, of sludge the total sum of potentially carcinogenic PAHs in the urban soil lowered by approximately 68% in comparison with the control plots. PAHs contamination of the urban soil samples resulted from the influence of coal, petroleum and biomass combustion. Moreover, PAHs can enter soil via at mospheric deposition.
Collapse
Affiliation(s)
- Elżbieta Wołejko
- Bialystok University of Technology, Department of Sanitary Biology and Biotechnology, Wiejska 45A Street, 15-351, Białystok, Poland.
| | - Urszula Wydro
- Bialystok University of Technology, Department of Sanitary Biology and Biotechnology, Wiejska 45A Street, 15-351, Białystok, Poland
| | - Agata Jabłońska-Trypuć
- Bialystok University of Technology, Department of Sanitary Biology and Biotechnology, Wiejska 45A Street, 15-351, Białystok, Poland
| | - Andrzej Butarewicz
- Bialystok University of Technology, Department of Sanitary Biology and Biotechnology, Wiejska 45A Street, 15-351, Białystok, Poland
| | - Tadeusz Łoboda
- Bialystok University of Technology, Department of Sanitary Biology and Biotechnology, Wiejska 45A Street, 15-351, Białystok, Poland
| |
Collapse
|
30
|
Viggi CC, Matturro B, Frascadore E, Insogna S, Mezzi A, Kaciulis S, Sherry A, Mejeha OK, Head IM, Vaiopoulou E, Rabaey K, Rossetti S, Aulenta F. Bridging spatially segregated redox zones with a microbial electrochemical snorkel triggers biogeochemical cycles in oil-contaminated River Tyne (UK) sediments. WATER RESEARCH 2017; 127:11-21. [PMID: 29020640 DOI: 10.1016/j.watres.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 09/19/2017] [Accepted: 10/01/2017] [Indexed: 06/07/2023]
Abstract
Marine sediments represent an important sink for a number of anthropogenic organic contaminants, including petroleum hydrocarbons following an accidental oil spill. Degradation of these compounds largely depends on the activity of sedimentary microbial communities linked to biogeochemical cycles, in which abundant elements such as iron and sulfur are shuttled between their oxidized and reduced forms. Here we show that introduction of a small electrically conductive graphite rod ("the electrochemical snorkel") into an oil-contaminated River Tyne (UK) sediment, so as to create an electrochemical connection between the anoxic contaminated sediment and the oxygenated overlying water, has a large impact on the rate of metabolic reactions taking place in the bulk sediment. The electrochemical snorkel accelerated sulfate reduction processes driven by organic contaminant oxidation and suppressed competitive methane-producing reactions. The application of a comprehensive suite of chemical, spectroscopic, biomolecular and thermodynamic analyses suggested that the snorkel served as a scavenger of toxic sulfide via a redox interaction with the iron cycle. Taken as a whole, the results of this work highlight a new strategy for controlling biological processes, such as bioremediation, through the manipulation of the electron flows in contaminated sediments.
Collapse
Affiliation(s)
| | - Bruna Matturro
- Water Research Institute (IRSA), National Research Council (CNR), Italy
| | | | | | - Alessio Mezzi
- Institute for the Study of Nanostructured Materials (ISMN), National Research Council (CNR), Italy
| | - Saulius Kaciulis
- Institute for the Study of Nanostructured Materials (ISMN), National Research Council (CNR), Italy
| | - Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Obioma K Mejeha
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Ian M Head
- School of Civil Engineering and Geosciences, Newcastle University, United Kingdom
| | - Eleni Vaiopoulou
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET), Ghent University, Belgium
| | - Simona Rossetti
- Water Research Institute (IRSA), National Research Council (CNR), Italy
| | - Federico Aulenta
- Water Research Institute (IRSA), National Research Council (CNR), Italy.
