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Su X, Bamba A, Zhang S, Zhang Y, Hashmi M, Lin H, Ding L. Revealing potential functions of VBNC bacteria in polycyclic aromatic hydrocarbons biodegradation. Lett Appl Microbiol 2018; 66:277-283. [DOI: 10.1111/lam.12853] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 01/13/2018] [Accepted: 01/14/2018] [Indexed: 12/12/2022]
Affiliation(s)
- X.M. Su
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
| | - A.M. Bamba
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
| | - S. Zhang
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
| | - Y.G. Zhang
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
| | - M.Z. Hashmi
- Department of Meteorology; COMSATS Institute of Information Technology; Islamabad Pakistan
| | - H.J. Lin
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
| | - L.X. Ding
- College of Geography and Environmental Science; Zhejiang Normal University; Jinhua China
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Cipullo S, Prpich G, Campo P, Coulon F. Assessing bioavailability of complex chemical mixtures in contaminated soils: Progress made and research needs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 615:708-723. [PMID: 28992498 DOI: 10.1016/j.scitotenv.2017.09.321] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 05/13/2023]
Abstract
Understanding the distribution, behaviour and interactions of complex chemical mixtures is key for providing the evidence necessary to make informed decisions and implement robust remediation strategies. Much of the current risk assessment frameworks applied to manage land contamination are based on total contaminant concentrations and the exposure assessments embedded within them do not explicitly address the partitioning and bioavailability of chemical mixtures. These oversights may contribute to an overestimation of both the eco-toxicological effects of the fractions and the mobility of contaminants. In turn, this may limit the efficacy of risk frameworks to inform targeted and proportionate remediation strategies. In this review we analyse the science surrounding bioavailability, its regulatory inclusion and the challenges of incorporating bioavailability in decision making process. While a number of physical and chemical techniques have proven to be valuable tools for estimating bioavailability of organic and inorganic contaminants in soils, doubts have been cast on its implementation into risk management soil frameworks mainly due to a general disagreement on the interchangeable use of bioavailability and bioaccessibility, and the associated methods which are still not standardised. This review focuses on the role of biotic and abiotic factors affecting bioavailability along with soil physicochemical properties and contaminant composition. We also included advantages and disadvantages of different extraction techniques and their implications for bioavailability quantitative estimation. In order to move forward the integration of bioavailability into site-specific risk assessments we should (1) account for soil and contaminant physicochemical characteristics and their effect on bioavailability; (2) evaluate receptor's potential exposure and uptake based on mild-extraction; (3) adopt a combined approach where chemical-techniques are used along with biological methods; (4) consider a simplified and cost-effective methodology to apply at regulatory and industry setting; (5) use single-contaminant exposure assessments to inform and predict complex chemical mixture behaviour and bioavailability.
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Affiliation(s)
- S Cipullo
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - G Prpich
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - P Campo
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK
| | - F Coulon
- Cranfield University, School of Water, Energy and Environment, Cranfield MK43 0AL, UK.
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Kijima K, Mita H, Kawakami M, Amada K. Role of CadC and CadD in the 2,4-dichlorophenoxyacetic acid oxygenase system of Sphingomonas agrestis 58-1. J Biosci Bioeng 2018; 125:649-653. [PMID: 29398549 DOI: 10.1016/j.jbiosc.2018.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/05/2017] [Accepted: 01/05/2018] [Indexed: 12/01/2022]
Abstract
In the present study, we confirm that 2,4-dichlorophenoxyacetic acid (2,4-D) oxygenase from Sphingomonas agrestis 58-1 belongs to the family of Rieske non-heme iron aromatic ring-hydroxylating oxygenases, which comprise a core enzyme (oxygenase), ferredoxin, and oxidoreductase. It has previously been shown that cadAB genes are necessary for the conversion of 2,4-D to 2,4-dichlorophenol; however, the respective roles of ferredoxin and oxidoreductase in the 2,4-D oxygenase system from S. agrestis 58-1 remain unknown. Using nucleotide sequence analysis of the plasmid pCADAB1 from Sphingomonas sp. ERG5, which degrades 4-chloro-2-methylphenoxyacetic acid and 2,4-D, Nielsen et al. identified orf95, upstream of cadA, and orf98, downstream of cadB, which were predicted and designated as cadD (oxidoreductase) and cadC (ferredoxin), respectively (Nielsen et al., PLoS One, 8, e83346, 2013). These designations were the result of sequence analysis; therefore, we constructed an expression system of CadABC and CadABCD in Escherichia coli and assayed their enzyme activities. Our findings indicate that CadC is essential for the activity of 2,4-D oxygenase and CadD promotes CadABC activity in recombinant E. coli cells.
