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Moratti CF, Yang SNN, Scott C, Coleman NV. Development of a whole-cell biosensor for ethylene oxide and ethylene. Microb Biotechnol 2024; 17:e14511. [PMID: 38925606 PMCID: PMC11197473 DOI: 10.1111/1751-7915.14511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Ethylene and ethylene oxide are widely used in the chemical industry, and ethylene is also important for its role in fruit ripening. Better sensing systems would assist risk management of these chemicals. Here, we characterise the ethylene regulatory system in Mycobacterium strain NBB4 and use these genetic parts to create a biosensor. The regulatory genes etnR1 and etnR2 and cognate promoter Petn were combined with a fluorescent reporter gene (fuGFP) in a Mycobacterium shuttle vector to create plasmid pUS301-EtnR12P. Cultures of M. smegmatis mc2-155(pUS301-EtnR12P) gave a fluorescent signal in response to ethylene oxide with a detection limit of 0.2 μM (9 ppb). By combining the epoxide biosensor cells with another culture expressing the ethylene monooxygenase, the system was converted into an ethylene biosensor. The co-culture was capable of detecting ethylene emission from banana fruit. These are the first examples of whole-cell biosensors for epoxides or aliphatic alkenes. This work also resolves long-standing questions concerning the regulation of ethylene catabolism in bacteria.
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Affiliation(s)
- Claudia F. Moratti
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Sui Nin Nicholas Yang
- School of Life and Environmental SciencesUniversity of SydneyCamperdownNew South WalesAustralia
| | - Colin Scott
- CSIRO Advanced Engineering Biology Future Science Platform, Black Mountain Research & Innovation ParkCanberraAustralian Capital TerritoryAustralia
| | - Nicholas V. Coleman
- School of Natural Sciences and ARC Centre of Excellence in Synthetic BiologyMacquarie UniversityNorth RydeNew South WalesAustralia
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Lu M, Sha Y, Kumar V, Xu Z, Zhai R, Jin M. Transcription factor-based biosensor: A molecular-guided approach for advanced biofuel synthesis. Biotechnol Adv 2024; 72:108339. [PMID: 38508427 DOI: 10.1016/j.biotechadv.2024.108339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental protection. Traditional engineering of cell factories for production of advanced biofuels lacks efficient high-throughput screening tools and regulating systems, impeding the improvement of cellular productivity and yield. Transcription factor-based biosensors have been widely applied to monitor and regulate microbial cell factory products due to the advantages of fast detection and in-situ screening. This review updates the design and application of transcription factor-based biosensors tailored for advanced biofuels and related intermediates. The construction and genetic parts selection principle of biosensors are discussed. Strategies to enhance the performance of biosensor, including regulating promoter strength and RBS strength, optimizing plasmid copy number, implementing genetic amplifier, and modulating the structure of transcription factor, have also been summarized. We further review the application of biosensors in high-throughput screening of new metabolic engineering targets, evolution engineering, confirmation of protein function, and dynamic regulation of metabolic flux for higher production of advanced biofuels. At last, we discuss the current limitations and future trends of transcription factor-based biosensors.
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Affiliation(s)
- Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuanyuan Sha
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, United Kingdom
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China.
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Kim HS, Suh MK, Kim JS, Do HE, Eom MK, Jin JS, Lee JS. Pseudomonas aestuarii sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 38047902 DOI: 10.1099/ijsem.0.006190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Two novel Pseudomonas strains, SA3-5T and SA3-6, were isolated from a tidal flat (getbol) in the Republic of Korea. Strains SA3-5T and SA3-6 were subjected to polyphasic characterization to determine their taxonomic affiliations. Cells were Gram-stain-negative, aerobic, rod-shaped and motile by using peritrichous flagella. Based on their 16S rRNA gene sequences, strains SA3-5T and SA3-6 exhibited a high degree of similarity (100 %) and were classified within the genus Pseudomonas. Furthermore, the closest related species to SA3-5T and SA3-6 were Pseudomonas taeanensis MS-3T (98.3 %). The ranges of average nucleotide identity and digital DNA-DNA hybridization values between SA3-5T and closely related species were 75.9-89.1% and 21.3-38.7%, respectively, both of which being below the thresholds for delineating novel strains. Strain SA3-5T and SA3-6 contained C16 : 1 ω6с and/or C16 : 1 ω7с (summed feature 3), C16 : 0 and C18 : 1 ω6с and/or C18 : 1 ω7с (summed feature 8) as the major fatty acids. The predominant respiratory quinone was Q-9. The DNA G+C content of strain SA3-5T was 62.5 mol%. Based on their combined phenotypic, chemotaxonomic and phylogenetic characterisitics, strains SA3-5T and SA3-6 represent a novel species of the genus Pseudomonas for which the name Pseudomonas aestuarii sp. nov. is proposed. The type strain is SA3-5T (=KCTC 92395T=JCM 35697T).
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Affiliation(s)
- Han Sol Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Min Kuk Suh
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Lifestyle Medicine, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do 54596, Republic of Korea
| | - Ji-Sun Kim
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Hyo Eun Do
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Mi Kyung Eom
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
| | - Jong-Sik Jin
- Department of Oriental Medicine Resources, Jeonbuk National University, 79 Gobong-ro, Iksan-si54596,Jeollabuk-do, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type CulturesKorea Research Institute of Bioscience and Biotechnology(KRIBB), Jeongeup-si, 181 Ipsin-gil, Jeollabuk-do 56212, Republic of Korea
- University of Science and Technology(UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Wang S, Yun Y, Tian X, Su Z, Liao Z, Li G, Ma T. HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132397. [PMID: 37639797 DOI: 10.1016/j.jhazmat.2023.132397] [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: 02/27/2023] [Revised: 08/10/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023]
Abstract
The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming. We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of homologous enzymes which took non-hydrocarbons as substrates to HMDB. The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data. HMDB is freely available at http://www.orgene.net/HMDB/.
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Affiliation(s)
- Shaojing Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuan Yun
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xuefeng Tian
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhaoying Su
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zitong Liao
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guoqiang Li
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin 300071, China.
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Ejenavi O, Teng T, Huang W, Wang X, Zhang W, Zhang D. Online detection of alkanes by a biological-phase microextraction and biosensing (BPME-BS) device. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131316. [PMID: 37003003 DOI: 10.1016/j.jhazmat.2023.131316] [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: 02/03/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 05/03/2023]
Abstract
Oil spill incidents occur frequently and threaten ecosystems and human health. Solid-phase microextraction allows direct alkane extraction from environmental matrices to improve the limit of detection but is unable to measure alkanes on site. A biological-phase microextraction and biosensing (BPME-BS) device was developed by immobilising an alkane chemotactic Acinetobacter bioreporter ADPWH_alk in agarose gel to achieve online alkane quantification with the aid of a photomultiplier. The BPME-BS device had a high enrichment factor (average 7.07) and a satisfactory limit of detection (0.075 mg/L) for alkanes. The quantification range was 0.1-100 mg/L, comparable to a gas chromatography flame ionisation detector and better than a bioreporter without immobilisation. ADPWH_alk cells in the BPME-BS device maintained good sensitivity under a wide range of environmental conditions, including pH (4.0-9.0), temperature (20-40 °C), and salinity (0.0-3.0%), and its response remained stable within 30 days at 4 °C. In a 7-day continual measurement, the BPME-BS device successfully visualised the dynamic concentration of alkanes, and a 7-day field test successfully captured an oil spill event, helping in source apportionment and on-scene law enforcement. Our work proved that the BPME-BS device is a powerful tool for online alkane measurement, showing substantial potential for fast detection and rapid response to oil spills on site and in situ.
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Affiliation(s)
- Odafe Ejenavi
- Lancaster Environment Centre, Lancaster University, LA1 4YQ, UK
| | - Tingting Teng
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Wenxin Huang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Xinzi Wang
- School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Wenjing Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, PR China; College of New Energy and Environment, Jilin University, Changchun 130012, PR China.
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Fenibo EO, Selvarajan R, Abia ALK, Matambo T. Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162951. [PMID: 36948313 DOI: 10.1016/j.scitotenv.2023.162951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 05/06/2023]
Abstract
Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C8-C16 medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Akebe Luther King Abia
- Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa; Environmental Research Foundation, Westville 3630, South Africa
| | - Tonderayi Matambo
- Institute for the Development of Energy for African Sustainability, University of South Africa, Roodepoort 1709, South Africa.