| |
Collapse
|
31
|
Kronenberg M, Trably E, Bernet N, Patureau D. Biodegradation of polycyclic aromatic hydrocarbons: Using microbial bioelectrochemical systems to overcome an impasse. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:509-523. [PMID: 28841503 DOI: 10.1016/j.envpol.2017.08.048] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/09/2017] [Accepted: 08/11/2017] [Indexed: 05/22/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are hardly biodegradable carcinogenic organic compounds. Bioremediation is a commonly used method for treating PAH contaminated environments such as soils, sediment, water bodies and wastewater. However, bioremediation has various drawbacks including the low abundance, diversity and activity of indigenous hydrocarbon degrading bacteria, their slow growth rates and especially a limited bioavailability of PAHs in the aqueous phase. Addition of nutrients, electron acceptors or co-substrates to enhance indigenous microbial activity is costly and added chemicals often diffuse away from the target compound, thus pointing out an impasse for the bioremediation of PAHs. A promising solution is the adoption of bioelectrochemical systems. They guarantee a permanent electron supply and withdrawal for microorganisms, thereby circumventing the traditional shortcomings of bioremediation. These systems combine biological treatment with electrochemical oxidation/reduction by supplying an anode and a cathode that serve as an electron exchange facility for the biocatalyst. Here, recent achievements in polycyclic aromatic hydrocarbon removal using bioelectrochemical systems have been reviewed. This also concerns PAH precursors: total petroleum hydrocarbons and diesel. Removal performances of PAH biodegradation in bioelectrochemical systems are discussed, focussing on configurational parameters such as anode and cathode designs as well as environmental parameters like porosity, salinity, adsorption and conductivity of soil and sediment that affect PAH biodegradation in BESs. The still scarcely available information on microbiological aspects of bioelectrochemical PAH removal is summarised here. This comprehensive review offers a better understanding of the parameters that affect the removal of PAHs within bioelectrochemical systems. In addition, future experimental setups are proposed in order to study syntrophic relationships between PAH degraders and exoelectrogens. This synopsis can help as guide for researchers in their choices for future experimental designs aiming at increasing the power densities and PAH biodegradation rates using microbial bioelectrochemistry.
Collapse
Affiliation(s)
| | - Eric Trably
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France
| | - Nicolas Bernet
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France
| | | |
Collapse
|
32
|
Dou J, Qin W, Ding A, Liu X, Zhu Y. iTRAQ-based proteomic profiling of a Microbacterium sp. strain during benzo(a)pyrene removal under anaerobic conditions. Appl Microbiol Biotechnol 2017; 101:8365-8377. [DOI: 10.1007/s00253-017-8536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 08/16/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
|
33
|
Qin W, Fan F, Zhu Y, Huang X, Ding A, Liu X, Dou J. Anaerobic biodegradation of benzo(a)pyrene by a novel Cellulosimicrobium cellulans CWS2 isolated from polycyclic aromatic hydrocarbon-contaminated soil. Braz J Microbiol 2017; 49:258-268. [PMID: 29102294 PMCID: PMC5913828 DOI: 10.1016/j.bjm.2017.04.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/23/2017] [Accepted: 04/25/2017] [Indexed: 12/14/2022] Open
Abstract
Cellulosimicrobium cellulans CWS2, a novel strain capable of utilizing benzo(a)pyrene (BaP) as the sole carbon and energy source under nitrate-reducing conditions, was isolated from PAH-contaminated soil. Temperature and pH significantly affected BaP biodegradation, and the strain exhibited enhanced biodegradation ability at temperatures above 30 °C and between pH 7 and 10. The highest BaP removal rate (78.8%) was observed in 13 days when the initial BaP concentration was 10 mg/L, and the strain degraded BaP at constant rate even at a higher concentration (50 mg/L). Metal exposure experimental results illustrated that Cd(II) was the only metal ion that significantly inhibited biodegradation of BaP. The addition of 0.5 and 1.0 g/L glucose enhanced BaP biodegradation, while the addition of low-molecular-weight organic acids with stronger acidity reduced BaP removal rates during co-metabolic biodegradation. The addition of phenanthrene and pyrene, which were degraded to some extent by the strain, showed no distinct effect on BaP biodegradation. Gas chromatography–mass spectrometry (GC-MS) analysis revealed that the five rings of BaP opened, producing compounds with one to four rings which were more bioavailable. Thus, the strain exhibited strong BaP degradation capability and has great potential in the remediation of BaP-/PAH-contaminated environments.