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Affiliation(s)
- Kumiko Kijima
- Division of Material Science and Production Engineering, Graduate School of Engineering, Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi, Fukuoka 811-0295, Japan
| | - Hajime Mita
- Department of Life, Environment and Material Science, Faculty of Engineering, Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi, Fukuoka 811-0295, Japan
| | - Mitsuyasu Kawakami
- Department of Life, Environment and Material Science, Faculty of Engineering, Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi, Fukuoka 811-0295, Japan
| | - Kei Amada
- Department of Life, Environment and Material Science, Faculty of Engineering, Fukuoka Institute of Technology, 3-30-1 Wajiro-Higashi, Higashi, Fukuoka 811-0295, Japan.
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Adam IKU, Duarte M, Pathmanathan J, Miltner A, Brüls T, Kästner M. Microbial communities in pyrene amended soil-compost mixture and fertilized soil. AMB Express 2017; 7:7. [PMID: 28050848 PMCID: PMC5209307 DOI: 10.1186/s13568-016-0306-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/11/2016] [Indexed: 12/11/2022] Open
Abstract
Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of 13C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.
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55
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Ding Q, Huang X, Hu H, Hong M, Zhang D, Wang K. Impact of pyrene and cadmium co-contamination on prokaryotic community in coastal sediment microcosms. CHEMOSPHERE 2017; 188:320-328. [PMID: 28888120 DOI: 10.1016/j.chemosphere.2017.08.124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Acute ecological impacts of co-contamination of polycyclic aromatic hydrocarbons (PAHs) and heavy metals on diversity and composition of coastal benthic prokaryotes were unclear. We took pyrene (Pyr) and cadmium (Cd) as the representatives and mimicked an eight-week exposure of moderate and high levels of Pyr, Cd and their mixtures. 16S rRNA amplicon sequencing was used to investigate interaction of the contaminants in temporal succession of prokaryotes. Generally, concentrations of Pyr and HCl-extractable Cd in the sediments were stable over time. Effects and interaction of Pyr and Cd on prokaryotic α-diversity were temporally- and dose-dependent with a decreasing trend in richness and Shannon index under various contamination regimes, particularly in the single-Cd contaminated groups at the early stage. Temporal variability and Pyr-induced pattern in prokaryotic composition were observed. However, Pyr and Cd showed a persistent interaction in prokaryotic composition after 7 days, altering successional trajectories of communities. The communities under Pyr contamination regardless of Cd could be at a developing stage for an active PAH-degrading community with appearance of a pioneer Cycloclasticus phylotype, persistently showing a strong correlation with Pyr level. The associations of phylotypes and Cd level were short-lived and weak, corresponding to the overall resistance of prokaryotic composition to Cd. In the high-throughput sequencing era, using microcosm experiment, we renewed the knowledge about how prokaryotes vary in terms of α-diversity, composition and specific taxa in response to co-contamination of model contaminants at a temporal scale.
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Affiliation(s)
- Qifang Ding
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Xiaolin Huang
- Zhejiang Mariculture Research Institute, Wenzhou, 325005, China
| | - Hanjing Hu
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Man Hong
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Demin Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China
| | - Kai Wang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo, 315211, China.
