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Lin R, Li H, Wu H, Ren H, Kong X, Lu Z. Resting for viability: Gordonia polyisoprenivorans ZM27, a robust generalist for petroleum bioremediation under hypersaline stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124618. [PMID: 39067736 DOI: 10.1016/j.envpol.2024.124618] [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: 04/12/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The intrinsic issue associated with the application of microbes for practical pollution remediation involves maintaining the expected activity of engaged strains or consortiums as effectively as that noted under laboratory conditions. Faced with various stress factors, degraders with dormancy ability are more likely to survive and exhibit degradation activity. In this study, a hydrocarbonoclastic and halotolerant strain, Gordonia polyisoprenivorans ZM27, was isolated via stimulation with resuscitation-promoting factor (Rpf). Long-term exposure to dual stresses of 10% NaCl and starvation induced ZM27 to enter a viable but nonculturable (VBNC)-like state, and ZM27 cells could be resuscitated upon Rpf stimulation. Notable changes in both morphological and physiological characteristics between VBNC-like ZM27 cells and resuscitated cells confirmed the response to Rpf and their robust resistance against harsh environments. Whole-genome sequencing and analysis indicated ZM27 could be a generalist degrader with dormancy ability. Subsequently, VBNC-like ZM27 was applied in a soil microcosm experiment to investigate the practical application potential under harsh conditions. VBNC-like ZM27 combined with Rpf stimulation exhibited the most effective biodegradation performance, and the initial n-hexadecane content (1000 mg kg-1) decreased by 63.29% after 14-day incubation. Based on 16S rRNA amplicon sequencing and analysis, Gordonia exhibited a positive response to Rpf stimulation. The relative abundance of genus Gordonia was negatively correlated with that of Alcanivorax, a genus of obligate hydrocarbon degrader with the greatest abundance during soil incubation. Based on the degradation profile and community analysis, generalist Gordonia may be more efficient in hydrocarbon degradation than specialist Alcanivorax under harsh conditions. The characteristics of ZM27, including its sustainable culturability under long-term stress, response to Rpf and robust performance in soil microcosms, are valuable for the remediation of petroleum pollution under stressful conditions. Our work validated the importance of dormancy and highlighted the underestimated role of low-activity degraders in petroleum remediation.
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Affiliation(s)
- Renzhang Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Hao Ren
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Xiangyu Kong
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China; Cancer Center, Zhejiang University, Hangzhou, 310058, China.
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Mohamed SF, Narayanan R. Enterobacter cloacae-mediated polymer biodegradation: in-silico analysis predicts broad spectrum degradation potential by Alkane monooxygenase. Biodegradation 2024; 35:969-991. [PMID: 39001975 DOI: 10.1007/s10532-024-10091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/03/2024] [Indexed: 07/15/2024]
Abstract
Plastic pollution poses a significant environmental challenge. In this study, the strain Enterobacter cloacae O5-E, a bacterium displaying polyethylene-degrading capabilities was isolated. Over a span of 30 days, analytical techniques including x-ray diffractometry, scanning electron microscopy, optical profilometry, hardness testing and mass spectrometric analysis were employed to examine alterations in the polymer. Results revealed an 11.48% reduction in crystallinity, a 50% decrease in hardness, and a substantial 25-fold increase in surface roughness resulting from the pits and cracks introduced in the polymer by the isolate. Additionally, the presence of degradational by-products revealed via gas chromatography ascertains the steady progression of degradation. Further, recognizing the pivotal role of alkane monooxygenase in plastic degradation, the study expanded to detect this enzyme in the isolate molecularly. Molecular docking studies were conducted to assess the enzyme's affinity with various polymers, demonstrating notable binding capability with most polymers, especially with polyurethane (- 5.47 kcal/mol). These findings highlight the biodegradation potential of Enterobacter cloacae O5-E and the crucial involvement of alkane monooxygenase in the initial steps of the degradation process, offering a promising avenue to address the global plastic pollution crisis.
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Affiliation(s)
- Shafana Farveen Mohamed
- Department of Genetic Engineering, School of Bioengineering and Faculty of Engineering and Technology, College of Engineering & Technology (CET), SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India
| | - Rajnish Narayanan
- Department of Genetic Engineering, School of Bioengineering and Faculty of Engineering and Technology, College of Engineering & Technology (CET), SRM Institute of Science and Technology, Kattankulathur, Kanchipuram, Chennai, Tamil Nadu, 603203, India.
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Frantsuzova E, Bogun A, Kopylova O, Vetrova A, Solyanikova I, Streletskii R, Delegan Y. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. BIOLOGY 2024; 13:339. [PMID: 38785821 PMCID: PMC11117675 DOI: 10.3390/biology13050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Olga Kopylova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
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Wang H, Guan F, Zhu Y, Pan Y, Liu Q, Liu Q, He W, Gong D, Tian J, Han D. Biofilm formation promoted biodegradation of polyethylene in Gordonia polyisoprenivorans B251 isolated from bacterial enrichment acclimated by hexadecane for two years. CHEMOSPHERE 2023; 344:140383. [PMID: 37832891 DOI: 10.1016/j.chemosphere.2023.140383] [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: 02/15/2023] [Revised: 08/31/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Polyethylene (PE) mulch films have been widely used in agriculture and led to a significant pollution in cultivated soils. It is desirable to develop the sustainable method for the degradation of PE. As an environment friendly approach, microbial or enzymatic degradation of PE could meet this demanding. Thus, more microbial strains are required for illustrating biodegrading pathway and developing efficient biological method. In this study, Gordonia polyisoprenivorans B251 capable of degrading PE was isolated from bacterial enrichment with hexadecane as a sole carbon source for two years, in which genus Gordonia had dominated. As revealed by microbial growth curve, the strain B251 had the highest growth rate than other tested strains in the mediums either with hexadecane or PE particles as sole carbon source. The formation of biofilms in both enriched culture and G. polyisoprenivorans B251 pure culture attached to PE film was observed. The capability for PE degradation of individual strain was screened by 30-day incubation with PE film and confirmed by the presence of hydroxyl, carbonyl, carbon-carbon double bond and ether groups in FT-IR analysis and cracks on the surface of PE film observed by scanning electron microscopy (SEM). Therefore, Gordonia polyisoprenivorans, reported as their degradation of environmental contaminants in previous study, were also identified in current study as a candidate for polyethylene biodegradation.
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Affiliation(s)
- Hongzhe Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Zhu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yanshuo Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qi Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qin Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqing He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Daozhi Gong
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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Xiang W, Hong S, Xue Y, Ma Y. Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91. Microorganisms 2023; 11:1537. [PMID: 37375039 DOI: 10.3390/microorganisms11061537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.