Collapse
Affiliation(s)
- Wei Qin
- Beijing Normal University, College of Water Sciences, Beijing, China
| | - Fuqiang Fan
- Memorial University of Newfoundland, Faculty of Engineering and Applied Science, Northern Region Persistent Organic Pollution Control Laboratory, St. John's, Canada
| | - Yi Zhu
- Beijing Normal University, College of Water Sciences, Beijing, China
| | - Xiaolong Huang
- Beijing Normal University, College of Water Sciences, Beijing, China
| | - Aizhong Ding
- Beijing Normal University, College of Water Sciences, Beijing, China
| | - Xiang Liu
- Tsinghua University, School of Environment, Beijing, China
| | - Junfeng Dou
- Beijing Normal University, College of Water Sciences, Beijing, China.
| |
Collapse
|
34
|
Yan S, Wu G. Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. J Appl Genet 2017; 58:545-563. [PMID: 28685384 PMCID: PMC5655620 DOI: 10.1007/s13353-017-0402-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/22/2017] [Accepted: 06/06/2017] [Indexed: 01/05/2023]
Abstract
Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene’s function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.
Collapse
Affiliation(s)
- Shaomin Yan
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Guang Wu
- Bioscience and Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China.
| |
Collapse
|
35
|
Weyrauch P, Zaytsev AV, Stephan S, Kocks L, Schmitz OJ, Golding BT, Meckenstock RU. Conversion of cis-2-carboxycyclohexylacetyl-CoA in the downstream pathway of anaerobic naphthalene degradation. Environ Microbiol 2017; 19:2819-2830. [PMID: 28574200 DOI: 10.1111/1462-2920.13806] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/27/2017] [Indexed: 11/29/2022]
Abstract
The cyclohexane derivative cis-2-(carboxymethyl)cyclohexane-1-carboxylic acid [(1R,2R)-/(1S,2S)-2-(carboxymethyl)cyclohexane-1-carboxylic acid] has previously been identified as metabolite in the pathway of anaerobic degradation of naphthalene by sulfate-reducing bacteria. We tested the corresponding CoA esters of isomers and analogues of this compound for conversion in cell free extracts of the anaerobic naphthalene degraders Desulfobacterium strain N47 and Deltaproteobacterium strain NaphS2. Conversion was only observed for the cis-isomer, verifying that this is a true intermediate and not a dead-end product. Mass-spectrometric analyses confirmed that conversion is performed by an acyl-CoA dehydrogenase and a subsequent hydratase yielding an intermediate with a tertiary hydroxyl-group. We propose that a novel kind of ring-opening lyase is involved in the further catabolic pathway proceeding via pimeloyl-CoA. In contrast to degradation pathways of monocyclic aromatic compounds where ring-cleavage is achieved via hydratases, this lyase might represent a new ring-opening strategy for the degradation of polycyclic compounds. Conversion of the potential downstream metabolites pimeloyl-CoA and glutaryl-CoA was proved in cell free extracts, yielding 2,3-dehydropimeloyl-CoA, 3-hydroxypimeloyl-CoA, 3-oxopimeloyl-CoA, glutaconyl-CoA, crotonyl-CoA, 3-hydroxybutyryl-CoA and acetyl-CoA as observable intermediates. This indicates a link to central metabolism via β-oxidation, a non-decarboxylating glutaryl-CoA dehydrogenase and a subsequent glutaconyl-CoA decarboxylase.