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56
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Wang C, Guo G, Huang Y, Hao H, Wang H. Salt Adaptation and Evolutionary Implication of a Nah-related PAHs Dioxygenase cloned from a Halophilic Phenanthrene Degrading Consortium. Sci Rep 2017; 7:12525. [PMID: 28970580 PMCID: PMC5624874 DOI: 10.1038/s41598-017-12979-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 09/14/2017] [Indexed: 12/05/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) pollutions often occur in marine and other saline environment, largely due to anthropogenic activities. However, study of the PAHs-degradation genotypes in halophiles is limited, compared with the mesophilic terrestrial PAHs degraders. In this study, a bacterial consortium (CY-1) was enriched from saline soil contaminated with crude oil using phenanthrene as the sole carbon source at 10% salinity. CY-1 was dominated by the moderate halophilic Marinobacter species, and its dominant PAHs ring-hydroxylating dioxygenase (RHD) genotypes shared high identity to the classic nah-related RHDs found in the mesophilic species. Further cloning of a 5.6-kb gene cluster from CY-1 unveiled the existence of a new type of PAHs degradation gene cluster (hpah), which most probably evolves from the nah-related gene clusters. Expression of the RHD in this gene cluster in E. coli lead to the discovery of its prominent salt-tolerant properties compared with two RHDs from mesophiles. As a common structural feature shared by all halophilic and halotolerant enzymes, higher abundance of acidic amino acids was also found on the surface of this RHD than its closest nah-related alleles. These results suggest evolution towards saline adaptation occurred after horizontal transfer of this hpah gene cluster into the halophiles.
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Affiliation(s)
- Chongyang Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Guang Guo
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,School of Environmental Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Yong Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Han Hao
- 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.
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Williams AK, Bacosa HP, Quigg A. The impact of dissolved inorganic nitrogen and phosphorous on responses of microbial plankton to the Texas City "Y" oil spill in Galveston Bay, Texas (USA). MARINE POLLUTION BULLETIN 2017; 121:32-44. [PMID: 28545863 DOI: 10.1016/j.marpolbul.2017.05.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/26/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Ongoing bioremediation research seeks to promote naturally occurring microbial polycyclic aromatic hydrocarbon (PAH) degradation during and after oil spill events. However, complex relationships among functionally different microbial groups, nutrients and PAHs remain unconstrained. We conducted a surface water survey and corresponding nutrient amendment bioassays following the Texas City "Y" oil spill in Galveston Bay, Texas. Resident microbial groups, defined as either heterotrophic or autotrophic were enumerated by flow cytometry. Heterotrophic abundance was increased by oil regardless of nutrient concentrations. Contrastingly, autotrophic abundance was inhibited by oil, but this reaction was less severe when nutrient concentrations were higher. Several PAH compounds were reduced in nutrient amended treatments relative to controls suggesting nutrient enhanced microbial PAH processing. These findings provide a first-look at nutrient limitation during microbial oil processing in Galveston Bay, an important step in understanding if nutrient additions would be a useful bioremediation strategy in this and other estuarine systems.
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Affiliation(s)
- Alicia K Williams
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; Texas A&M University, Department of Oceanography, 797 Lamar Street, College Station, TX 77840, USA.
| | - Hernando P Bacosa
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; The University of Texas at Austin, Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Antonietta Quigg
- Texas A&M University at Galveston, Department of Marine Biology, 200 Seawolf Parkway, Galveston, TX 77554, USA; Texas A&M University, Department of Oceanography, 797 Lamar Street, College Station, TX 77840, USA
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58
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Segura A, Hernández-Sánchez V, Marqués S, Molina L. Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 590-591:381-393. [PMID: 28285855 DOI: 10.1016/j.scitotenv.2017.02.180] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 05/15/2023]
Abstract
Novosphingobium sp. HR1a is able to grow using diverse polycyclic aromatic hydrocarbons (PAHs) as the sole carbon sources. We have identified two transposons that contain genes encoding several ring-hydroxylating dioxygenases and we have demonstrated the crucial role of one of these dioxygenases in the PAH metabolism in this strain; a mutant in the large subunit of this dioxygenase was unable to growth with 2-, 3-, or 4-rings aromatic hydrocarbons. Using a construction of lacZ gene fused with the pathway promoter, we determined that the expression of the dioxygenase gene was specifically induced in the presence of some PAHs and intermediates of their metabolic pathway. In silico analysis of the ORFs within the transposons and construction of the corresponding knock-out mutants allowed us to identify the main regulatory protein involved in PAH degradation in Novosphingobium sp. HR1a. To our knowledge this is the first time that a regulatory protein controlling the degradation pathway of high-molecular weight PAHs has been investigated. A deeper knowledge of the regulatory circuits that control the expression of PAH degradation has allowed us to design two biosensors for monitoring environments contaminated with oil-derived mixtures. Novosphingobium sp. HR1a (pKSR-1), the biosensor based on the promoter of the regulatory protein PahR, was more sensitive and faster in the detection of aromatic contaminants in environmental samples than Novosphingobium sp. HR1a (pKSA-1), the biosensor that is based on the PAHs-dioxygenase promoter (PpahA). Novosphingobium sp. HR1a (pKSR-1) was able to detect PAHs in the range of μgl-1 (ppb).