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Schultes FPJ, Haarmann M, Tischler D, Mügge C. Primary alcohols as substrates or products in whole-cell biocatalysis: Toxicity for Escherichia coli expression strains. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Pseudomonas veronii strain 7-41 degrading medium-chain n-alkanes and polycyclic aromatic hydrocarbons. Sci Rep 2022; 12:20527. [PMID: 36443410 PMCID: PMC9705281 DOI: 10.1038/s41598-022-25191-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Pollution of the environment by crude oil and oil products (represented by various types of compounds, mainly aliphatic, mono- and polyaromatic hydrocarbons) poses a global problem. The strain Pseudomonas veronii 7-41 can grow on medium-chain n-alkanes (C8-C12) and polycyclic aromatic hydrocarbons such as naphthalene. We performed a genetic analysis and physiological/biochemical characterization of strain 7-41 cultivated in a mineral medium with decane, naphthalene or a mixture of the hydrocarbons. The genes responsible for the degradation of alkanes and PAHs are on the IncP-7 conjugative plasmid and are organized into the alk and nah operons typical of pseudomonads. A natural plasmid carrying functional operons for the degradation of two different classes of hydrocarbons was first described. In monosubstrate systems, 28.4% and 68.8% of decane and naphthalene, respectively, were biodegraded by the late stationary growth phase. In a bisubstrate system, these parameters were 25.4% and 20.8% by the end of the exponential growth phase. Then the biodegradation stopped, and the bacterial culture started dying due to the accumulation of salicylate (naphthalene-degradation metabolite), which is toxic in high concentrations. The activity of the salicylate oxidation enzymes was below the detection limit. These results indicate that the presence of decane and a high concentration of salicylate lead to impairment of hydrocarbon degradation by the strain.
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de Oliveira HL, Dias GM, Neves BC. Genome sequence of Pseudomonas aeruginosa PA1-Petro—A role model of environmental adaptation and a potential biotechnological tool. Heliyon 2022; 8:e11566. [DOI: 10.1016/j.heliyon.2022.e11566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/12/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
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Wang S, Li G, Liao Z, Liu T, Ma T. A novel alkane monooxygenase ( alkB) clade revealed by massive genomic survey and its dissemination association with IS elements. PeerJ 2022; 10:e14147. [PMID: 36193440 PMCID: PMC9526415 DOI: 10.7717/peerj.14147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
Background Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids. Methods To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters. Results A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters. Conclusions We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.
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Affiliation(s)
- Shaojing Wang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guoqiang Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Zitong Liao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Tongtong Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Ting Ma
- College of Life Sciences, Nankai University, Tianjin, China
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Bacterial Isolates from Greek Sites and Their Efficacy in Degrading Petroleum. SUSTAINABILITY 2022. [DOI: 10.3390/su14159562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a major organic pollutant, not only because they do not self-degenerate but also because they accumulate in the food chain and give rise to serious repercussions in terms of biodiversity sustainability. Petroleum-degrading bacteria have long been used as a promising solution in the effort to biodegrade crude oil. In this study, new isolates from specific Greek environments displaying various levels of crude oil contamination, as well as isolates belonging to the ATHUBA collection, were thoroughly investigated for their capacity to degrade crude oil. Furthermore, the presence of nahH and alkJ genes in the above bacterial isolates, as well as their ability to form agglomerates or release surfactants, was investigated. Two consortia were formed, and their ability to degrade crude oil was tested, achieving similar degrading capacities as those observed with the individual strains. A Pseudomonas plecoglossicida isolate demonstrated the highest percentage (76.7%) ability to degrade crude oil. The biodegradation rate of this isolate was further evaluated by measuring the alkanes/hopanes ratio over a period of ten days, exhibiting a higher degradation rate in short-chain (C11–C21) alkanes, whereas a decrease in the ratio was observed when the number of carbons in petroleum increased. This is the first detailed report on bacterial communities in oil-polluted areas of Greece that contain a variety of bacteria with the ability to degrade PAHs in contaminated sites and may provide a novel alternative to various bioremediation processes or be used as inocula in autochthonous bioaugmentation procedures for crude oil biodegradation.
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Góngora E, Chen YJ, Ellis M, Okshevsky M, Whyte L. Hydrocarbon bioremediation on Arctic shorelines: Historic perspective and roadway to the future. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119247. [PMID: 35390417 DOI: 10.1016/j.envpol.2022.119247] [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] [Received: 11/12/2021] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Climate change has become one of the greatest concerns of the past few decades. In particular, global warming is a growing threat to the Canadian high Arctic and other polar regions. By the middle of this century, an increase in the annual mean temperature of 1.8 °C-2.7 °C for the Canadian North is predicted. Rising temperatures lead to a significant decrease of the sea ice area covered in the Northwest Passage. As a consequence, a surge of maritime activity in that region increases the risk of hydrocarbon pollution due to accidental fuel spills. In this review, we focus on bioremediation approaches on Arctic shorelines. We summarize historical experimental spill studies conducted at Svalbard, Baffin Island, and the Kerguelen Archipelago, and review contemporary studies that used modern omics techniques in various environments. We discuss how omics approaches can facilitate our understanding of Arctic shoreline bioremediation and identify promising research areas that should be further explored. We conclude that specific environmental conditions strongly alter bioremediation outcomes in Arctic environments and future studies must therefore focus on correlating these diverse parameters with the efficacy of hydrocarbon biodegradation.
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Affiliation(s)
- Esteban Góngora
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Madison Ellis
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Mira Okshevsky
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
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Nikel PI, Benedetti I, Wirth NT, de Lorenzo V, Calles B. Standardization of regulatory nodes for engineering heterologous gene expression: a feasibility study. Microb Biotechnol 2022; 15:2250-2265. [PMID: 35478326 PMCID: PMC9328736 DOI: 10.1111/1751-7915.14063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 12/21/2022] Open
Abstract
The potential of LacI/Ptrc, XylS/Pm, AlkS/PalkB, CprK/PDB3 and ChnR/PchnB regulatory nodes, recruited from both Gram‐negative and Gram‐positive bacteria, as the source of parts for formatting expression cargoes following the Standard European Vector Architecture (SEVA) has been examined. The five expression devices, which cover most known regulatory configurations in bacteria were assembled within exactly the same plasmid backbone and bearing the different functional segments arrayed in an invariable DNA scaffold. Their performance was then analysed in an Escherichia coli strain of reference through the readout of a fluorescence reporter gene that contained strictly identical translation signal elements. This approach allowed us to describe and compare the cognate expression systems with quantitative detail. The constructs under scrutiny diverged considerably in their capacity, expression noise, inducibility and ON/OFF ratios. Inspection of such a variance exposed the different constraints that rule the optimal arrangement of functional DNA segments in each case. The data highlighted also the ease of standardizing inducer‐responsive devices subject to transcriptional activation as compared to counterparts based on repressors. The study resulted in a defined collection of formatted expression cargoes lacking any cross talk while offering a panoply of choices to potential users and help interoperability of the specific constructs.
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Affiliation(s)
- Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Ilaria Benedetti
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, 2800, Denmark
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Belén Calles
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
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Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence. Appl Microbiol Biotechnol 2022; 106:3153-3171. [PMID: 35396956 DOI: 10.1007/s00253-022-11906-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/29/2022] [Indexed: 11/02/2022]
Abstract
The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.