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Affiliation(s)
- Wei Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Hong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Frantsuzova E, Bogun A, Solomentsev V, Vetrova A, Streletskii R, Solyanikova I, Delegan Y. Whole Genome Analysis and Assessment of the Metabolic Potential of Gordonia rubripertincta Strain 112, a Degrader of Aromatic and Aliphatic Compounds. BIOLOGY 2023; 12:biology12050721. [PMID: 37237534 DOI: 10.3390/biology12050721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/28/2023]
Abstract
The application of Gordonia strains in biotechnologies of environmental purification as degraders of pollutants of different chemical structures is an interesting research topic. The strain Gordonia rubripertincta 112 (IEGM112) is capable of utilizing diesel fuel, alkanes, and aromatic compounds. The aim of this work was to study the potential of G. rubripertincta 112 as a degrader of aromatic and aliphatic compounds and analyze its complete genome in comparison with other known G. rubripertincta strains. The genome had a total length of 5.28 Mb and contained 4861 genes in total, of which 4799 were coding sequences (CDS). The genome contained 62 RNA genes in total, of which 50 were tRNAs, three were ncRNAs, and nine were rRNAs. The strain bears plasmid elements with a total length of 189,570 nucleotides (plasmid p1517). The strain can utilize 10.79 ± 1.17% of hexadecane and 16.14 ± 0.16% of decane over 3 days of cultivation. In the genome of the strain, we have found metabolic pathways of alkane (cytochrome P450 hydroxylases) and catechol (ortho- and meta-pathways) degradation. These results will help us to further approach the fundamental study of the processes occurring in the strain cells and to enrich our knowledge of the catabolic capabilities of G. rubripertincta.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Viktor Solomentsev
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of Russian Academy of Sciences" (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
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Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains. Microorganisms 2022; 11:microorganisms11010004. [PMID: 36677296 PMCID: PMC9861168 DOI: 10.3390/microorganisms11010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon-carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.
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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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Abstract
Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.
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Hoang SA, Lamb D, Seshadri B, Sarkar B, Cheng Y, Wang L, Bolan NS. Petroleum hydrocarbon rhizoremediation and soil microbial activity improvement via cluster root formation by wild proteaceae plant species. CHEMOSPHERE 2021; 275:130135. [PMID: 33984915 DOI: 10.1016/j.chemosphere.2021.130135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/26/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Rhizoremediation potential of different wild plant species for total (aliphatic) petroleum hydrocarbon (TPH)-contaminated soils was investigated. Three-week-old seedlings of Acacia inaequilatera, Acacia pyrifolia, Acacia stellaticeps, Banksia seminuda, Chloris truncata, Hakea prostrata, Hardenbergia violacea, and Triodia wiseana were transplanted in a soil contaminated with diesel and engine oil as TPH at pollution levels of 4,370 (TPH1) and 7,500 (TPH2) mg kg-1, and an uncontaminated control (TPH0). After 150 days, the presence of TPH negatively affected the plant growth, but the growth inhibition effect varied between the plant species. Plant growth and associated root biomass influenced the activity of rhizo-microbiome. The presence of B. seminuda, C. truncata, and H. prostrata significantly increased the TPH removal rate (up to 30% compared to the unplanted treatment) due to the stimulation of rhizosphere microorganisms. No significant difference was observed between TPH1 and TPH2 regarding the plant tolerance and rhizoremediation potentials of the three plant species. The presence of TPH stimulated cluster root formation in B. seminuda and H. prostrata which was associated with enhanced TPH remediation of these two members of Proteaceae family. These results indicated that B. seminuda, C. truncata, and H. prostrata wild plant species could be suitable candidates for the rhizoremediation of TPH-contaminated soil.
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Affiliation(s)
- Son A Hoang
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia; Division of Urban Infrastructural Engineering, Mien Trung University of Civil Engineering, Phu Yen, 56000, Viet Nam
| | - Dane Lamb
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, PO Box 18, Callaghan, NSW, 2308, Australia; The Global Innovation Centre for Advanced Nanotechnology, University of Newcastle, Callaghan, NSW, Australia
| | - Balaji Seshadri
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, PO Box 18, Callaghan, NSW, 2308, Australia
| | - Binoy Sarkar
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, United Kingdom
| | - Ying Cheng
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, PO Box 18, Callaghan, NSW, 2308, Australia
| | - Liang Wang
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, PO Box 18, Callaghan, NSW, 2308, Australia
| | - Nanthi S Bolan
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, PO Box 18, Callaghan, NSW, 2308, Australia.
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Development and Genetic Engineering of Hyper-Producing Microbial Strains for Improved Synthesis of Biosurfactants. Mol Biotechnol 2021; 63:267-288. [PMID: 33523418 DOI: 10.1007/s12033-021-00302-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Current research energies are fixated on the synthesis of environmentally friendly and non-hazardous products, which include finding and recognizing biosurfactants that can substitute synthetic surfactants. Microbial biosurfactants are surface-active compounds synthesized intracellularly or extracellularly. To use biosurfactants in various industries, it is essential to understand scientific engagements that demonstrate its potentials as real advancement in the 21st century. Other than applying a substantial effect on the world economic market, engineered hyper-producing microbial strains in combination with optimized cultivation parameters have made it probable for many industrial companies to receive the profits of 'green' biosurfactant innovation. There needs to be an emphasis on the worldwide state of biosurfactant synthesis, expression of biosurfactant genes in expressive host systems, the recent developments, and prospects in this line of research. Thus, molecular dynamics with respect to genetic engineering of biosynthetic genes are proposed as new biotechnological tools for development, improved synthesis, and applications of biosurfactants. For example, mutant and hyper-producing recombinants have been designed efficaciously to advance the nature, quantity, and quality of biosurfactants. The fastidious and deliberate investigation will prompt a comprehension of the molecular dynamics and phenomena in new microorganisms. Throughout the decade, valuable data on the molecular genetics of biosurfactant have been produced, and this solid foundation would encourage application-oriented yields of the biosurfactant production industry and expand its utilization in diverse fields. Therefore, the conversations among different interdisciplinary experts from various scientific interests such as microbiology, biochemistry, molecular biology, and genetics are indispensable and significant to accomplish these objectives.