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Affiliation(s)
- Ana Segura
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Spain
| | - Verónica Hernández-Sánchez
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Spain
| | - Silvia Marqués
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Spain
| | - Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008, Spain.
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59
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Han X, Hu H, Shi X, Zhang L, He J. Effects of different agricultural wastes on the dissipation of PAHs and the PAH-degrading genes in a PAH-contaminated soil. CHEMOSPHERE 2017; 172:286-293. [PMID: 28086156 DOI: 10.1016/j.chemosphere.2017.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 12/05/2016] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Land application of agricultural wastes is considered as a promising bioremediation approach for cleaning up soils contaminated by aged polycyclic aromatic hydrocarbons (PAHs). However, it remains largely unknown about how microbial PAH-degraders, which play a key role in the biodegradation of soil PAHs, respond to the amendments of agricultural wastes. Here, a 90-day soil microcosm study was conducted to compare the effects of three agricultural wastes (i.e. WS, wheat stalk; MCSW, mushroom cultivation substrate waste; and CM, cow manure) on the dissipation of aged PAHs and the abundance and community structure of PAH-degrading microorganisms. The results showed that all the three agricultural wastes accelerated the dissipation of aged PAHs and significantly increased abundances of the bacterial 16S rRNA and PAH-degrading genes (i.e. pdo1 and nah). CM and MCSW with lower ratios of C:N eliminated soil PAHs more efficiently than WS with a high ratio of C:N. Low molecular weight PAHs were dissipated more quickly than those with high molecular weight. Phylogenetic analysis revealed that all of the nah and C12O clones were affiliated within Betaproteobacteria and Gammaproteobacteria, and application of agricultural wastes significantly changed the community structure of the microorganisms harboring nah and C12O genes, particularly in the CM treatment. Taken together, our findings suggest that the three tested agricultural wastes could accelerate the degradation of aged PAHs most likely through changing the abundances and community structure of microbial PAH degraders.
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Affiliation(s)
- Xuemei Han
- School of Resources and Environment, University of Jinan, Jinan, 250100, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
| | - Xiuzhen Shi
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Limei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Jizheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, 3010, Victoria, Australia.
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60
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Aydin S, Karaçay HA, Shahi A, Gökçe S, Ince B, Ince O. Aerobic and anaerobic fungal metabolism and Omics insights for increasing polycyclic aromatic hydrocarbons biodegradation. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2016.12.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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61
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Obi CC, Adebusoye SA, Amund OO, Ugoji EO, Ilori MO, Hedman CJ, Hickey WJ. Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment. Appl Microbiol Biotechnol 2017; 101:4299-4314. [PMID: 28190100 DOI: 10.1007/s00253-017-8151-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 01/12/2023]
Abstract
Coastal sediments contaminated by polycyclic aromatic hydrocarbons (PAHs) can be candidates for remediation via an approach like land farming. Land farming converts naturally anaerobic sediments to aerobic environments, and the response of microbial communities, in terms of community structure alterations and corresponding effects on biodegradative activities, is unknown. A key goal of this study was to determine if different sediments exhibited common patterns in microbial community responses that might serve as indicators of PAH biodegradation. Sediments from three stations in the Lagos Lagoon (Nigeria) were used in microcosms, which were spiked with a mixture of four PAH, then examined for PAH biodegradation and for shifts in microbial community structure by analysis of diversity in PAH degradation genes and Illumina sequencing of 16S rRNA genes. PAH biodegradation was similar in all sediments, yet each exhibited unique microbiological responses and there were no microbial indicators of PAH bioremediation common to all sediments.