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15
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Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas. Folia Microbiol (Praha) 2022; 67:591-604. [PMID: 35318574 DOI: 10.1007/s12223-022-00966-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/15/2022] [Indexed: 11/04/2022]
Abstract
One of the most frequently used methods for elimination of oil pollution is the use of biological preparations based on oil-degrading microorganisms. Such microorganisms often relate to bacteria of the genus Pseudomonas. Pseudomonads are ubiquitous microorganisms that often have the ability to oxidize various pollutants, including oil hydrocarbons. To date, individual biochemical pathways of hydrocarbon degradation and the organization of the corresponding genes have been studied in detail. Almost all studies of this kind have been performed on degraders of individual hydrocarbons belonging to a single particular class. Microorganisms capable of simultaneous degradation of aliphatic and aromatic hydrocarbons are very poorly studied. Most of the works on such objects have been devoted only to phenotype characteristic and some to genetic studies. To identify the patterns of interaction of several metabolic systems depending on the growth conditions, the most promising are such approaches as transcriptomics and proteomics, which make it possible to obtain a comprehensive assessment of changes in the expression of hundreds of genes and proteins at the same time. This review summarizes the existing data on bacteria of the genus Pseudomonas capable of the simultaneous oxidation of hydrocarbons of different classes (alkanes, monoaromatics, and polyaromatics) and presents the most important results obtained in the studies on the biodegradation of hydrocarbons by representatives of this genus using methods of transcriptomic and proteomic analyses.
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16
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Williams SC, Luongo D, Orman M, Vizcarra CL, Austin RN. An alkane monooxygenase (AlkB) family in which all electron transfer partners are covalently bound to the oxygen-activating hydroxylase. J Inorg Biochem 2022; 228:111707. [PMID: 34990970 PMCID: PMC8799515 DOI: 10.1016/j.jinorgbio.2021.111707] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/13/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
Abstract
Alkane monooxygenase (AlkB) is a non-heme diiron enzyme that catalyzes the hydroxylation of alkanes. It is commonly found in alkanotrophic organisms that can live on alkanes as their sole source of carbon and energy. Activation of AlkB occurs via two-electron reduction of its diferric active site, which facilitates the binding, activation, and cleavage of molecular oxygen for insertion into an inert CH bond. Electrons are typically supplied by NADH via a rubredoxin reductase (AlkT) to a rubredoxin (AlkG) to AlkB, although alternative electron transfer partners have been observed. Here we report a family of AlkBs in which both electron transfer partners (a ferredoxin and a ferredoxin reductase) appear as an N-terminal gene fusion to the hydroxylase (ferr_ferrR_AlkB). This enzyme catalyzes the hydroxylation of medium chain alkanes (C6-C14), with a preference for C10-C12. It requires only NADH for activity. It is present in a number of bacteria that are known to be human pathogens. A survey of the genome neighborhoods in which is it found suggest it may be involved in alkane metabolism, perhaps facilitating growth of pathogens in non-host environments.
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Williams SC, Austin RN. An Overview of the Electron-Transfer Proteins That Activate Alkane Monooxygenase (AlkB). Front Microbiol 2022; 13:845551. [PMID: 35295299 PMCID: PMC8918992 DOI: 10.3389/fmicb.2022.845551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Alkane-oxidizing enzymes play an important role in the global carbon cycle. Alkane monooxygenase (AlkB) oxidizes most of the medium-chain length alkanes in the environment. The first AlkB identified was from P. putida GPo1 (initially known as P. oleovorans) in the early 1970s, and it continues to be the family member about which the most is known. This AlkB is found as part of the OCT operon, in which all of the key proteins required for growth on alkanes are present. The AlkB catalytic cycle requires that the diiron active site be reduced. In P. putida GPo1, electrons originate from NADH and arrive at AlkB via the intermediacy of a flavin reductase and an iron–sulfur protein (a rubredoxin). In this Mini Review, we will review what is known about the canonical arrangement of electron-transfer proteins that activate AlkB and, more importantly, point to several other arrangements that are possible. These other arrangements include the presence of a simpler rubredoxin than what is found in the canonical arrangement, as well as two other classes of AlkBs with fused electron-transfer partners. In one class, a rubredoxin is fused to the hydroxylase and in another less well-explored class, a ferredoxin reductase and a ferredoxin are fused to the hydroxylase. We review what is known about the biochemistry of these electron-transfer proteins, speculate on the biological significance of this diversity, and point to key questions for future research.
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Affiliation(s)
| | - Rachel Narehood Austin
- Department of Chemistry, Barnard College, Columbia University, New York City, NY, United States
- *Correspondence: Rachel Narehood Austin,
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18
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Moratti CF, Scott C, Coleman NV. Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review. Front Bioeng Biotechnol 2022; 9:804234. [PMID: 35083206 PMCID: PMC8784404 DOI: 10.3389/fbioe.2021.804234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.
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Affiliation(s)
- Claudia F. Moratti
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
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19
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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20
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Calm and Frenzy: marine obligate hydrocarbonoclastic bacteria sustain ocean wellness. Curr Opin Biotechnol 2021; 73:337-345. [PMID: 34768202 DOI: 10.1016/j.copbio.2021.09.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/03/2022]
Abstract
According to current estimates, the annual volume of crude oil entering the ocean due to both anthropogenic activities and naturally occurring seepages reaches approximately 8.3 million metric tons. Huge discharges from accidents have caused large-scale environmental disasters with extensive damage to the marine ecosystem. The natural clean-up of petroleum spills in marine environments is carried out primarily by naturally occurring obligate hydrocarbonoclastic bacteria (OHCB). The natural hosts of OHCB include a range of marine primary producers, unicellular photosynthetic eukaryotes and cyanobacteria, which have been documented as both, suppliers of hydrocarbon-like compounds that fuel the 'cryptic' hydrocarbon cycle and as a source of isolation of new OHCB. A very new body of evidence suggests that OHCB are not only the active early stage colonizers of plastics and hence the important component of the ocean's 'plastisphere' but also encode an array of enzymes experimentally proven to act on petrochemical and bio-based polymers.
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21
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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22
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Pal S, Dutta A, Sarkar J, Roy A, Sar P, Kazy SK. Exploring the diversity and hydrocarbon bioremediation potential of microbial community in the waste sludge of Duliajan oil field, Assam, India. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:50074-50093. [PMID: 33945094 DOI: 10.1007/s11356-021-13744-6] [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: 07/05/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Microbial community analysis of crude oil containing sludge collected from Duliajan oil field, Assam, India, showed the predominance of hydrocarbon-degrading bacteria such as Pseudomonas (20.1%), Pseudoxanthomonas (15.8%), Brevundimonas (1.6%), and Bacillus (0.8%) alongwith anaerobic, fermentative, nitrogen-fixing, nitrate-, sulfate-, and metal-reducing, syntrophic bacteria, and methanogenic archaea. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis indicated gene collection for potential hydrocarbon degradation, lipid, nitrogen, sulfur, and methane metabolism. The culturable microbial community was predominated by Pseudomonas and Bacillus with the metabolic potential for utilizing diverse hydrocarbons, crude oil, and actual petroleum sludge as sole carbon source during growth and tolerating various environmental stresses prevailing in such contaminated sites. More than 90% of the isolated strains could produce biosurfactant and exhibit catechol 2,3-dioxygenase activity. Nearly 30% of the isolates showed alkane hydroxylase activity with the maximum specific activity of 0.54 μmol min-1 mg-1. The study provided better insights into the microbial diversity and functional potential within the crude oil containing sludge which could be exploited for in situ bioremediation of contaminated sites.
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Affiliation(s)
- Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
- School of Bio Science, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713209, India.
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23
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Eze MO, Hose GC, George SC, Daniel R. Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany. AMB Express 2021; 11:89. [PMID: 34125309 PMCID: PMC8203775 DOI: 10.1186/s13568-021-01250-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 01/21/2023] Open
Abstract
The pollution of terrestrial and aquatic environments by petroleum contaminants, especially diesel fuel, is a persistent environmental threat requiring cost-effective and environmentally sensitive remediation approaches. Bioremediation is one such approach, but is dependent on the availability of microorganisms with the necessary metabolic abilities and environmental adaptability. The aim of this study was to examine the microbial community in a petroleum contaminated site, and isolate organisms potentially able to degrade hydrocarbons. Through successive enrichment of soil microorganisms from samples of an historic petroleum contaminated site in Wietze, Germany, we isolated a bacterial consortium using diesel fuel hydrocarbons as sole carbon and energy source. The 16S rRNA gene analysis revealed the dominance of Alphaproteobacteria. We further reconstructed a total of 18 genomes from both the original soil sample and the isolated consortium. The analysis of both the metagenome of the consortium and the reconstructed metagenome-assembled genomes show that the most abundant bacterial genus in the consortium, Acidocella, possess many of the genes required for the degradation of diesel fuel aromatic hydrocarbons, which are often the most toxic component. This can explain why this genus proliferated in all the enrichment cultures. Therefore, this study reveals that the microbial consortium isolated in this study and its dominant genus, Acidocella, could potentially serve as an effective inoculum for the bioremediation of sites polluted with diesel fuel or other organic contaminants.