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Catania V, Lopresti F, Cappello S, Scaffaro R, Quatrini P. Innovative, ecofriendly biosorbent-biodegrading biofilms for bioremediation of oil- contaminated water. N Biotechnol 2020; 58:25-31. [PMID: 32485241 DOI: 10.1016/j.nbt.2020.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/24/2023]
Abstract
Immobilization of microorganisms capable of degrading specific contaminants significantly promotes bioremediation processes. In this study, innovative and ecofriendly biosorbent-biodegrading biofilms have been developed in order to remediate oil-contaminated water. This was achieved by immobilizing hydrocarbon-degrading gammaproteobacteria and actinobacteria on biodegradable oil-adsorbing carriers, based on polylactic acid and polycaprolactone electrospun membranes. High capacities for adhesion and proliferation of bacterial cells were observed by scanning electron microscopy. The bioremediation efficiency of the systems, tested on crude oil and quantified by gas chromatography, showed that immobilization increased hydrocarbon biodegradation by up to 23 % compared with free living bacteria. The resulting biosorbent biodegrading biofilms simultaneously adsorbed 100 % of spilled oil and biodegraded more than 66 % over 10 days, with limited environmental dispersion of cells. Biofilm-mediated bioremediation, using eco-friendly supports, is a low-cost, low-impact, versatile tool for bioremediation of aquatic systems.
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Affiliation(s)
- Valentina Catania
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, blg. 16, 90128, Palermo, Italy
| | - Francesco Lopresti
- Dept. of Engineering, University of Palermo, Viale delle Scienze, blg. 6, 90128, Palermo, Italy
| | - Simone Cappello
- Institute for Biological Resources and Marine Biotechnology, National Research Council (CNR) of Messina, Spianata San Raineri, 86, 98121, Messina, Italy
| | - Roberto Scaffaro
- Dept. of Engineering, University of Palermo, Viale delle Scienze, blg. 6, 90128, Palermo, Italy
| | - Paola Quatrini
- Dept. of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, blg. 16, 90128, Palermo, Italy.
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13
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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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Jimoh AA, Lin J. Biosurfactant: A new frontier for greener technology and environmental sustainability. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109607. [PMID: 31505408 DOI: 10.1016/j.ecoenv.2019.109607] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/13/2019] [Accepted: 08/22/2019] [Indexed: 05/26/2023]
Abstract
Petroleum hydrocarbons, oil, heavy metals pollution is becoming additional severe problem due to the growing call for crude oil and crude oil products related products in several fields of application. Such pollution have fascinated much considerations and attractions as it leads to ecological damages in both marines, aquatic and terrestrial ecosystems. Thus, different techniques including chemical surfactants and complex technologies have been proposed for their clean up from the environment, which in turn has detrimental effects on the environment. As of late, biosurfactant compounds have added much deliberation since they are considered as a reasonable option and eco-accommodating materials for remediation technology. The present society is confronting a few difficulties of usage, authorizing ecological protection and environmental change for the next generations. Biosurfactants hold the special property of minimizing and reducing the interfacial tension of liquids. Such features endure biosurfactants to afford a major part in emulsification, de-emulsification, biodegradability, foam formation, washing performance, surface activity, and detergent formulation, which have potential applications in the diverse industrial set-up. Conversations on cost-effective technologies, renewable materials, novel synthesis, downstream, upstream, emerging characterization techniques, molecular, and genetical engineering are substantial to produce biosurfactant of quality and quantity. Therefore, greater attention is being paid to biosurfactant production by identifying their environmental, and biotechnological applications. Be that as it may, the extravagant cost drew in with biosurfactants biotechnological synthesis and recovery can hamper their application in those areas. Notwithstanding these costs, biosurfactants can be used as these parts shows outstandingly high benefits that can at present beat the expenses incurred in the initial purification and downstream processes. Biosurfactant production by microorganisms is relatively considered one of the crucial know-how for improvement, growth, advancement, and environmental sustainability of the 21st century. There is a developing conversation around environmental safety and the significant role that biosurfactants will progressively play soon, for instance, the use of renewable by-products as substrates, potential reduction, re-use and recycling of waste and waste products. The review confers the usefulness of biosurfactants in the removal of environmental contaminants and, consequently, expanding environmental safety and drive towards greener technology.
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Affiliation(s)
- Abdullahi Adekilekun Jimoh
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X 54001, Durban, South Africa.
| | - Johnson Lin
- Discipline of Microbiology, School of Life Sciences, University of KwaZulu-Natal (Westville), Private Bag X 54001, Durban, South Africa
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Complete Genome Sequence of Rhodococcus erythropolis X5, a Psychrotrophic Hydrocarbon-Degrading Biosurfactant-Producing Bacterium. Microbiol Resour Announc 2019; 8:8/48/e01234-19. [PMID: 31776221 PMCID: PMC6883108 DOI: 10.1128/mra.01234-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content). Rhodococcus erythropolis X5 is a psychrotrophic (cold-adapted) hydrocarbon-degrading bacterium, as it showed effective n-alkane destruction at low positive temperatures. Here, the genome of strain X5 was completely sequenced; it consists of a 6,472,161-bp circular chromosome (62.25% GC content) and a 526,979-bp linear plasmid, pRhX5-526k (62.37% GC content).
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Delegan Y, Sargsyan A, Hovhannisyan N, Babayan B, Petrikov K, Vainstein M. Analysis of genome sequence and trehalose lipid production peculiarities of the thermotolerant Gordonia
strain. J Basic Microbiol 2019; 60:14-21. [DOI: 10.1002/jobm.201900439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Yanina Delegan
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
| | - Armen Sargsyan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
| | - Nelli Hovhannisyan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
- Institute of Pharmacy; Yerevan State University; Yerevan Armenia
| | - Bella Babayan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
| | - Kirill Petrikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
| | - Mikhail Vainstein
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
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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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18
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Sowani H, Kulkarni M, Zinjarde S. Harnessing the catabolic versatility of Gordonia species for detoxifying pollutants. Biotechnol Adv 2019; 37:382-402. [DOI: 10.1016/j.biotechadv.2019.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 01/12/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
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19
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Silva NM, de Oliveira AMSA, Pegorin S, Giusti CE, Ferrari VB, Barbosa D, Martins LF, Morais C, Setubal JC, Vasconcellos SP, da Silva AM, de Oliveira JCF, Pascon RC, Viana-Niero C. Characterization of novel hydrocarbon-degrading Gordonia paraffinivorans and Gordonia sihwensis strains isolated from composting. PLoS One 2019; 14:e0215396. [PMID: 30998736 PMCID: PMC6472744 DOI: 10.1371/journal.pone.0215396] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/01/2019] [Indexed: 01/10/2023] Open
Abstract
Hydrocarbons are important environmental pollutants, and the isolation and characterization of new microorganisms with the ability to degrade these compounds are important for effective biodegradation. In this work we isolated and characterized several bacterial isolates from compost, a substrate rich in microbial diversity. The isolates were obtained from selective culture medium containing n-hexadecane, aiming to recover alkane-degraders. Six isolates identified as Gordonia by MALDI-TOF and 16S rRNA sequencing had the ability to degrade n-hexadecane in three days. Two isolates were selected for genomic and functional characterization, Gordonia paraffinivorans (MTZ052) and Gordonia sihwensis (MTZ096). The CG-MS results showed distinct n-hexadecane degradation rates for MTZ052 and MTZ096 (86% and 100% respectively). The genome sequence showed that MTZ052 encodes only one alkane degrading gene cluster, the CYP153 system, while MTZ096 harbors both the Alkane Hydroxylase (AH) and the CYP153 systems. qPCR showed that both gene clusters are induced by the presence of n-hexadecane in the growth medium, suggesting that G. paraffinivorans and G. sihwensis use these systems for degradation. Altogether, our results indicate that these Gordonia isolates have a good potential for biotransformation of hydrocarbons.