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Affiliation(s)
- Chioma C Obi
- Department of Microbiology, University of Lagos, Lagos, Nigeria.
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA.
| | | | | | - Esther O Ugoji
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | - Mathew O Ilori
- Department of Microbiology, University of Lagos, Lagos, Nigeria
| | | | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department of Soil Science, University of Wisconsin-Madison, Madison, WI, USA
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Biswas B, Sarkar B, Naidu R. Bacterial mineralization of phenanthrene on thermally activated palygorskite: A 14C radiotracer study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 579:709-717. [PMID: 27863871 DOI: 10.1016/j.scitotenv.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/31/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Clay-bacterial interaction can significantly influence the biodegradation of organic contaminants in the environment. A moderate heat treatment of palygorskite could alter the physicochemical properties of the clay mineral and thus support the growth and function of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria. By using 14C-labelled phenanthrene and a model bacterium Burkholderia sartisoli, we studied the mineralization of phenanthrene on the surface of a moderately heat-treated (up to 400°C) palygorskite. The heat treatment at 400°C induced a reduction of binding sites (e.g., by the elimination of organic matter and/or channel shrinkage) in the palygorskite and thus imparted a weaker sequestration of phenanthrene on its surface and within the pores. As a result, a supplement with the thermally modified palygorskite (400°C) significantly increased (20-30%; p<0.05) the biomineralization of total phenanthrene in a simulated soil slurry system. These results are highly promising to develop a clay mineral based technology for the bioremediation of PAH contaminants in water and soil environments.
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Affiliation(s)
- Bhabananda Biswas
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, SA 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, ACT Building, University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Binoy Sarkar
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, SA 5095, Australia.
| | - Ravi Naidu
- Cooperative Research Centre for Contamination Assessment and Remediation of the Environment, ACT Building, University of Newcastle, Callaghan, NSW 2308, Australia; Global Centre for Environmental Remediation (GCER), Faculty of Science and Information Technology, University of Newcastle, Callaghan, NSW 2308, Australia.
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63
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Zhu F, Storey S, Ashaari MM, Clipson N, Doyle E. Benzo(a)pyrene degradation and microbial community responses in composted soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:5404-5414. [PMID: 28025788 DOI: 10.1007/s11356-016-8251-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
Benzo(a)pyrene degradation was compared in soil that was either composted, incubated at a constant temperature of 22 °C, or incubated under a temperature regime typical of a composting process. After 84 days, significantly more (61%) benzo(a)pyrene was removed from composted soil compared to soils incubated at a constant temperature (29%) or at composting temperatures (46%). Molecular fingerprinting approaches indicated that in composted soils, bacterial community changes were driven by both temperature and organic amendment, while fungal community changes were primarily driven by temperature. Next-generation sequencing data revealed that the bacterial community in composted soil was dominated by Actinobacteria (order Actinomycetales), Firmicutes (class Bacilli), and Proteobacteria (classes Gammaproteobacteria and Alphaproteobacteria), regardless of whether benzo(a)pyrene was present or not. The relative abundance of unclassified Actinomycetales (Actinobacteria) was significantly higher in composted soil when degradation was occurring, indicating a potential role for these organisms in benzo(a)pyrene metabolism. This study provides baseline data for employing straw-based composting strategies for the removal of high molecular weight PAHs from soil and contributes to the knowledge of how microbial communities respond to incubation conditions and pollutant degradation.
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Affiliation(s)
- Fengxiao Zhu
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Sean Storey
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Mardiana Mohd Ashaari
- Department of Biotechnology, Kulliyah of Science, International Islamic University Malaysia, Kuantan, Malaysia
| | - Nicholas Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Dublin, Ireland.