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Affiliation(s)
- Michael O Eze
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University of Göttingen, 37077, Göttingen, Germany.
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Grant C Hose
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Simon C George
- Department of Earth and Environmental Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University of Göttingen, 37077, Göttingen, Germany
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24
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Ibrahim S, Gupta RK, War AR, Hussain B, Kumar A, Sofi T, Noureldeen A, Darwish H. Degradation of chlorpyriphos and polyethylene by endosymbiotic bacteria from citrus mealybug. Saudi J Biol Sci 2021; 28:3214-3224. [PMID: 34121858 PMCID: PMC8176133 DOI: 10.1016/j.sjbs.2021.03.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/14/2021] [Accepted: 03/22/2021] [Indexed: 11/22/2022] Open
Abstract
Chlorpyriphos is one of the major organophosphorus pesticides used widely to control a range of insect pests across several crops. This insecticide is hazardous to the environment and toxic to mammals, thus, it is essential to remove the same from the environment. Similarly, use of polythene is also increasing day by day. Therefore, it is highly important to identify ways to degrade chlorpyriphos and other pesticides from the environment. We studied the degradation of chlorpyriphos and polyethylene by Citrus mealybug (Planococcus citri) bacterial endosymbionts such as Bacillus licheniformis, Pseudomonas cereus, Pseudomonas putida and Bacillus subtilis. This investigation revealed that bacterial endosymbionts use the polythene as a source of carbon and solubilize them by their enzymatic machinery. The degradation of polyethylene by endosymbionts showed a significant reduction in weight of polyethylene sheet after 15, 30 and 45 days of treatment. The SEM images showed localized degradation of the polyethylene around the bacterial cells in the biofilm. Further, the tensile strength (percentage elongation) was significantly reduced after 45 days of incubation. The weight of paraffin wax showed significant reduction in B. cereus. A significant reduction in total amount of chlorpyriphos in soil was observed at an interval of 7, 14 and 21 days after treatment by the bacterial isolates. Among the bacteria, B. cereus and P. putida were found to be most effective. The results from this study show that endosymbionts can be significantly implicated in degrading chlorpyriphos and polyethylene from the environment.
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Affiliation(s)
- Shahida Ibrahim
- Division of Entomology, SKUAST-J, Chatta-180009, Jammu, Jammu and Kashmir, India
| | - Rakesh Kumar Gupta
- Division of Entomology, SKUAST-J, Chatta-180009, Jammu, Jammu and Kashmir, India
| | - Abdul Rasheed War
- World Vegetable Center, ICRISAT Campus, Patancheru-502324, Hyderabad, Telangana, India
| | - Barkat Hussain
- Division of Entomology, SKUAST-K, Shalimar Campus-190025, Srinagar, Jammu and Kashmir, India
| | - Amit Kumar
- Instrumentation Division, Indian Institute of Integrative Medicine, Canal Road-180001, Jammu, Jammu and Kashmir, India
| | - Tariq Sofi
- Division of Plant Pathology, SKUAST-K, Shalimar-190025, Srinagar, Jammu and Kashmir, India
| | - Ahmad Noureldeen
- Department of Biology, College of Sciences, Taif University, P.O. Box 21944, Saudi Arabia
| | - Hadeer Darwish
- Department of Biotechnology, College of Sciences, Taif University, Taif 21944, Saudi Arabia
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25
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Bretschneider L, Wegner M, Bühler K, Bühler B, Karande R. One-pot synthesis of 6-aminohexanoic acid from cyclohexane using mixed-species cultures. Microb Biotechnol 2021; 14:1011-1025. [PMID: 33369139 PMCID: PMC8085927 DOI: 10.1111/1751-7915.13744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
6-Aminohexanoic acid (6AHA) is a vital polymer building block for Nylon 6 production and an FDA-approved orphan drug. However, its production from cyclohexane is associated with several challenges, including low conversion and yield, and severe environmental issues. We aimed at overcoming these challenges by developing a bioprocess for 6AHA synthesis. A mixed-species approach turned out to be most promising. Thereby, Pseudomonas taiwanensis VLB120 strains harbouring an upstream cascade converting cyclohexane to either є-caprolactone (є-CL) or 6-hydroxyhexanoic acid (6HA) were combined with Escherichia coli JM101 strains containing the corresponding downstream cascade for the further conversion to 6AHA. ε-CL was found to be a better 'shuttle molecule' than 6HA enabling higher 6AHA formation rates and yields. Mixed-species reaction performance with 4 g l-1 biomass, 10 mM cyclohexane, and an air-to-aqueous phase ratio of 23 combined with a repetitive oxygen feeding strategy led to complete substrate conversion with 86% 6AHA yield and an initial specific 6AHA formation rate of 7.7 ± 0.1 U gCDW -1 . The same cascade enabled 49% 7-aminoheptanoic acid yield from cycloheptane. This combination of rationally engineered strains allowed direct 6AHA production from cyclohexane in one pot with high conversion and yield under environmentally benign conditions.
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Affiliation(s)
- Lisa Bretschneider
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Martin Wegner
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Katja Bühler
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Bruno Bühler
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
| | - Rohan Karande
- Department of Solar MaterialsHelmholtz‐Centre for Environmental Research –UFZPermoserstrasse 15Leipzig04318Germany
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26
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Liu J, Zhao B, Lan Y, Ma T. Enhanced degradation of different crude oils by defined engineered consortia of Acinetobacter venetianus RAG-1 mutants based on their alkane metabolism. BIORESOURCE TECHNOLOGY 2021; 327:124787. [PMID: 33556770 DOI: 10.1016/j.biortech.2021.124787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial consortia offer an attractive biodegradation strategy for removing hydrocarbons from oil-contaminated sites. In this study, we explored the degradation properties of Acinetobacter venetianus strain RAG-1 (RAG-1). RAG-1 effectively degrades three crude oils with excellent emulsification activity and cell surface hydrophobicity, while exhibiting broad environmental tolerance. RAG-1 accepts a range of alkane substrates (C10-C38) using three alkane hydroxylases (AlkMa, AlkMb, and AlmA). Bacterial mutant with alkMa or alkMb deletion enhanced degradation of C10-C20 or C22-C32 n-alkanes, respectively. Based on the substrate metabolism of the mutants, adjustable and targeted consortia consisting of ΔalkMa/almA and ΔalkMb were constructed, achieving enhanced degradation (10 days) of light crude oil (73.42% to 88.65%), viscous crude oil (68.40% to 90.05%), and high waxy crude oil (47.46% to 60.52%) compared with the single wild-type strain. The degradation properties of RAG-1 and the engineered consortia strategy may have potential use in microbial biodegradation applications.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Bo Zhao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yazheng Lan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China; Tianjin Engineering Technology Center of Green Manufacturing Biobased Materials, Tianjin 300071, China.