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Affiliation(s)
- Natalia Maria Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Stefania Pegorin
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, Diadema, Brazil
| | - Camila Escandura Giusti
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vitor Batista Ferrari
- Departamento de Ciências Farmacêuticas da Universidade Federal de São Paulo, Diadema, Brazil
| | - Deibs Barbosa
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Carlos Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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Solyanikova IP, Golovleva LA. Hexadecane and Hexadecane-Degrading Bacteria: Mechanisms of Interaction. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261718060152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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21
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Djahnit N, Chernai S, Catania V, Hamdi B, China B, Cappello S, Quatrini P. Isolation, characterization and determination of biotechnological potential of oil-degrading bacteria from Algerian centre coast. J Appl Microbiol 2019; 126:780-795. [PMID: 30586234 DOI: 10.1111/jam.14185] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/31/2018] [Accepted: 12/20/2018] [Indexed: 11/26/2022]
Abstract
AIMS The Algerian coastline is exposed to several types of pollution, including hydrocarbons. The aim of this work was to isolate oil-degrading bacteria and to explore the intrinsic bioremediation potential of part of its contaminated harbour. METHODS AND RESULTS A collection of 119 strains, capable to grow on mineral medium supplemented with hydrocarbons, were obtained from polluted sediment and seawater collected from Sidi Fredj harbour (Algiers). Twenty-three strains were selected for further studies. Sequencing of the 16S rRNA gene showed that most isolates belong to genera of hydrocarbonoclastic bacteria (Alcanivorax), generalist hydrocarbons degraders (Marinobacter, Pseudomonas, Gordonia, Halomonas, Erythrobacter and Brevibacterium) and other bacteria not known as hydrocarbon degraders (Xanthomarina) but were able to degrade hydrocarbons. Strains related to Marinobacter and Alcanivorax were frequently isolated from our samples and resulted the most effective in degrading crude oil. Screening of catabolic genes alkB and xylA revealed the presence of alkB gene in several bacterial strains; one isolate harboured both catabolic genes while other isolates carried none of the studied genes. However, they grew in the presence of crude oil implying the existence of other biodegradation pathways. CONCLUSIONS The samples of seawater and sediment from the Algerian coast contain high level of hydrocarbon-degrading bacteria that could be interesting and useful for future bioremediation purposes. SIGNIFICANCE AND IMPACT OF THE STUDY This investigation demonstrates the diversity of hydrocarbon-degrading bacteria from a marine-contaminated area in Algeria, and their variable biodegradation abilities.
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Affiliation(s)
- N Djahnit
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - S Chernai
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - V Catania
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - B Hamdi
- Laboratoire de Conservation et de Valorisation des Ressources Marines, Ecole Nationale Supérieure des Sciences de la Mer et l'Aménagement du Littoral, ENSSMAL, Alger, Algérie
| | - B China
- Sciensano, J. Wytsmanstreet, Brussels, Belgium
| | - S Cappello
- Istituto per l'Ambiente Marino Costiero (IAMC) - C.N.R. U.O.S. di Messina Sp., Messina, Italy
| | - P Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
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Yang R, Zhang G, Li S, Moazeni F, Li Y, Wu Y, Zhang W, Chen T, Liu G, Zhang B, Wu X. Degradation of crude oil by mixed cultures of bacteria isolated from the Qinghai-Tibet plateau and comparative analysis of metabolic mechanisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:1834-1847. [PMID: 30456621 DOI: 10.1007/s11356-018-3718-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
This study investigates the biodegradation of crude oil by a mixed culture of bacteria isolated from the Qinghai-Tibet plateau using gas chromatography-mass spectrometer (GC-MS) and the gravimetric method. The results showed that a mixed culture has a stronger ability to degrade hydrocarbon than pure cultures. Once both Nocardia soli Y48 and Rhodococcus erythropolis YF28-1 (8) were present in a culture, the culture demonstrated the highest crude oil removal efficiency of almost 100% after 10 days of incubation at 20 °C. Moreover, further analysis of the degradation mechanisms used by the above strains, which revealed utilization of different n-alkane substrates, indicated the diversity of evolution and variations in different strains, as well as the importance of multiple metabolic mechanisms for alkane degradation. Therefore, it is concluded that a mixed culture of Y48 and YF28-1 (8) strains can provide a more effective method for bioremediation of hydrocarbon-contaminated soil in permafrost regions.
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Affiliation(s)
- Ruiqi Yang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Shiweng Li
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, 730070, China
| | - Faegheh Moazeni
- School of Science Engineering and Technology, Penn State Harrisburg University, Middletown, PA, 17057, USA
| | - Yunshi Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yongna Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China.
| | - Binglin Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, 730000, Gansu Province, China
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23
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Delegan YA, Valentovich LN, Shafieva SM, Ganbarov KG, Filonov AE, Vainstein MB. Characterization and genomic analysis of highly efficient thermotolerant oil-degrading bacterium Gordonia sp. 1D. Folia Microbiol (Praha) 2018; 64:41-48. [PMID: 29951843 DOI: 10.1007/s12223-018-0623-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/06/2018] [Indexed: 10/28/2022]
Abstract
A thermotolerant bacterial strain 1D isolated from refinery oil-contaminated soil was identified as Gordonia sp. based on the analysis of 16S rRNA and gyrB gene sequences. The strain was found to utilize crude oil, diesel fuel, and a wide spectrum of alkanes at temperatures up to 50 °C. Strain 1D is the first representative of Gordonia amicalis capable of utilizing alkanes of chain length up to С36 at a temperature of 45-50 °C. The degree of crude oil degradation by Gordonia sp. 1D at 45 °C was 38% in liquid medium and 40% in soil (with regard to abiotic loss). There are no examples of so effective hydrocarbon-oxidizing thermotolerant Gordonia in the world literature. The 1D genome analysis revealed the presence of two alkane hydroxylase gene clusters, genes of dibenzothiophene cleavage, and the cleavage of salicylate and gentisate - naphthalene metabolism intermediates. The highly efficient thermotolerant strain Gordonia sp. 1D can be used in remediation of oil-contaminated soils in hot climates.