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Zhao JK, Li XM, Ai GM, Deng Y, Liu SJ, Jiang CY. Reconstruction of metabolic networks in a fluoranthene-degrading enrichments from polycyclic aromatic hydrocarbon polluted soil. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:90-98. [PMID: 27415596 DOI: 10.1016/j.jhazmat.2016.06.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/26/2016] [Accepted: 06/27/2016] [Indexed: 06/06/2023]
Abstract
Microbial degradation of polycyclic aromatic hydrocarbons (PAHs) is the primary process of removing PAHs from environments. The metabolic pathway of PAHs in pure cultures has been intensively studied, but cooperative metabolisms at community-level remained to be explored. In this study, we determined the dynamic composition of a microbial community and its metabolic intermediates during fluoranthene degradation using high-throughput metagenomics and gas chromatography-mass spectrometry (GC-MS), respectively. Subsequently, a cooperative metabolic network for fluoranthene degradation was constructed. The network shows that Mycobacterium contributed the majority of ring-hydroxylating and -cleavage dioxygenases, while Diaphorobacter contributed most of the dehydrogenases. Hyphomicrobium, Agrobacterium, and Sphingopyxis contributed to genes encoding enzymes involved in downstream reactions of fluoranthene degradation. The contributions of various microbial groups were calculated with the PICRUSt program. The contributions of Hyphomicrobium to alcohol dehydrogenases were 62.4% in stage 1 (i.e., when fluoranthene was rapidly removed) and 76.8% in stage 3 (i.e., when fluoranthene was not detectable), respectively; the contribution of Pseudomonas were 6.6% in stage 1 and decreased to 1.2% in subsequent stages. To the best of the author's knowledge, this report describes the first cooperative metabolic network to predict the contributions of various microbial groups during PAH-degradation at community-level.
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Affiliation(s)
- Jian-Kang Zhao
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ming Li
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Guo-Min Ai
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China
| | - Ye Deng
- Research Center of Ecological and Environmental Science, CAS, Beijing, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources at Institute of Microbiology, CAS, Beijing 100101, China; IMCAS-RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
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65
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Duran R, Cravo-Laureau C. Role of environmental factors and microorganisms in determining the fate of polycyclic aromatic hydrocarbons in the marine environment. FEMS Microbiol Rev 2016; 40:814-830. [PMID: 28201512 PMCID: PMC5091036 DOI: 10.1093/femsre/fuw031] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/28/2015] [Accepted: 07/24/2016] [Indexed: 11/14/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are widespread in marine ecosystems and originate from natural sources and anthropogenic activities. PAHs enter the marine environment in two main ways, corresponding to chronic pollution or acute pollution by oil spills. The global PAH fluxes in marine environments are controlled by the microbial degradation and the biological pump, which plays a role in particle settling and in sequestration through bioaccumulation. Due to their low water solubility and hydrophobic nature, PAHs tightly adhere to sediments leading to accumulation in coastal and deep sediments. Microbial assemblages play an important role in determining the fate of PAHs in water and sediments, supporting the functioning of biogeochemical cycles and the microbial loop. This review summarises the knowledge recently acquired in terms of both chronic and acute PAH pollution. The importance of the microbial ecology in PAH-polluted marine ecosystems is highlighted as well as the importance of gaining further in-depth knowledge of the environmental services provided by microorganisms.
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Affiliation(s)
- Robert Duran
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, MELODY group, Université de Pau et des Pays de l'Adour, Pau Cedex, France
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66
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Kästner M, Nowak KM, Miltner A, Schäffer A. (Multiple) Isotope probing approaches to trace the fate of environmental chemicals and the formation of non-extractable ‘bound’ residues. Curr Opin Biotechnol 2016; 41:73-82. [DOI: 10.1016/j.copbio.2016.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022]
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67
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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68
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Adrion AC, Nakamura J, Shea D, Aitken MD. Screening Nonionic Surfactants for Enhanced Biodegradation of Polycyclic Aromatic Hydrocarbons Remaining in Soil After Conventional Biological Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:3838-45. [PMID: 26919662 PMCID: PMC4973855 DOI: 10.1021/acs.est.5b05243] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A total of five nonionic surfactants (Brij 30, Span 20, Ecosurf EH-3, polyoxyethylene sorbitol hexaoleate, and R-95 rhamnolipid) were evaluated for their ability to enhance PAH desorption and biodegradation in contaminated soil after treatment in an aerobic bioreactor. Surfactant doses corresponded to aqueous-phase concentrations below the critical micelle concentration in the soil-slurry system. The effect of surfactant amendment on soil (geno)toxicity was also evaluated for Brij 30, Span 20, and POESH using the DT40 B-lymphocyte cell line and two of its DNA-repair-deficient mutants. Compared to the results from no-surfactant controls, incubation of the bioreactor-treated soil with all surfactants increased PAH desorption, and all except R-95 substantially increased PAH biodegradation. POESH had the greatest effect, removing 50% of total measured PAHs. Brij 30, Span 20, and POESH were particularly effective at enhancing biodegradation of four- and five-ring PAHs, including five of the seven carcinogenic PAHs, with removals up to 80%. Surfactant amendment also significantly enhanced the removal of alkyl-PAHs. Most treatments significantly increased soil toxicity. Only the no-surfactant control and Brij 30 at the optimum dose significantly decreased soil genotoxicity, as evaluated with either mutant cell line. Overall, these findings have implications for the feasibility of bioremediation to achieve cleanup levels for PAHs in soil.