Collapse
Affiliation(s)
- Philip Weyrauch
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrey V Zaytsev
- School of Chemistry, Newcastle University, Newcastle, UK.,Health and Life Sciences, Northumberland University, Newcastle, UK
| | - Susanne Stephan
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Lena Kocks
- Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany
| | | | | |
Collapse
|
36
|
Ghattas AK, Fischer F, Wick A, Ternes TA. Anaerobic biodegradation of (emerging) organic contaminants in the aquatic environment. WATER RESEARCH 2017; 116:268-295. [PMID: 28347952 DOI: 10.1016/j.watres.2017.02.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 05/22/2023]
Abstract
Although strictly anaerobic conditions prevail in several environmental compartments, up to now, biodegradation studies with emerging organic contaminants (EOCs), such as pharmaceuticals and personal care products, have mainly focused on aerobic conditions. One of the reasons probably is the assumption that the aerobic degradation is more energetically favorable than degradation under strictly anaerobic conditions. Certain aerobically recalcitrant contaminants, however, are biodegraded under strictly anaerobic conditions and little is known about the organisms and enzymatic processes involved in their degradation. This review provides a comprehensive survey of characteristic anaerobic biotransformation reactions for a variety of well-studied, structurally rather simple contaminants (SMOCs) bearing one or a few different functional groups/structural moieties. Furthermore it summarizes anaerobic degradation studies of more complex contaminants with several functional groups (CMCs), in soil, sediment and wastewater treatment. While strictly anaerobic conditions are able to promote the transformation of several aerobically persistent contaminants, the variety of observed reactions is limited, with reductive dehalogenations and the cleavage of ether bonds being the most prevalent. Thus, it becomes clear that the transferability of degradation mechanisms deduced from culture studies of SMOCs to predict the degradation of CMCs, such as EOCs, in environmental matrices is hampered due the more complex chemical structure bearing different functional groups, different environmental conditions (e.g. matrix, redox, pH), the microbial community (e.g. adaptation, competition) and the low concentrations typical for EOCs.
Collapse
Affiliation(s)
- Ann-Kathrin Ghattas
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Ferdinand Fischer
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Arne Wick
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology (BfG), D-56068 Koblenz, Am Mainzer Tor 1, Germany.
| |
Collapse
|
37
|
Biodegradation of benzo(a)pyrene by Microbacterium sp. strain under denitrification: Degradation pathway and effects of limiting electron acceptors or carbon source. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.02.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
38
|
Hofmann R, Grösbacher M, Griebler C. Mini Sediment Columns and Two-Dimensional Sediment Flow-Through Microcosms: Versatile Experimental Systems for Studying Biodegradation of Organic Contaminants in Groundwater Ecosystems. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/8623_2016_210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
|
39
|
Meckenstock RU, Boll M, Mouttaki H, Koelschbach JS, Cunha Tarouco P, Weyrauch P, Dong X, Himmelberg AM. Anaerobic Degradation of Benzene and Polycyclic Aromatic Hydrocarbons. J Mol Microbiol Biotechnol 2016; 26:92-118. [DOI: 10.1159/000441358] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aromatic hydrocarbons such as benzene and polycyclic aromatic hydrocarbons (PAHs) are very slowly degraded without molecular oxygen. Here, we review the recent advances in the elucidation of the first known degradation pathways of these environmental hazards. Anaerobic degradation of benzene and PAHs has been successfully documented in the environment by metabolite analysis, compound-specific isotope analysis and microcosm studies. Subsequently, also enrichments and pure cultures were obtained that anaerobically degrade benzene, naphthalene or methylnaphthalene, and even phenanthrene, the largest PAH currently known to be degradable under anoxic conditions. Although such cultures grow very slowly, with doubling times of around 2 weeks, and produce only very little biomass in batch cultures, successful proteogenomic, transcriptomic and biochemical studies revealed novel degradation pathways with exciting biochemical reactions such as for example the carboxylation of naphthalene or the ATP-independent reduction of naphthoyl-coenzyme A. The elucidation of the first anaerobic degradation pathways of naphthalene and methylnaphthalene at the genetic and biochemical level now opens the door to studying the anaerobic metabolism and ecology of anaerobic PAH degraders. This will contribute to assessing the fate of one of the most important contaminant classes in anoxic sediments and aquifers.