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Furlan JPR, Lopes R, Stehling EG. Whole-genome sequence-based analysis of the Paenibacillus aquistagni strain DK1, a polyethylene-degrading bacterium isolated from landfill. World J Microbiol Biotechnol 2021; 37:80. [PMID: 33839943 DOI: 10.1007/s11274-021-03045-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 03/29/2021] [Indexed: 11/25/2022]
Abstract
Polyethylene-degrading bacteria have been emerging as a rational and safe alternative in bioremediation strategies. In this context, some Paenibacillus species produce enzymes involved in the biodegradation of pollutants. Among the enzymes involved in the biodegradation of polyethylene, the alkane hydroxylases, encoded by alkB homologous genes, play a key role in this process. Therefore, this study aimed to identify and perform a genomic investigation of the first polyethylene-degrading Paenibacillus sp. strain, named DK1. The whole-genome sequence-based analysis revealed that the DK1 strain belonged to the species Paenibacillus aquistagni and shared a total of 4327 CDSs with P. aquistagni strain 11. On the other hand, a comparison of the gene clusters showed that DK1 strain harbored a genetic context surrounding the alkB-like gene similar to that found in Pseudomonas sp. strains. The percentage of similarity ranged from 47.88 to 99.76% among all complete amino acid sequences of AlkB-like proteins analyzed. Nevertheless, the predicted amino acid sequences of AlkB-like contained typical structural motifs of alkane hydroxylases, such as His boxes and the HYG motif. These findings associated with the previously reported phenotypic results highlighted the potential of P. aquistagni strain DK1 to biodegrade polyethylene. Therefore, further studies focusing on the biochemical and structural properties of the AlkB-like protein from Paenibacillus may also contribute to the development of sustainable bioremediation strategies.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Ralf Lopes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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28
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Soares-Castro P, Soares F, Santos PM. Current Advances in the Bacterial Toolbox for the Biotechnological Production of Monoterpene-Based Aroma Compounds. Molecules 2020; 26:molecules26010091. [PMID: 33379215 PMCID: PMC7794910 DOI: 10.3390/molecules26010091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
Monoterpenes are plant secondary metabolites, widely used in industrial processes as precursors of important aroma compounds, such as vanillin and (-)-menthol. However, the physicochemical properties of monoterpenes make difficult their conventional conversion into value-added aromas. Biocatalysis, either by using whole cells or enzymes, may overcome such drawbacks in terms of purity of the final product, ecological and economic constraints of the current catalysis processes or extraction from plant material. In particular, the ability of oxidative enzymes (e.g., oxygenases) to modify the monoterpene backbone, with high regio- and stereo-selectivity, is attractive for the production of "natural" aromas for the flavor and fragrances industries. We review the research efforts carried out in the molecular analysis of bacterial monoterpene catabolic pathways and biochemical characterization of the respective key oxidative enzymes, with particular focus on the most relevant precursors, β-pinene, limonene and β-myrcene. The presented overview of the current state of art demonstrates that the specialized enzymatic repertoires of monoterpene-catabolizing bacteria are expanding the toolbox towards the tailored and sustainable biotechnological production of values-added aroma compounds (e.g., isonovalal, α-terpineol, and carvone isomers) whose implementation must be supported by the current advances in systems biology and metabolic engineering approaches.
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29
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Li H, Zhang D, Luo J, Jones KC, Martin FL. Applying Raman Microspectroscopy to Evaluate the Effects of Nutrient Cations on Alkane Bioavailability to Acinetobacter baylyi ADP1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15800-15810. [PMID: 33274919 DOI: 10.1021/acs.est.0c04944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Contamination with petroleum hydrocarbons causes extensive damage to ecological systems. On oil-contaminated sites, alkanes are major components; many indigenous bacteria can access and/or degrade alkanes. However, their ability to do so is affected by external properties of the soil, including nutrient cations. This study used Raman microspectroscopy to study how nutrient cations affect alkanes' bioavailability to Acinetobacter baylyi ADP1 (a known degrader). Treated with Na, K, Mg, and Ca at 10 mM, A. baylyi was exposed to seven n-alkanes (decane, dodecane, tetradecane, hexadecane, nonadecane, eicosane, and tetracosane) and one alkane mixture (mineral oil). Raman spectral analysis indicated that bioavailability of alkanes varied with carbon chain lengths, and additional cations altered the bacterial response to n-alkanes. Sodium significantly increased the bacterial affinity toward decane and dodecane, and K and Mg enhanced the bioavailability of tetradecane and hexadecane. In contrast, the bacterial response was inhibited by Ca for all alkanes. Similar results were observed in mineral oil exposure. Our study employed Raman spectral assay to offer a deep insight into how nutrient cations affect the bioavailability of alkanes, suggesting that nutrient cations can play a key role in influencing the harmful effects of hydrocarbons and could be optimized to enhance the bioremediation strategy.
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Affiliation(s)
- Hanbing Li
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Dayi Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- School of Environment, Tsinghua University, Beijing 100086, China
| | - Jun Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
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30
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Xu A, Wang D, Ding Y, Zheng Y, Wang B, Wei Q, Wang S, Yang L, Ma LZ. Integrated Comparative Genomic Analysis and Phenotypic Profiling of Pseudomonas aeruginosa Isolates From Crude Oil. Front Microbiol 2020; 11:519. [PMID: 32300337 PMCID: PMC7145413 DOI: 10.3389/fmicb.2020.00519] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/10/2020] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa is an environmental microorganism that can thrive in diverse ecological niches including plants, animals, water, soil, and crude oil. It also one of the microorganism widely used in tertiary recovery of crude oil and bioremediation. However, the genomic information regarding the mechanisms of survival and adapation of this bacterium in crude oil is still limited. In this study, three Pseudomonads strains (named as IMP66, IMP67, and IMP68) isolated from crude oil were taken for whole-genome sequencing by using a hybridized PacBio and Illumina approach. The phylogeny analysis showed that the three strains were all P. aeruginosa species and clustered in clade 1, the group with PAO1 as a representitive. Subsequent comparative genomic analysis revealed a high degree of individual genomic plasticity, with a probable alkane degradation genomic island, one type I-F CRISPR-Cas system and several prophages integrated into their genomes. Nine genes encoding alkane hydroxylases (AHs) homologs were found in each strain, which might enable these strains to degrade alkane in crude oil. P. aeruginosa can produce rhamnolipids (RLs) biosurfactant to emulsify oil, which enables their survival in crude oil enviroments. Our previous report showed that IMP67 and IMP68 were high RLs producers, while IMP66 produced little RLs. Genomic analysis suggested that their RLs yield was not likely due to differences at genetic level. We then further analyzed the quorum sensing (QS) signal molecules that regulate RLs synthesis. IMP67 and IMP68 produced more N-acyl-homoserine lactones (AHLs) signal molecules than that of PAO1 and IMP66, which could explain their high RLs yield. This study provides evidence for adaptation of P. aeruginosa in crude oil and proposes the potential application of IMP67 and IMP68 in microbial-enhanced oil recovery and bioremediation.
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Affiliation(s)
- Anming Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Di Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Jurong West, Singapore
| | - Yaqian Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bo Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qing Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Luyan Z Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environ Microbiol 2020; 22:1870-1883. [PMID: 32090431 PMCID: PMC7318663 DOI: 10.1111/1462-2920.14956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
In cold marine environments, the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8, which utilizes aliphatic alkanes almost exclusively as substrates, dominates microbial communities following oil spills. In this study, LC–MS/MS shotgun proteomics was used to identify changes in the proteome induced during growth on n‐alkanes and in cold temperatures. Specifically, proteins with significantly higher relative abundance during growth on tetradecane (n‐C14) at 16°C and 4°C have been quantified. During growth on n‐C14, O. antarctica expressed a complete pathway for the terminal oxidation of n‐alkanes including two alkane monooxygenases, two alcohol dehydrogenases, two aldehyde dehydrogenases, a fatty‐acid‐CoA ligase, a fatty acid desaturase and associated oxidoreductases. Increased biosynthesis of these proteins ranged from 3‐ to 21‐fold compared with growth on a non‐hydrocarbon control. This study also highlights mechanisms O. antarctica may utilize to provide it with ecological competitiveness at low temperatures. This was evidenced by an increase in spectral counts for proteins involved in flagella structure/output to overcome higher viscosity, flagella rotation to accumulate cells and proline metabolism to counteract oxidative stress, during growth at 4°C compared with 16°C. Such species‐specific understanding of the physiology during hydrocarbon degradation can be important for parameterizing models that predict the fate of marine oil spills.
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Affiliation(s)
- Benjamin H Gregson
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Peter N Golyshin
- School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, UK.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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32
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Medić A, Lješević M, Inui H, Beškoski V, Kojić I, Stojanović K, Karadžić I. Efficient biodegradation of petroleum n-alkanes and polycyclic aromatic hydrocarbons by polyextremophilic Pseudomonas aeruginosa san ai with multidegradative capacity. RSC Adv 2020; 10:14060-14070. [PMID: 35498501 PMCID: PMC9051604 DOI: 10.1039/c9ra10371f] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/30/2020] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas aeruginosa san ai degraded individual selected petroleum compounds: n-hexadecane, n-nonadecane, fluorene, phenanthrene, and pyrene with high efficiency, at initial concentrations of 20 mg L−1 and in seven days.