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Affiliation(s)
- Alden C. Adrion
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431
| | - Jun Nakamura
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431
| | - Damian Shea
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| | - Michael D. Aitken
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7431
- Corresponding author (T: 1-919-966-1024; F: 1-919-966-7911; )
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69
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Promising approaches towards biotransformation of polycyclic aromatic hydrocarbons with Ascomycota fungi. Curr Opin Biotechnol 2016; 38:1-8. [DOI: 10.1016/j.copbio.2015.12.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022]
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70
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Wang X, Koehler SA, Wilking JN, Sinha NN, Cabeen MT, Srinivasan S, Seminara A, Rubinstein S, Sun Q, Brenner MP, Weitz DA. Probing phenotypic growth in expanding Bacillus subtilis biofilms. Appl Microbiol Biotechnol 2016; 100:4607-15. [PMID: 27003268 DOI: 10.1007/s00253-016-7461-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/26/2016] [Accepted: 03/10/2016] [Indexed: 12/19/2022]
Abstract
We develop an optical imaging technique for spatially and temporally tracking biofilm growth and the distribution of the main phenotypes of a Bacillus subtilis strain with a triple-fluorescent reporter for motility, matrix production, and sporulation. We develop a calibration procedure for determining the biofilm thickness from the transmission images, which is based on Beer-Lambert's law and involves cross-sectioning of biofilms. To obtain the phenotype distribution, we assume a linear relationship between the number of cells and their fluorescence and determine the best combination of calibration coefficients that matches the total number of cells for all three phenotypes and with the total number of cells from the transmission images. Based on this analysis, we resolve the composition of the biofilm in terms of motile, matrix-producing, sporulating cells and low-fluorescent materials which includes matrix and cells that are dead or have low fluorescent gene expression. We take advantage of the circular growth to make kymograph plots of all three phenotypes and the dominant phenotype in terms of radial distance and time. To visualize the nonlocal character of biofilm growth, we also make kymographs using the local colonization time. Our technique is suitable for real-time, noninvasive, quantitative studies of the growth and phenotype distribution of biofilms which are either exposed to different conditions such as biocides, nutrient depletion, dehydration, or waste accumulation.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, 100083, China. .,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
| | - Stephan A Koehler
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - James N Wilking
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717-3920, USA
| | - Naveen N Sinha
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Matthew T Cabeen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Siddarth Srinivasan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Agnese Seminara
- CNRS, LPMC UMR 7336, Université Nice Sophia Antipolis, Parc Valrose, 06108, Nice, France
| | - Shmuel Rubinstein
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Qingping Sun
- Department of Mechanical Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA. .,Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
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71
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Kästner M, Miltner A. Application of compost for effective bioremediation of organic contaminants and pollutants in soil. Appl Microbiol Biotechnol 2016; 100:3433-49. [PMID: 26921182 DOI: 10.1007/s00253-016-7378-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 01/27/2023]
Abstract
Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as 'stimulants' of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a 'metabolic memory' within developing and mature compost materials. Compost addition can thus be considered as a 'super-bioaugmentation' with a complex natural mixture of degrading microorganisms, combined with a 'biostimulation' by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.