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Affiliation(s)
- Yanina A Delegan
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, Pushchino, 142290, Russia.
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, 2 Kuprevich str, 220141, Minsk, Belarus
| | - Samira M Shafieva
- Baku State University, 23 Academic Zahid Khalilov str, AZ 1148, Baku, Azerbaijan
| | | | - Andrey E Filonov
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, Pushchino, 142290, Russia
| | - Mikhail B Vainstein
- FSBIS G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 5 Prospekt Nauki, Pushchino, 142290, Russia
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Chiciudean I, Nie Y, Tănase AM, Stoica I, Wu XL. Complete genome sequence of Tsukamurella sp. MH1: A wide-chain length alkane-degrading actinomycete. J Biotechnol 2017; 268:1-5. [PMID: 29292131 DOI: 10.1016/j.jbiotec.2017.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 02/07/2023]
Abstract
Tsukamurella sp. strain MH1, capable to use a wide range of n-alkanes as the only carbon source, was isolated from petroleum-contaminated soil (Pitești, Romania) and its complete genome was sequenced. The 4,922,396 bp genome contains only one circular chromosome with a G + C content of 71.12%, much higher than the type strains of this genus (68.4%). Based on the 16S rRNA genes sequence similarity, strain MH1 was taxonomically identified as Tsukamurella carboxydivorans. Genome analyses revealed that strain MH1 is harboring only one gene encoding for the alkB-like hydroxylase, arranged in a complete alkane monooxygenase operon. This is the first complete genome of the specie T. carboxydivorans, which will provide insights into the potential of Tsukamurella sp. MH1 and related strains for bioremediation of petroleum hydrocarbons-contaminated sites and into the environmental role of these bacteria.
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Affiliation(s)
- Iulia Chiciudean
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China; Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China.
| | - Ana-Maria Tănase
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest 060101, Romania.
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, PR China.
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25
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Cheremnykh KM, Grishko VV, Ivshin IB. Bacterial degradation of ecotoxic dehydroabietic acid. CATALYSIS IN INDUSTRY 2017. [DOI: 10.1134/s207005041704002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Polycaprolactone-based scaffold for oil-selective sorption and improvement of bacteria activity for bioremediation of polluted water. Eur Polym J 2017. [DOI: 10.1016/j.eurpolymj.2017.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Catania V, Sarà G, Settanni L, Quatrini P. Bacterial communities in sediment of a Mediterranean marine protected area. Can J Microbiol 2017; 63:303-311. [DOI: 10.1139/cjm-2016-0406] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Biodiversity is crucial in preservation of ecosystems, and bacterial communities play an indispensable role for the functioning of marine ecosystems. The Mediterranean marine protected area (MPA) “Capo Gallo–Isola delle Femmine” was instituted to preserve marine biodiversity. The bacterial diversity associated with MPA sediment was compared with that from sediment of an adjacent harbour exposed to intense nautical traffic. The MPA sediment showed higher diversity with respect to the impacted site. A 16S rDNA clone library of the MPA sediment allowed the identification of 7 phyla: Proteobacteria (78%), Firmicutes (11%), Acidobacteria (3%), Actinobacteria (3%), Bacteroidetes (2%), Planctomycetes (2%), and Cyanobacteria (1%). Analysis of the hydrocarbon (HC)-degrading bacteria was performed using enrichment cultures. Most of the MPA sediment isolates were affiliated with Gram-positive G+C rich bacteria, whereas the majority of taxa in the harbour sediment clustered with Alpha- and Gammaproteobacteria; no Gram-positive HC degraders were isolated from the harbour sediment. Our results show that protection probably has an influence on bacterial diversity, and suggest the importance of monitoring the effects of protection at microbial level as well. This study creates a baseline of data that can be used to assess changes over time in bacterial communities associated with a Mediterranean MPA.
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Affiliation(s)
- Valentina Catania
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Gianluca Sarà
- Dipartimento di Scienze della Terra e del Mare (DISTEM), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
| | - Luca Settanni
- Dipartimento di Scienze Agrarie e Forestali (SAF), Università degli Studi di Palermo, Viale delle Scienze Ed.4 - 90128 Palermo, Italia
| | - Paola Quatrini
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università degli Studi di Palermo, Viale delle Scienze Ed.16 - 90128 Palermo, Italia
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Tourova TP, Sokolova DS, Semenova EM, Shumkova ES, Korshunova AV, Babich TL, Poltaraus AB, Nazina TN. Detection of n-alkane biodegradation genes alkB and ladA in thermophilic hydrocarbon-oxidizing bacteria of the genera Aeribacillus and Geobacillus. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716060199] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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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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Wang H, Wang B, Dong W, Hu X. Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures. Sci Rep 2016; 6:34588. [PMID: 27698451 PMCID: PMC5048299 DOI: 10.1038/srep34588] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/15/2016] [Indexed: 01/05/2023] Open
Abstract
Crude oil is a complex mixture of hydrocarbons with different structures; its components vary in bioavailability and toxicity. It is important to understand how bacterial communities response to different hydrocarbons and their co-acclimation in the process of degradation. In this study, microcosms with the addition of structurally different hydrocarbons were setup to investigate the successions of bacterial communities and the interactions between different bacterial taxa. Hydrocarbons were effectively degraded in all microcosms after 40 days. High-throughput sequencing offered a great quantity of data for analyzing successions of bacterial communities. The results indicated that the bacterial communities responded dramatically different to various hydrocarbons. KEGG database and PICRUSt were applied to predict functions of individual bacterial taxa and networks were constructed to analyze co-acclimations between functional bacterial groups. Almost all functional genes catalyzing degradation of different hydrocarbons were predicted in bacterial communities. Most of bacterial taxa were believed to conduct biodegradation processes via interactions with each other. This study addressed a few investigated area of bacterial community responses to structurally different organic pollutants and their co-acclimation and interactions in the process of biodegradation. The study could provide useful information to guide the bioremediation of crude oil pollution.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Bin Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Wenwen Dong
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Costal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
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Singh P, Chachan S, Singhi D, Srivastava P. Isolation and molecular characterization of a stationary phase promoter useful for gene expression in Gordonia. Gene 2016; 591:153-160. [DOI: 10.1016/j.gene.2016.07.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/29/2016] [Accepted: 07/05/2016] [Indexed: 11/25/2022]
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Mikolasch A, Reinhard A, Alimbetova A, Omirbekova A, Pasler L, Schumann P, Kabisch J, Mukasheva T, Schauer F. From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects. J Basic Microbiol 2016; 56:1252-1273. [PMID: 27624187 DOI: 10.1002/jobm.201600300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/06/2016] [Indexed: 12/30/2022]
Abstract
Heavy contamination of soils by crude oil is omnipresent in areas of oil recovery and exploitation. Bioremediation by indigenous plants in cooperation with hydrocarbon degrading microorganisms is an economically and ecologically feasible means to reclaim contaminated soils. To study the effects of indigenous soil bacteria capable of utilizing oil hydrocarbons on biomass production of plants growing in oil-contaminated soils eight bacterial strains were isolated from contaminated soils in Kazakhstan and characterized for their abilities to degrade oil components. Four of them, identified as species of Gordonia and Rhodococcus turned out to be effective degraders. They produced a variety of organic acids from oil components, of which 59 were identified and 7 of them are hitherto unknown acidic oil metabolites. One of them, Rhodococcus erythropolis SBUG 2054, utilized more than 140 oil components. Inoculating barley seeds together with different combinations of these bacterial strains restored normal growth of the plants on contaminated soils, demonstrating the power of this approach for bioremediation. Furthermore, we suggest that the plant promoting effect of these bacteria is not only due to the elimination of toxic oil hydrocarbons but possibly also to the accumulation of a variety of organic acids which modulate the barley's rhizosphere environment.