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Affiliation(s)
- Ana Medić
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - Marija Lješević
- Department of Chemistry
- Institute of Chemistry, Technology and Metallurgy
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | | | - Ivan Kojić
- Innovation Center of the Faculty of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
| | | | - Ivanka Karadžić
- Department of Chemistry
- Faculty of Medicine
- University of Belgrade
- 11000 Belgrade
- Serbia
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33
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Gibu N, Kasai D, Ikawa T, Akiyama E, Fukuda M. Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1. Microorganisms 2019; 7:microorganisms7110479. [PMID: 31652785 PMCID: PMC6921075 DOI: 10.3390/microorganisms7110479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/16/2022] Open
Abstract
Gram-positive actinomycete Rhodococcus jostii RHA1 is able to grow on C10 to C19 n-alkanes as a sole source of carbon and energy. To clarify, the n-alkane utilization pathway-a cluster of 5 genes (alkBrubA1A2BalkU) which appeared to be involved in n-alkane degradation-was identified and the transcriptional regulation of these genes was characterized. Reverse transcription-PCR analyses revealed that these genes constituted an operon and were transcribed in the presence of n-alkane. Inactivation of alkB led to the absence of the ability to utilize n-undecane. The alkB mutation resulted in reduction of growth rates on C10 and C12 n-alkanes; however, growths on C13 to C19 n-alkanes were not affected by this mutation. These results suggested that alkB was essential for the utilization of C10 to C12 n-alkanes. Inactivation of alkU showed the constitutive expression of alkB. Purified AlkU is able to bind to the putative promoter region of alkB, suggesting that AlkU played a role in repression of the transcription of alk operon. The results of this study indicated that alkB was involved in the medium-chain n-alkanes degradation of strain RHA1 and the transcription of alk operon was negatively regulated by alkU-encoded regulator. This report is important to understand the n-alkane degradation pathway of R. jostii, including the transcriptional regulation of alk gene cluster.
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Affiliation(s)
- Namiko Gibu
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan.
| | - Takumi Ikawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Emiko Akiyama
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan
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34
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Gregson BH, Metodieva G, Metodiev MV, McKew BA. Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2 T. Environ Microbiol 2019; 21:2347-2359. [PMID: 30951249 PMCID: PMC6850023 DOI: 10.1111/1462-2920.14620] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/19/2019] [Indexed: 02/02/2023]
Abstract
Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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35
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Ji N, Wang X, Yin C, Peng W, Liang R. CrgA Protein Represses AlkB2 Monooxygenase and Regulates the Degradation of Medium-to-Long-Chain n-Alkanes in Pseudomonas aeruginosa SJTD-1. Front Microbiol 2019; 10:400. [PMID: 30915046 PMCID: PMC6422896 DOI: 10.3389/fmicb.2019.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
AlkB monooxygenases in bacteria are responsible for the hydroxylation of medium- and long-chain n-alkanes. In this study, one CrgA protein of Pseudomonas aeruginosa SJTD-1, a member of LysR family, was proved to regulate AlkB2 monooxygenase and the degradation of medium-to-long-chain n-alkanes (C14-C20) by directly binding to the upstream of alkB2 gene. Two specific sites for CrgA binding were found in the promoter region of alkB2 gene, and the imperfect mirror repeat (IIR) structure was proved critical for CrgA recognition and binding. Hexadecyl CoA and octadecyl CoA could effectively release the CrgA binding and start the transcription of alkB2 gene, implying a positive regulation of metabolic intermediate. In the presence of medium-to-long-chain n-alkanes (C14-C20), deletion of crgA gene could enhance the transcription and expression of AlkB2 monooxygenase significantly; and in n-octadecane culture, strain S1ΔalkB1&crgA grew more vigorously than strain S1 ΔalkB1 &crgA . Almost no regulation of CrgA protein was observed to alkB1 gene in vitro and in vivo. Therefore, CrgA acted as a negative regulator for the medium-to-long-chain n-alkane utilization in P. aeruginosa SJTD-1. The work will promote the regulation mechanism study of n-alkane degradation in bacteria and help the bioremediation method development for petroleum pollution.
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Affiliation(s)
- Nannan Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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36
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Wang H, Yang Y, Xu J, Kong D, Li Y. iTRAQ-based comparative proteomic analysis of differentially expressed proteins in Rhodococcus sp. BAP-1 induced by fluoranthene. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 169:282-291. [PMID: 30458394 DOI: 10.1016/j.ecoenv.2018.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
To reveal the molecular mechanism at the level of regulation of proteins in Rhodococcus sp. BAP-1 induced by fluoranthene comparative proteomic analysis was performed on proteins extracted from fluoranthene-exposed cells on 1 d, 3 d, 6 d and 8 d compared with control cells using isobaric tags for relative and absolute quantization (iTRAQ) labeling and LC-MS/MS analysis to access differentially expressed proteins. As a result, we detected a total of 897 significantly differentially expressed proteins, including 30 shared proteins in four comparison clusters. We were able to short-list 190, 329, 101 and 90 proteins that were over-represented, and 394, 234, 65 and 49 under-represented proteins, in 1d/control, 3d/control, 6d/control and 8d/control comparisons, respectively. Functional analysis relied on Clusters of Orthologous Groups (COG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that fluoranthene significantly altered the expression of proteins involved in metabolic and biosynthesis processes. Furthermore, BAP-1 up-regulates aldehyde dehydrogenase, cytochrome c oxidase, and oligopeptide transport ATP-binding protein, while down-regulates several other proteins in order to adapt to fluoranthene exposure. These findings provide important clues to reveal fluoranthene degradation mechanism in BAP-1 and promote its bioremediation applications.
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Affiliation(s)
- Hongqi Wang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Yan Yang
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Jie Xu
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Dekang Kong
- College of Water Sciences, Beijing Normal University, 100875 Beijing, China
| | - Yi Li
- College of Environment and Resource, Guangxi Normal University, 541004 Guilin, Guangxi, China.
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37
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Differential Protein Expression During Growth on Medium Versus Long-Chain Alkanes in the Obligate Marine Hydrocarbon-Degrading Bacterium Thalassolituus oleivorans MIL-1. Front Microbiol 2018; 9:3130. [PMID: 30619200 PMCID: PMC6304351 DOI: 10.3389/fmicb.2018.03130] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 02/02/2023] Open
Abstract
The marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, United Kingdom.,School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, United Kingdom
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, United Kingdom
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38
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Sun JQ, Xu L, Liu XY, Zhao GF, Cai H, Nie Y, Wu XL. Functional Genetic Diversity and Culturability of Petroleum-Degrading Bacteria Isolated From Oil-Contaminated Soils. Front Microbiol 2018; 9:1332. [PMID: 29973925 PMCID: PMC6019457 DOI: 10.3389/fmicb.2018.01332] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
In this study, we compared the culturability of aerobic bacteria isolated from long-term oil-contaminated soils via enrichment and direct-plating methods; bacteria were cultured at 30°C or ambient temperatures. Two soil samples were collected from two sites in the Shengli oilfield located in Dongying, China. One sample (S0) was close to the outlet of an oil-production water treatment plant, and the other sample (S1) was located 500 m downstream of the outlet. In total, 595 bacterial isolates belonging to 56 genera were isolated, distributed in Actinobacteria, Firmicutes, Bacterioidetes, and Proteobacteria. It was interesting that Actinobacteria and Firmicutes were not detected from the 16S rRNA gene clone library. The results suggested the activation of rare species during culture. Using the enrichment method, 239 isolates (31 genera) and 96 (22 genera) isolates were obtained at ambient temperatures and 30°C, respectively, from S0 soil. Using the direct-plating method, 97 isolates (15 genera) and 163 isolates (20 genera) were obtained at ambient temperatures and 30°C, respectively, from two soils. Of the 595 isolates, 244 isolates (41.7% of total isolates) could degrade n-hexadecane. A greater number of alkane-degraders was isolated at ambient temperatures using the enrichment method, suggesting that this method could significantly improve bacterial culturability. Interestingly, the proportion of alkane degrading isolates was lower in the isolates obtained using enrichment method than that obtained using direct-plating methods. Considering the greater species diversity of isolates obtained via the enrichment method, this technique could be used to increase the diversity of the microbial consortia. Furthermore, phenol hydroxylase genes (pheN), medium-chain alkane monooxygenases genes (alkB and CYP153A), and long-chain alkane monooxygenase gene (almA) were detected in 60 isolates (11 genotypes), 91 isolates (27 genotypes) and 93 isolates (24 genotypes), and 34 isolates (14 genotypes), respectively. This study could provide new insights into microbial resources from oil fields or other environments, and this information will be beneficial for bioremediation of petroleum contamination and for other industrial applications.