Collapse
|
40
|
Insights into the Anaerobic Biodegradation Pathway of n-Alkanes in Oil Reservoirs by Detection of Signature Metabolites. Sci Rep 2015; 5:9801. [PMID: 25966798 PMCID: PMC4429370 DOI: 10.1038/srep09801] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 03/16/2015] [Indexed: 11/28/2022] Open
Abstract
Anaerobic degradation of alkanes in hydrocarbon-rich environments has been documented
and different degradation strategies proposed, of which the most encountered one is
fumarate addition mechanism, generating alkylsuccinates as specific biomarkers.
However, little is known about the mechanisms of anaerobic degradation of alkanes in
oil reservoirs, due to low concentrations of signature metabolites and lack of mass
spectral characteristics to allow identification. In this work, we used a
multidisciplinary approach combining metabolite profiling and selective gene assays
to establish the biodegradation mechanism of alkanes in oil reservoirs. A total of
twelve production fluids from three different oil reservoirs were collected and
treated with alkali; organic acids were extracted, derivatized with ethanol to form
ethyl esters and determined using GC-MS analysis. Collectively, signature metabolite
alkylsuccinates of parent compounds from C1 to C8 together with their (putative)
downstream metabolites were detected from these samples. Additionally, metabolites
indicative of the anaerobic degradation of mono- and poly-aromatic hydrocarbons
(2-benzylsuccinate, naphthoate, 5,6,7,8-tetrahydro-naphthoate) were also observed.
The detection of alkylsuccinates and genes encoding for alkylsuccinate synthase
shows that anaerobic degradation of alkanes via fumarate addition occurs in oil
reservoirs. This work provides strong evidence on the in situ anaerobic
biodegradation mechanisms of hydrocarbons by fumarate addition.
Collapse
|
41
|
Marine Oil-Degrading Microorganisms and Biodegradation Process of Petroleum Hydrocarbon in Marine Environments: A Review. Curr Microbiol 2015; 71:220-8. [PMID: 25917503 DOI: 10.1007/s00284-015-0825-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
Abstract
Due to the toxicity of petroleum compounds, the increasing accidents of marine oil spills/leakages have had a significant impact on our environment. Recently, different remedial techniques for the treatment of marine petroleum pollution have been proposed, such as bioremediation, controlled burning, skimming, and solidifying. (Hedlund and Staley in Int J Syst Evol Microbiol 51:61-66, 2001). This review introduces an important remedial method for marine oil pollution treatment-bioremediation technique-which is considered as a reliable, efficient, cost-effective, and eco-friendly method. First, the necessity of bioremediation for marine oil pollution was discussed. Second, this paper discussed the species of oil-degrading microorganisms, degradation pathways and mechanisms, the degradation rate and reaction model, and the factors affecting the degradation. Last, several suggestions for the further research in the field of marine oil spill bioremediation were proposed.