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Affiliation(s)
- Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Anja Miltner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
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72
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Acosta-González A, Marqués S. Bacterial diversity in oil-polluted marine coastal sediments. Curr Opin Biotechnol 2016; 38:24-32. [PMID: 26773654 DOI: 10.1016/j.copbio.2015.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/27/2022]
Abstract
Marine environments harbour a persistent microbial seed which can be shaped by changes of the environmental conditions such as contamination by petroleum components. Oil spills, together with small but continuous discharges of oil from transportation and recreational activities, are important sources of hydrocarbon pollution within the marine realm. Consequently, prokaryotic communities have become well pre-adapted toward oil pollution, and many microorganisms that are exposed to its presence develop an active degradative response. The natural attenuation of oil pollutants, as has been demonstrated in many sites, is modulated according to the intrinsic environmental properties such as the availability of terminal electron acceptors and elemental nutrients, together with the degree of pollution and the type of hydrocarbon fractions present. Whilst dynamics in the bacterial communities in the aerobic zones of coastal sediments are well characterized and the key players in hydrocarbon biodegradation have been identified, the subtidal ecology of the anaerobic community is still not well understood. However, current data suggest common patterns of response in these ecosystems.
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Affiliation(s)
- Alejandro Acosta-González
- Grupo de Investigación en Bioprospección (GIBP), Facultad de Ingeniería, Universidad de La Sabana, Autopista Norte km 7, Chía, Cundinamarca, Colombia
| | - Silvia Marqués
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Environmental Protection, Profesor Albareda 1, E-18008 Granada, Spain.
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73
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Drevinskas T, Mickienė R, Maruška A, Stankevičius M, Tiso N, Mikašauskaitė J, Ragažinskienė O, Levišauskas D, Bartkuvienė V, Snieškienė V, Stankevičienė A, Polcaro C, Galli E, Donati E, Tekorius T, Kornyšova O, Kaškonienė V. Downscaling the in vitro test of fungal bioremediation of polycyclic aromatic hydrocarbons: methodological approach. Anal Bioanal Chem 2015; 408:1043-53. [DOI: 10.1007/s00216-015-9191-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/08/2015] [Accepted: 11/12/2015] [Indexed: 01/05/2023]
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74
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Tauler M, Vila J, Nieto JM, Grifoll M. Key high molecular weight PAH-degrading bacteria in a soil consortium enriched using a sand-in-liquid microcosm system. Appl Microbiol Biotechnol 2015; 100:3321-36. [DOI: 10.1007/s00253-015-7195-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/19/2015] [Accepted: 11/22/2015] [Indexed: 12/31/2022]
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75
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Messina E, Denaro R, Crisafi F, Smedile F, Cappello S, Genovese M, Genovese L, Giuliano L, Russo D, Ferrer M, Golyshin P, Yakimov MM. Genome sequence of obligate marine polycyclic aromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME, isolated from petroleum deposits of the sunken tanker Amoco Milford Haven, Mediterranean Sea. Mar Genomics 2015; 25:11-13. [PMID: 26508673 DOI: 10.1016/j.margen.2015.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/11/2015] [Accepted: 10/21/2015] [Indexed: 01/11/2023]
Abstract
Cycloclasticus sp. 78-ME isolated from petroleum deposits of the sunken tanker “Amoco Milford Haven” (Gulf of Genoa, Ligurian Sea, Italy) could effectively degrade polycyclic aromatic hydrocarbons of up to five condensed rings. The genome of 78-ME was sequenced and analysed to gain insights into its remarkable degrading capacities. It comprises two circular replicons, the 2,613,078 bp chromosome and the plasmid of 42,347 bp, with 41.84% and 53.28% of the G + C content respectively. A total of 2585 protein-coding genes were obtained, and three large operons with more than fifteen enzymes belonging to four different classes of ring-cleavage dioxygenases were found.
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Affiliation(s)
- Enzo Messina
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | | | | | - Simone Cappello
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | - Maria Genovese
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | | | - Laura Giuliano
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | - Daniela Russo
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | | | - Peter Golyshin
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 UW, Gwynedd, United Kingdom
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy.
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76
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Degradation of 13C-labeled pyrene in soil-compost mixtures and fertilized soil. Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6822-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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