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Affiliation(s)
- Annett Mikolasch
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Anne Reinhard
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Anna Alimbetova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Anel Omirbekova
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Lisa Pasler
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Kabisch
- Institute of Biochemistry, University Greifswald, 17487, Greifswald, Germany
| | - Togzhan Mukasheva
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Frieder Schauer
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Greifswald, Germany
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33
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Liang JL, Nie Y, Wang M, Xiong G, Wang YP, Maser E, Wu XL. Regulation of alkane degradation pathway by a TetR family repressor via an autoregulation positive feedback mechanism in a Gram-positiveDietziabacterium. Mol Microbiol 2015; 99:338-59. [DOI: 10.1111/mmi.13232] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Jie-Liang Liang
- Department of Energy and Resources Engineering; College of Engineering; Peking University; Beijing 100871 China
| | - Yong Nie
- Department of Energy and Resources Engineering; College of Engineering; Peking University; Beijing 100871 China
| | - Miaoxiao Wang
- Department of Energy and Resources Engineering; College of Engineering; Peking University; Beijing 100871 China
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists; University Medical School; Schleswig-Holstein, Campus Kiel Kiel 24105 Germany
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research; College of Life Sciences; Peking University; Beijing 100871 China
| | - Edmund Maser
- Institute of Toxicology and Pharmacology for Natural Scientists; University Medical School; Schleswig-Holstein, Campus Kiel Kiel 24105 Germany
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering; College of Engineering; Peking University; Beijing 100871 China
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34
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Tsuboi S, Yamamura S, Nakajima-Kambe T, Iwasaki K. Diversity of alkane hydroxylase genes on the rhizoplane of grasses planted in petroleum-contaminated soils. SPRINGERPLUS 2015; 4:526. [PMID: 26405645 PMCID: PMC4575313 DOI: 10.1186/s40064-015-1312-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 09/07/2015] [Indexed: 11/10/2022]
Abstract
The study investigated the diversity and genotypic features of alkane hydroxylase genes on rhizoplanes of grasses planted in artificial petroleum-contaminated soils to acquire new insights into the bacterial communities responsible for petroleum degradation in phytoremediation. Four types of grass (Cynodon dactylon, two phenotypes of Zoysia japonica, and Z. matrella) were used. The concentrations of total petroleum hydrocarbon effectively decreased in the grass-planted systems compared with the unplanted system. Among the representative alkane hydroxylase genes alkB, CYP153, almA and ladA, the first two were detected in this study, and the genotypes of both genes were apparently different among the systems studied. Their diversity was also higher on the rhizoplanes of the grasses than in unplanted oil-contaminated soils. Actinobacteria-related genes in particular were among the most diverse alkane hydroxylase genes on the rhizoplane in this study, indicating that they are one of the main contributors to degrading alkanes in oil-contaminated soils during phytoremediation. Actinobacteria-related alkB genes and CYP153 genes close to the genera Parvibaculum and Aeromicrobium were found in significant numbers on the rhizoplanes of grasses. These results suggest that the increase in diversity and genotype differences of the alkB and CYP153 genes are important factors affecting petroleum hydrocarbon-degrading ability during phytoremediation.
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Affiliation(s)
- Shun Tsuboi
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan ; National Institute for Environmental Studies (NIES), Center for Environmental Biology and Ecosystem Studies, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Shigeki Yamamura
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Toshiaki Nakajima-Kambe
- Faculty of Life and Environmental Sciences (Bioindustrial Sciences), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Japan
| | - Kazuhiro Iwasaki
- National Institute for Environmental Studies (NIES), Center for Regional Environmental Research, 16-2 Onogawa, Tsukuba, 305-8506 Japan
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35
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Metabolic responses of Rhodococcus erythropolis PR4 grown on diesel oil and various hydrocarbons. Appl Microbiol Biotechnol 2015; 99:9745-59. [DOI: 10.1007/s00253-015-6936-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
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36
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Mikolasch A, Omirbekova A, Schumann P, Reinhard A, Sheikhany H, Berzhanova R, Mukasheva T, Schauer F. Enrichment of aliphatic, alicyclic and aromatic acids by oil-degrading bacteria isolated from the rhizosphere of plants growing in oil-contaminated soil from Kazakhstan. Appl Microbiol Biotechnol 2015; 99:4071-84. [PMID: 25592733 DOI: 10.1007/s00253-014-6320-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/09/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
Three microbial strains were isolated from the rhizosphere of alfalfa (Medicago sativa), grass mixture (Festuca rubra, 75 %; Lolium perenne, 20 %; Poa pratensis, 10 %), and rape (Brassica napus) on the basis of their high capacity to use crude oil as the sole carbon and energy source. These isolates used an unusually wide spectrum of hydrocarbons as substrates (more than 80), including n-alkanes with chain lengths ranging from C12 to C32, monomethyl- and monoethyl-substituted alkanes (C12-C23), n-alkylcyclo alkanes with alkyl chain lengths from 4 to 18 carbon atoms, as well as substituted monoaromatic and diaromatic hydrocarbons. These three strains were identified as Gordonia rubripertincta and Rhodococcus sp. SBUG 1968. During their transformation of this wide range of hydrocarbon substrates, a very large number of aliphatic, alicyclic, and aromatic acids was detected, 44 of them were identified by GC/MS analyses, and 4 of them are described as metabolites for the first time. Inoculation of plant seeds with these highly potent bacteria had a beneficial effect on shoot and root development of plants which were grown on oil-contaminated sand.