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Affiliation(s)
- Ji-Quan Sun
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Lian Xu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xue-Ying Liu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Gui-Fang Zhao
- School of Environment, Tsinghua University, Beijing, China
| | - Hua Cai
- School of Environment, Tsinghua University, Beijing, China
| | - Yong Nie
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiao-Lei Wu
- Department of Energy & Resources Engineering, College of Engineering, Peking University, Beijing, China
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39
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LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation in Pseudomonas aeruginosa. Appl Environ Microbiol 2018; 84:AEM.00626-18. [PMID: 29678916 DOI: 10.1128/aem.00626-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/15/2018] [Indexed: 12/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa strain PAO1 is able to use a variety of organic pollutants as growth substrates, including the anionic detergent sodium dodecyl sulfate (SDS) and long-chain alkanes. While the enzymes initiating SDS and alkane degradation are well known, the subsequent enzymatic steps for degradation of the derived primary long-chain alcohols have not yet been identified. By evaluating genes specifically induced during growth with SDS, a gene cluster encoding a putative alcohol dehydrogenase (PA0364/LaoA), a probable inner membrane protein (PA0365/LaoB), and a presumable aldehyde dehydrogenase (PA0366/LaoC) was identified and designated the Lao (long-chain-alcohol/aldehyde-oxidation) system. Growth experiments with deletion mutants with SDS, 1-dodecanol, and alkanes revealed that LaoA and LaoB are involved in the degradation of primary long-chain alcohols. Moreover, detection of 1-dodecanol oxidation in cell extracts by activity staining revealed an interdependency of LaoA and LaoB for efficient 1-dodecanol oxidation. An in silico analysis yielded no well-characterized homologue proteins for LaoA and LaoB. Furthermore, a gene adjacent to the lao gene cluster encodes a putative transcriptional regulator (PA0367/LaoR). A laoR deletion mutant exhibited constitutive expression of LaoA and LaoB, indicating that LaoR is a repressor for the expression of laoABC Taken together, these results showed that the proteins LaoA and LaoB constitute a novel oxidation system for long-chain alcohols derived from pollutants.IMPORTANCE The versatile and highly adaptive bacterium Pseudomonas aeruginosa is able to colonize a variety of habitats, including anthropogenic environments, where it is often challenged with toxic compounds. Its ability to degrade such compounds and to use them as growth substrates can significantly enhance spreading of this opportunistic pathogen in hygienic settings, such as clinics or water distribution systems. Thus, knowledge about the metabolism of P. aeruginosa can contribute to novel approaches for preventing its growth and reducing nosocomial infections. As the Lao system is important for the degradation of two different classes of pollutants, the identification of these novel enzymes can be a useful contribution for developing effective antibacterial strategies.
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40
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Draft Genome Sequence of n-Alkane-Utilizing Acinetobacter sp. Strain BS1, Isolated from Ethane Oxidation Culture. GENOME ANNOUNCEMENTS 2018; 6:6/22/e00465-18. [PMID: 29853505 PMCID: PMC5981037 DOI: 10.1128/genomea.00465-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft whole-genome sequence of a bacterial strain, Acinetobacter sp. strain BS1, isolated from black soil during ethane oxidation culture. Medium- or long-chain alkane oxidation-related genes were identified; however, the short-chain alkane monooxygenase was not detected.
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41
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Fu X, Zhang J, Li T, Zhang M, Li J, Kan B. The Outer Membrane Protein OmpW Enhanced V. cholerae Growth in Hypersaline Conditions by Transporting Carnitine. Front Microbiol 2018; 8:2703. [PMID: 29403450 PMCID: PMC5786537 DOI: 10.3389/fmicb.2017.02703] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/29/2017] [Indexed: 11/13/2022] Open
Abstract
Pathogenic marine bacteria are found in environments and food sources with high salt concentrations, which the bacteria must effectively manage for their survival. Several mechanisms, such as the transport of ions and compatible solutes as well as changes in aerobic and anaerobic respiration, confer salt tolerance to bacteria. In this study, we found that the outer membrane protein OmpW was related to salt stress in Vibrio cholerae and that ompW gene transcription and expression were up-regulated in cultures containing high NaCl concentrations. Deletion of ompW resulted in reduced V. cholerae growth in hypersaline culture conditions. Supplements of the compatible solutes betaine, L-carnitine, or L-lysine enhanced the growth of V. cholerae in hypersaline media. Supplements of betaine or L-lysine had the same growth enhancement effect on the ompW-deletion mutant cultured in hypersaline media, whereas L-carnitine supplementation did not restore mutant growth. In addition, the uptake of L-carnitine was decreased in the ompW-deletion mutant. Our study showed that among the multiplex factors that enhance the hypersaline tolerance of V. cholerae, OmpW also plays a role by transporting L-carnitine.
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Affiliation(s)
- Xiuping Fu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingyun Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tianyi Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mei Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jie Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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42
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Tribelli PM, Rossi L, Ricardi MM, Gomez-Lozano M, Molin S, Raiger Iustman LJ, Lopez NI. Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach. ACTA ACUST UNITED AC 2018; 45:15-23. [DOI: 10.1007/s10295-017-1987-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/01/2017] [Indexed: 01/25/2023]
Abstract
Abstract
Diesel fuel is one of the most important sources of hydrocarbon contamination worldwide. Its composition consists of a complex mixture of n-alkanes, branched alkanes and aromatic compounds. Hydrocarbon degradation in Pseudomonas species has been mostly studied under aerobic conditions; however, a dynamic spectrum of oxygen availability can be found in the environment. Pseudomonas extremaustralis, an Antarctic bacterium isolated from a pristine environment, is able to degrade diesel fuel and presents a wide microaerophilic metabolism. In this work RNA-deep sequence experiments were analyzed comparing the expression profile in aerobic and microaerophilic cultures. Interestingly, genes involved in alkane degradation, including alkB, were over-expressed in micro-aerobiosis in absence of hydrocarbon compounds. In minimal media supplemented with diesel fuel, n-alkanes degradation (C13–C19) after 7 days was observed under low oxygen conditions but not in aerobiosis. In-silico analysis of the alkB promoter zone showed a putative binding sequence for the anaerobic global regulator, Anr. Our results indicate that some diesel fuel components can be utilized as sole carbon source under microaerophilic conditions for cell maintenance or slow growth in a Pseudomonas species and this metabolism could represent an adaptive advantage in polluted environments.
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Affiliation(s)
- Paula M Tribelli
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Leticia Rossi
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Martiniano M Ricardi
- 0000 0001 0056 1981 grid.7345.5 Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET), Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires C1428EGA Buenos Aires Argentina
| | - Maria Gomez-Lozano
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Søren Molin
- 0000 0001 2181 8870 grid.5170.3 Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Hørsholm Denmark
| | - Laura J Raiger Iustman
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
| | - Nancy I Lopez
- 0000 0001 0056 1981 grid.7345.5 Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Intendente Guiraldes, 2160 C1428EGA Buenos Aires Argentina
- 0000 0001 1945 2152 grid.423606.5 IQUIBICEN, CONICET Buenos Aires Argentina
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43
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Ito M, Kambe H, Kishino S, Muramatsu M, Ogawa J. A search for microorganisms producing medium-chain alkanes from aldehydes. J Biosci Bioeng 2017; 125:87-91. [PMID: 28869193 DOI: 10.1016/j.jbiosc.2017.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/10/2017] [Accepted: 08/04/2017] [Indexed: 10/19/2022]
Abstract
Microorganisms with medium-chain alkane-producing activity are promising for the bio-production of drop-in fuel. In this study, we screened for microorganisms producing tridecane from tetradecanal. The activity of aldehyde decarbonylation was found in a wide range of microbes. In particular, the genus Klebsiella in the Enterobacteriaceae family was found to have a high ability to produce alkanes from aldehydes via enzyme catalyzed reaction.