Collapse
|
42
|
Anyika C, Abdul Majid Z, Ibrahim Z, Zakaria MP, Yahya A. The impact of biochars on sorption and biodegradation of polycyclic aromatic hydrocarbons in soils--a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:3314-3341. [PMID: 25345923 DOI: 10.1007/s11356-014-3719-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
Amending polycyclic aromatic hydrocarbon (PAH)-contaminated soils with biochar may be cheaper and environmentally friendly than other forms of organic materials. This has led to numerous studies on the use of biochar to either bind or stimulate the microbial degradation of organic compounds in soils. However, very little or no attention have been paid to the fact that biochars can give simultaneous impact on PAH fate processes, such as volatilization, sorption and biodegradation. In this review, we raised and considered the following questions: How does biochar affect microbes and microbial activities in the soil? What are the effects of adding biochar on sorption of PAHs? What are the effects of adding biochar on degradation of PAHs? What are the factors that we can manipulate in the laboratory to enhance the capability of biochars to degrade PAHs? A triphasic concept of how biochar can give simultaneous impact on PAH fate processes in soils was proposed, which involves rapid PAH sorption into biochar, subsequent desorption and modification of soil physicochemical properties by biochar, which in turn stimulates microbial degradation of the desorbed PAHs. It is anticipated that biochar can give simultaneous impact on PAH fate processes in soils.
Collapse
Affiliation(s)
- Chinedum Anyika
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310, UTM Johor, Malaysia
| | | | | | | | | |
Collapse
|
43
|
Kümmel S, Herbst FA, Bahr A, Duarte M, Pieper DH, Jehmlich N, Seifert J, von Bergen M, Bombach P, Richnow HH, Vogt C. Anaerobic naphthalene degradation by sulfate-reducing Desulfobacteraceae from various anoxic aquifers. FEMS Microbiol Ecol 2015; 91:fiv006. [PMID: 25764566 DOI: 10.1093/femsec/fiv006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAH) are widespread and persistent environmental contaminants, especially in oxygen-free environments. The occurrence of anaerobic PAH-degrading bacteria and their underlying metabolic pathways are rarely known. In this study, PAH degraders were enriched in laboratory microcosms under sulfate-reducing conditions using groundwater and sediment samples from four PAH-contaminated aquifers. Five enrichment cultures were obtained showing sulfate-dependent naphthalene degradation. Mineralization of naphthalene was demonstrated by the formation of sulfide concomitant with the depletion of naphthalene and the development of (13)C-labeled CO2 from [(13)C6]-naphthalene. 16S rRNA gene and metaproteome analyses revealed that organisms related to Desulfobacterium str. N47 were the main naphthalene degraders in four enrichment cultures. Protein sequences highly similar to enzymes of the naphthalene degradation pathway of N47 were identified, suggesting that naphthalene was activated by a carboxylase, and that the central metabolite 2-naphthoyl-CoA was further reduced by two reductases. The data indicate an importance of members of the family Desulfobacteraceae for naphthalene degradation under sulfate-reducing conditions in freshwater environments.
Collapse
Affiliation(s)
- Steffen Kümmel
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany
| | - Florian-Alexander Herbst
- UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Arne Bahr
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Márcia Duarte
- Helmholtz Centre for Infection Research - HZI, Microbial Interactions and Processes Research Group, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dietmar H Pieper
- Helmholtz Centre for Infection Research - HZI, Microbial Interactions and Processes Research Group, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Nico Jehmlich
- UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Jana Seifert
- University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany University of Hohenheim, Faculty of Agricultural Sciences, Emil-Wolff-Straße 8-10, D-70599 Stuttgart, Germany
| | - Martin von Bergen
- University of Freiburg, Faculty of Biology, Schaenzlestraße 1, D-79104 Freiburg, Germany UFZ - Helmholtz Centre for Environmental Research, Department of Metabolomics, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Petra Bombach
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Hans H Richnow
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| | - Carsten Vogt
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstraße 15, D-04318 Leipzig, Germany
| |
Collapse
|
44
|
Liang L, Song X, Kong J, Shen C, Huang T, Hu Z. Anaerobic biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a facultative anaerobe Pseudomonas sp. JP1. Biodegradation 2014; 25:825-33. [PMID: 25091324 DOI: 10.1007/s10532-014-9702-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/22/2014] [Indexed: 11/29/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are harmful persistent organic pollutants, while the high-molecular-weight (HMW) PAHs are even more detrimental to the environment and human health. However, microbial anaerobic degradation of HMW PAHs has rarely been reported. One facultative anaerobe Pseudomonas sp. JP1 was isolated from Shantou Bay, Shantou, China, which could degrade a variety of HMW PAHs. After 40 days cultivation with strain JP1, anaerobic biodegradation rate of benzo[a]pyrene (BaP), fluoranthene, and phenanthrene was 30, 47, and 5 %, respectively. Consumption of nitrate as the electron acceptor was confirmed by N-(1-naphthyl) ethylenediamine spectrophotometry. Supplementation of sodium sulfite, maltose, or glycine, and in a salinity of 0-20 ‰ significantly stimulated anaerobic degradation of BaP. Lastly, the anaerobic degradation metabolites of BaP by strain JP1 were investigated using GC/MS, and the degradation pathway was proposed. This study is helpful for further studies on the mechanism of anaerobic biodegradation of PAHs.