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Affiliation(s)
- Annett Mikolasch
- Department of Applied Microbiology, Institute of Microbiology, University Greifswald, Friedrich-Ludwig-Jahn-Str. 15, 17487, Greifswald, Germany,
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Zampolli J, Collina E, Lasagni M, Di Gennaro P. Biodegradation of variable-chain-length n-alkanes in Rhodococcus opacus R7 and the involvement of an alkane hydroxylase system in the metabolism. AMB Express 2014; 4:73. [PMID: 25401074 PMCID: PMC4230829 DOI: 10.1186/s13568-014-0073-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/05/2014] [Indexed: 01/31/2023] Open
Abstract
Rhodococcus opacus R7 is a Gram-positive bacterium isolated from a polycyclic aromatic hydrocarbon contaminated soil for its versatile metabolism; indeed the strain is able to grow on naphthalene, o-xylene, and several long- and medium-chain n-alkanes. In this work we determined the degradation of n-alkanes in Rhodococcus opacus R7 in presence of n-dodecane (C12), n-hexadecane (C16), n-eicosane (C20), n-tetracosane (C24) and the metabolic pathway in presence of C12. The consumption rate of C12 was 88%, of C16 was 69%, of C20 was 51% and of C24 it was 78%. The decrement of the degradation rate seems to be correlated to the length of the aliphatic chain of these hydrocarbons. On the basis of the metabolic intermediates determined by the R7 growth on C12, our data indicated that R. opacus R7 metabolizes medium-chain n-alkanes by the primary alcohol formation. This represents a difference in comparison with other Rhodococcus strains, in which a mixture of the two alcohols was observed. By GC-MSD analysis we also identified the monocarboxylic acid, confirming the terminal oxidation. Moreover, the alkB gene cluster from R. opacus R7 was isolated and its involvement in the n-alkane degradation system was investigated by the cloning of this genomic region into a shuttle-vector E. coli-Rhodococcus to evaluate the alkane hydroxylase activity. Our results showed an increased biodegradation of C12 in the recombinant strain R. erythropolis AP (pTipQT1-alkR7) in comparison with the wild type strain R. erythropolis AP. These data supported the involvement of the alkB gene cluster in the n-alkane degradation in the R7 strain.
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Jain CK, Gupta M, Prasad Y, Wadhwa G, Sharma SK. Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights. J Mol Model 2014; 20:2340. [PMID: 24990796 DOI: 10.1007/s00894-014-2340-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 06/08/2014] [Indexed: 12/23/2022]
Abstract
The degradation of hydrocarbons plays an important role in the eco-balancing of petroleum products, pesticides and other toxic products in the environment. The degradation of hydrocarbons by microbes such as Geobacillus thermodenitrificans, Burkhulderia, Gordonia sp. and Acinetobacter sp. has been studied intensively in the literature. The present study focused on the in silico protein engineering of alkane monooxygenase (ladA)-a protein involved in the alkane degradation pathway. We demonstrated the improvement in substrate binding energy with engineered ladA in Burkholderia thailandensis MSMB121. We identified an ortholog of ladA monooxygenase found in B. thailandensis MSMB121, and showed it to be an enzyme involved in an alkane degradation pathway studied extensively in Geobacillus thermodenitrificans. Homology modeling of the three-dimensional structure of ladA was performed with a crystal structure (protein databank ID: 3B9N) as a template in MODELLER 9v11, and further validated using PROCHECK, VERIFY-3D and WHATIF tools. Specific amino acids were substituted in the region corresponding to amino acids 305-370 of ladA protein, resulting in an enhancement of binding energy in different alkane chain molecules as compared to wild protein structures in the docking experiments. The substrate binding energy with the protein was calculated using Vina (Implemented in VEGAZZ). Molecular dynamics simulations were performed to study the dynamics of different alkane chain molecules inside the binding pockets of wild and mutated ladA. Here, we hypothesize an improvement in binding energies and accessibility of substrates towards engineered ladA enzyme, which could be further facilitated for wet laboratory-based experiments for validation of the alkane degradation pathway in this organism.
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Affiliation(s)
- Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA, Uttar Pradesh, 201307, India,
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Luo Q, Hiessl S, Poehlein A, Daniel R, Steinbüchel A. Insights into the microbial degradation of rubber and gutta-percha by analysis of the complete genome of Nocardia nova SH22a. Appl Environ Microbiol 2014; 80:3895-907. [PMID: 24747905 PMCID: PMC4054215 DOI: 10.1128/aem.00473-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/14/2014] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.
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Affiliation(s)
- Quan Luo
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany King Abdulaziz University, Faculty of Biology, Jeddah, Saudi Arabia
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40
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Nie Y, Chi CQ, Fang H, Liang JL, Lu SL, Lai GL, Tang YQ, Wu XL. Diverse alkane hydroxylase genes in microorganisms and environments. Sci Rep 2014; 4:4968. [PMID: 24829093 PMCID: PMC4021335 DOI: 10.1038/srep04968] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/07/2014] [Indexed: 11/08/2022] Open
Abstract
AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.
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Affiliation(s)
- Yong Nie
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Chang-Qiao Chi
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Hui Fang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Jie-Liang Liang
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - She-Lian Lu
- College of Engineering, Peking University, Beijing 100871, P. R. China
| | - Guo-Li Lai
- College of Engineering, Peking University, Beijing 100871, P. R. China
- Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, China
| | - Yue-Qin Tang
- College of Engineering, Peking University, Beijing 100871, P. R. China
- College of Architecture and Environment, Sichuan University, Chengdu, 610065, China
| | - Xiao-Lei Wu
- College of Engineering, Peking University, Beijing 100871, P. R. China
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Procópio L, de Cassia Pereira e Silva M, van Elsas JD, Seldin L. Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain. Braz J Microbiol 2013; 44:633-41. [PMID: 24294263 PMCID: PMC3833169 DOI: 10.1590/s1517-83822013000200044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022] Open
Abstract
The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.