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Affiliation(s)
- Masakazu Ito
- Future Project Division, Frontier Research Center, Toyota Motor Corporation, 1 Toyota-cho, Toyota, Aichi 471-8572, Japan
| | - Hiromi Kambe
- Toyota Biotechnology and Afforestation Laboratory, Toyota Motor Corporation, 1099 Marune, Kurozasa-cho, Miyoshi, Aichi 470-0201 Japan
| | - Shigenobu Kishino
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayoshi Muramatsu
- Future Project Division, Frontier Research Center, Toyota Motor Corporation, 1 Toyota-cho, Toyota, Aichi 471-8572, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
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44
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Toshchakov SV, Korzhenkov AA, Chernikova TN, Ferrer M, Golyshina OV, Yakimov MM, Golyshin PN. The genome analysis of Oleiphilus messinensis ME102 (DSM 13489 T) reveals backgrounds of its obligate alkane-devouring marine lifestyle. Mar Genomics 2017; 36:41-47. [PMID: 28802691 PMCID: PMC5847120 DOI: 10.1016/j.margen.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 11/24/2022]
Abstract
Marine bacterium Oleiphilus messinensis ME102 (DSM 13489T) isolated from the sediments of the harbor of Messina (Italy) is a member of the order Oceanospirillales, class Gammaproteobacteria, representing the physiological group of marine obligate hydrocarbonoclastic bacteria (OHCB) alongside the members of the genera Alcanivorax, Oleispira, Thalassolituus, Cycloclasticus and Neptunomonas. These organisms play a crucial role in the natural environmental cleanup in marine systems. Despite having the largest genome (6.379.281 bp) among OHCB, O. messinensis exhibits a very narrow substrate profile. The alkane metabolism is pre-determined by three loci encoding for two P450 family monooxygenases, one of which formed a cassette with ferredoxin and alcohol dehydrogenase encoding genes and alkane monoxygenase (AlkB) gene clustered with two genes for rubredoxins and NAD+-dependent rubredoxin reductase. Its genome contains the largest numbers of genomic islands (15) and mobile genetic elements (140), as compared with more streamlined genomes of its OHCB counterparts. Among hydrocarbon-degrading Oceanospirillales, O. messinensis encodes the largest array of proteins involved in the signal transduction for sensing and responding to the environmental stimuli (345 vs 170 in Oleispira antarctica, the bacterium with the second highest number). This must be an important trait to adapt to the conditions in marine sediments with a high physico-chemical patchiness and heterogeneity as compared to those in the water column.
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Affiliation(s)
| | | | | | - Manuel Ferrer
- Institute of Catalysis CSIC, Campus Cantoblanco, 28049 Madrid, Spain
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK
| | - Michail M Yakimov
- Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia; Institute for Coastal Marine Environment, CNR, 98122 Messina, Italy
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, Gwynedd, UK.
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45
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Draft Genome Sequence of Bacillus licheniformis VSD4, a Diesel Fuel-Degrading and Plant Growth-Promoting Phyllospheric Bacterium. GENOME ANNOUNCEMENTS 2017; 5:5/11/e00027-17. [PMID: 28302775 PMCID: PMC5356052 DOI: 10.1128/genomea.00027-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report here the 4.19-Mb draft genome sequence of Bacillus licheniformis VSD4, a Gram-positive bacterium of the Bacillaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. Knowledge about its genome will help to evaluate its potential as an inoculant in phylloremediation applications.
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46
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Li H, Martin FL, Zhang D. Quantification of Chemotaxis-Related Alkane Accumulation in Acinetobacter baylyi Using Raman Microspectroscopy. Anal Chem 2017; 89:3909-3918. [DOI: 10.1021/acs.analchem.6b02297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hanbing Li
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
| | - Francis Luke Martin
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
- School
of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, U.K
| | - Dayi Zhang
- Lancaster
Environment Centre, Lancaster University, Lancaster LA1 4YQ, U.K
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47
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Salam LB, Obayori SO, Nwaokorie FO, Suleiman A, Mustapha R. Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:7139-7159. [PMID: 28093673 DOI: 10.1007/s11356-017-8364-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/02/2017] [Indexed: 06/06/2023]
Abstract
Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.
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Affiliation(s)
- Lateef B Salam
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria.
| | - Sunday O Obayori
- Department of Microbiology, Lagos State University, Ojo, Lagos, Nigeria
| | - Francisca O Nwaokorie
- Department of Medical Laboratory Science, College of Medicine, University of Lagos, Akoka, Lagos, Nigeria
| | - Aisha Suleiman
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
| | - Raheemat Mustapha
- Microbiology Unit, Department of Biological Sciences, Al-Hikmah University, Ilorin, Kwara, Nigeria
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48
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Long H, Wang Y, Chang S, Liu G, Chen T, Huo G, Zhang W, Wu X, Tai X, Sun L, Zhang B. Diversity of crude oil-degrading bacteria and alkane hydroxylase (alkB) genes from the Qinghai-Tibet Plateau. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:116. [PMID: 28220441 DOI: 10.1007/s10661-017-5798-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 01/23/2017] [Indexed: 06/06/2023]
Abstract
The aim of this study was to survey the response of the microbial community to crude oil and the diversity of alkane hydroxylase (alkB) genes in soil samples from the Qinghai-Tibet Plateau (QTP). The enrichment cultures and clone libraries were used. Finally, 53 isolates and 94 alkB sequences were obtained from 10 pristine soil samples after enrichment at 10 °C with crude oil as sole carbon source. The isolates fell into the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, with the dominance of Pseudomonas and Acinetobacter. The composition of degraders was different from polar habitats where Acinetobacter sp. is not a predominant responder of alkane degradative microbial communities. Phylogenetic analysis showed that the alkB genes from isolates and enrichment communities formed eight clusters and mainly related with alkB genes of Pseudomonas, Rhodococcus, and Acinetobacter. The alkB gene diversity in the QTP was lower than marine environments and polar soil samples. In particular, a total of 10 isolates exhibiting vigorous growth with crude oil could detect no crude oil degradation-related gene sequences, such as alkB, P450, almA, ndoB, and xylE genes. The Shannon-Wiener index of the alkB clone libraries from the QTP ranged from 1.00 to 2.24 which is similar with polar pristine soil samples but lower than that of contaminated soils. These results indicated that the Pseudomonas, Acinetobacter, and Rhodococcus genera are the candidate for in situ bioremediation, and the environment of QTP may be still relatively uncontaminated by crude oil.
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Affiliation(s)
- Haozhi Long
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Yilin Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Sijing Chang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China.
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China.
- State Key Laboratory of Cryospheric Sciences, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China.
| | - Guanghua Huo
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Xisheng Tai
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Likun Sun
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
| | - Baogui Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, Gansu, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, Gansu, 730000, China
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49
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Draft Genome Sequence of Rhodococcus erythropolis VSD3, a Diesel Fuel-Degrading and Plant Growth-Promoting Bacterium Isolated from Hedera helix Leaves. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01680-16. [PMID: 28232452 PMCID: PMC5323631 DOI: 10.1128/genomea.01680-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We report here the 6.55-Mb draft genome sequence of Rhodococcus erythropolis VSD3, a Gram-positive bacterium of the Nocardiaceae family, isolated from leaves of Hedera helix growing at a high-traffic city center in Belgium. The exploration of its genome will contribute to the assessment of its application as an inoculant in phylloremediation approaches.
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50
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Gkorezis P, Daghio M, Franzetti A, Van Hamme JD, Sillen W, Vangronsveld J. The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front Microbiol 2016; 7:1836. [PMID: 27917161 PMCID: PMC5116465 DOI: 10.3389/fmicb.2016.01836] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.
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Affiliation(s)
- Panagiotis Gkorezis
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Matteo Daghio
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
- Department of Biological Sciences, Thompson Rivers University, KamloopsBC, Canada
| | - Andrea Franzetti
- Department of Environmental Sciences, University of Milano-BicoccaMilano, Italy
| | | | - Wouter Sillen
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt UniversityDiepenbeek, Belgium
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