Collapse
Affiliation(s)
- Lei Liang
- College of Science, Shantou University, 243 Daxue Road, Shantou, 515063, Guangdong, China
| | | | | | | | | | | |
Collapse
|
45
|
Mass spectrometric screening and identification of acidic metabolites in fulvic acid fractions of contaminated groundwater. Anal Bioanal Chem 2014; 406:3415-29. [DOI: 10.1007/s00216-014-7783-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
|
46
|
Morris BE, Gissibl A, Kümmel S, Richnow HH, Boll M. A PCR-based assay for the detection of anaerobic naphthalene degradation. FEMS Microbiol Lett 2014; 354:55-9. [DOI: 10.1111/1574-6968.12429] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 11/27/2022] Open
Affiliation(s)
- Brandon E.L. Morris
- Institute for Biology II - Microbiology; University of Freiburg; Freiburg Germany
| | - Alexander Gissibl
- Institute for Biology II - Microbiology; University of Freiburg; Freiburg Germany
| | - Steffen Kümmel
- Institute for Biology II - Microbiology; University of Freiburg; Freiburg Germany
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry; Helmholtz Centre for Environmental Research - UFZ; Leipzig Germany
| | - Matthias Boll
- Institute for Biology II - Microbiology; University of Freiburg; Freiburg Germany
| |
Collapse
|
47
|
Adelaja O, Keshavarz T, Kyazze G. Enhanced biodegradation of phenanthrene using different inoculum types in a microbial fuel cell. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300089] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Oluwaseun Adelaja
- Department of Molecular and Applied Biosciences; Applied Biotechnology Research Group; University of Westminster; London UK
| | - Tajalli Keshavarz
- Department of Molecular and Applied Biosciences; Applied Biotechnology Research Group; University of Westminster; London UK
| | - Godfrey Kyazze
- Department of Molecular and Applied Biosciences; Applied Biotechnology Research Group; University of Westminster; London UK
| |
Collapse
|
48
|
Liu Y, Hua X. Degradation of acenaphthylene and anthracene by chemically modified laccase from Trametes versicolor. RSC Adv 2014. [DOI: 10.1039/c4ra02807d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We are studying the chemically modified laccase from Trametes versicolor for use in the in vitro oxidation of two polycyclic aromatic hydrocarbons (PAHs), acenaphthylene and anthracene, in combination with 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as a redox mediator.
Collapse
Affiliation(s)
- Yulong Liu
- Department of Basic Teaching
- Yancheng Institute of Technology
- Yancheng, China
| | - Xiufu Hua
- Department of Scientific Research and Development
- Tsinghua University
- , China
| |
Collapse
|
49
|
Eberlein C, Estelmann S, Seifert J, von Bergen M, Müller M, Meckenstock RU, Boll M. Identification and characterization of 2-naphthoyl-coenzyme A reductase, the prototype of a novel class of dearomatizing reductases. Mol Microbiol 2013; 88:1032-9. [PMID: 23646996 DOI: 10.1111/mmi.12238] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2013] [Indexed: 11/30/2022]
Abstract
The enzymatic dearomatization of aromatic ring systems by reduction represents a highly challenging redox reaction in biology and plays a key role in the degradation of aromatic compounds under anoxic conditions. In anaerobic bacteria, most monocyclic aromatic growth substrates are converted to benzoyl-coenzyme A (CoA), which is then dearomatized to a conjugated dienoyl-CoA by ATP-dependent or -independent benzoyl-CoA reductases. It was unresolved whether or not related enzymes are involved in the anaerobic degradation of environmentally relevant polycyclic aromatic hydrocarbons (PAHs). In this work, a previously unknown dearomatizing 2-naphthoyl-CoA reductase was purified from extracts of the naphthalene-degrading, sulphidogenic enrichment culture N47. The oxygen-tolerant enzyme dearomatized the non-activated ring of 2-naphthoyl-CoA by a four-electron reduction to 5,6,7,8-tetrahydro-2-naphthoyl-CoA. The dimeric 150 kDa enzyme complex was composed of a 72 kDa subunit showing sequence similarity to members of the flavin-containing 'old yellow enzyme' family. NCR contained FAD, FMN, and an iron-sulphur cluster as cofactors. Extracts of Escherichia coli expressing the encoding gene catalysed 2-naphthoyl-CoA reduction. The identified NCR is a prototypical enzyme of a previously unknown class of dearomatizing arylcarboxyl-CoA reductases that are involved in anaerobic PAH degradation; it fundamentally differs from known benzoyl-CoA reductases.
Collapse
Affiliation(s)
- Christian Eberlein
- Institute for Biology II, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | | | | | | | | | | | | |
Collapse
|
50
|
Gao S, Seo JS, Wang J, Keum YS, Li J, Li QX. Multiple degradation pathways of phenanthrene by Stenotrophomonas maltophilia C6. INTERNATIONAL BIODETERIORATION & BIODEGRADATION 2013; 79:98-104. [PMID: 23539472 PMCID: PMC3607548 DOI: 10.1016/j.ibiod.2013.01.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Stenotrophomonas maltophilia strain C6, capable of utilizing phenanthrene as a sole source of carbon and energy, was isolated from creosote-contaminated sites at Hilo, Hawaii. Twenty-two metabolites of phenanthrene, covering from dihydrodiol to protocatechuic acid, were isolated and characterized. Phenanthrene was degraded via an initial dioxygenation on 1,2-, 3,4-, and 9,10-C, where the 3,4-dioxygenation and subsequent metabolisms were most dominant. The metabolic pathways were further branched by ortho- and meta-cleavage of phenanthrenediols to produce 1-hydroxy-2-naphthoic acid, 2-hydroxy-1-naphthoic acid, and naphthalene-1,2-dicarboxylic acid. These intermediates were then transformed to naphthalene-1,2-diol. 1-Hydroxy-2-naphthoic acid was also degraded via a direct ring cleavage. Naphthalene-1,2-diol underwent primarily ortho-cleavage to produce trans-2-carboxycinnamic acid and then to form phthalic acid, 4,5-dihydroxyphthalic acid and protocatechuic acid. Accumulation of salicylic acid in prolonged incubation indicated that a limited extent of meta-cleavage of naphthalene-1, 2-diol also occurred. This is the first study of detailed phenanthrene metabolic pathways by Stenotrophomonas maltophilia.
Collapse
Affiliation(s)
- Shumei Gao
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 YuanMingYuan West Road, Beijing 100193, China
| | - Jong-Su Seo
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Jun Wang
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Young-Soo Keum
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Jianqiang Li
- College of Agriculture and Biotechnology, China Agricultural University, No. 2 YuanMingYuan West Road, Beijing 100193, China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA
- Correspondence to: Qing X. Li, Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822, USA. Phone: 808-956-2011, Fax: 808-956-3542,
| |
Collapse
|