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Affiliation(s)
- Luciano Procópio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Ilha do Fundão, Rio de Janeiro, RJ, Brazil. ; Department of Microbial Ecology, University of Groningen, Kerklaan, Haren, The Netherlands
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42
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Bertrand EM, Keddis R, Groves JT, Vetriani C, Austin RN. Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents. Front Microbiol 2013; 4:109. [PMID: 23825470 PMCID: PMC3695450 DOI: 10.3389/fmicb.2013.00109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/16/2013] [Indexed: 12/21/2022] Open
Abstract
Six aerobic alkanotrophs (organism that can metabolize alkanes as their sole carbon source) isolated from deep-sea hydrothermal vents were characterized using the radical clock substrate norcarane to determine the metalloenzyme and reaction mechanism used to oxidize alkanes. The organisms studied were Alcanivorax sp. strains EPR7 and MAR14, Marinobacter sp. strain EPR21, Nocardioides sp. strains EPR26w, EPR28w, and Parvibaculum hydrocarbonoclasticum strain EPR92. Each organism was able to grow on n-alkanes as the sole carbon source and therefore must express genes encoding an alkane-oxidizing enzyme. Results from the oxidation of the radical-clock diagnostic substrate norcarane demonstrated that five of the six organisms (EPR7, MAR14, EPR21, EPR26w, and EPR28w) used an alkane hydroxylase functionally similar to AlkB to catalyze the oxidation of medium-chain alkanes, while the sixth organism (EPR92) used an alkane-oxidizing cytochrome P450 (CYP)-like protein to catalyze the oxidation. DNA sequencing indicated that EPR7 and EPR21 possess genes encoding AlkB proteins, while sequencing results from EPR92 confirmed the presence of a gene encoding CYP-like alkane hydroxylase, consistent with the results from the norcarane experiments.
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Affiliation(s)
- Erin M Bertrand
- Department of Chemistry, Bates College Lewiston, ME, USA ; Microbial and Environmental Genomics, J. Craig Venter Institute San Diego, CA, USA
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43
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Wang Y, San KY, Bennett GN. Cofactor engineering for advancing chemical biotechnology. Curr Opin Biotechnol 2013; 24:994-9. [PMID: 23611567 DOI: 10.1016/j.copbio.2013.03.022] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 03/21/2013] [Accepted: 03/22/2013] [Indexed: 11/26/2022]
Abstract
Cofactors provide redox carriers for biosynthetic reactions, catabolic reactions and act as important agents in transfer of energy for the cell. Recent advances in manipulating cofactors include culture conditions or additive alterations, genetic modification of host pathways for increased availability of desired cofactor, changes in enzyme cofactor specificity, and introduction of novel redox partners to form effective circuits for biochemical processes and biocatalysts. Genetic strategies to employ ferredoxin, NADH and NADPH most effectively in natural or novel pathways have improved yield and efficiency of large-scale processes for fuels and chemicals and have been demonstrated with a variety of microbial organisms.
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Affiliation(s)
- Yipeng Wang
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
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44
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Distribution of Hydrocarbon-Degrading Bacteria in the Soil Environment and Their Contribution to Bioremediation. Appl Biochem Biotechnol 2013; 170:329-39. [DOI: 10.1007/s12010-013-0170-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 02/28/2013] [Indexed: 11/26/2022]
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Characterization of a CYP153 alkane hydroxylase gene in a Gram-positive Dietzia sp. DQ12-45-1b and its "team role" with alkW1 in alkane degradation. Appl Microbiol Biotechnol 2013; 98:163-73. [PMID: 23504079 DOI: 10.1007/s00253-013-4821-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 02/26/2013] [Indexed: 01/07/2023]
Abstract
CYP153 and AlkB-like hydroxylases were recently discovered in Gram-positive alkane-degrading bacteria. However, it is unclear whether they cooperate with each other in alkane degradation as they do in Gram-negative bacteria. In this paper, we cloned the CYP153 gene from a representative Gram-positive alkane-degrading bacterium, Dietzia sp. DQ12-45-1b. The CYP153 gene transcription in Dietzia sp. DQ12-45-1b and heterologous expression in alkB gene knockout mutant strain Pseudomonas fluorescens KOB2∆1 both confirmed the functions of CYP153 on C6-C10 n-alkanes degradation, but not on longer chain-length n-alkanes. In addition, substrate-binding analysis of the purified CYP153 protein revealed different substrate affinities to C6-C16 n-alkanes, confirming n-alkanes binding to CYP153 protein. Along with AlkW1, an AlkB-like alkane hydroxylase in Dietzia sp. DQ12-45-1b, a teamwork pattern was found in n-alkane degradation, i.e. CYP153 was responsible for hydroxylating n-alkanes shorter than C10 while AlkW1 was responsible for those longer than C14. Further sequence analysis suggested that the high horizontal gene transfer (HGT) potential of CYP153 genes may be universal in Gram-positive alkane-degrading actinomycetes that contain both alkB and CYP153 genes.
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46
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Drzyzga O. The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential. Crit Rev Microbiol 2012; 38:300-16. [PMID: 22551505 DOI: 10.3109/1040841x.2012.668134] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This review about the genus Gordonia provides a current overview of recent research on a young genus that was introduced in the year 1997 ( Stackebrandt et al., 1997 ). This emerging genus has attracted increasing environmental, industrial, biotechnological and medical interest during the last few years, in particular due to the capabilities of its members to degrade, transform, and synthesize organic compounds as well as to the pathogenic effects that have been described in many case studies. The number of publications about Gordonia has increased significantly after the year 2004 (the year of the first Gordonia review published by Arenskötter et al.) describing 13 new validly published species (type strains), many newly described physiological and metabolic capabilities, new patent applications and many new case reports of bacterial infections. Members of the genus Gordonia are widely distributed in nature and it is therefore important to unravel the species richness and metabolic potential of gordoniae in future studies to demonstrate their environmental impact especially on the degradation of persistent organic compounds and their ecological participation in the carbon cycle of organic material in soil and water. This review summarizes mainly the current state of importance and potential of the members of this genus for the environmental and biotechnological industry ("the strengthsâ) and briefly its pathogenic impact to humans ("the weaknessesâ).
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Affiliation(s)
- Oliver Drzyzga
- Department of Biochemistry and Molecular Biology I, Complutense University of Madrid, Madrid, Spain.
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47
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Gallo G, Lo Piccolo L, Renzone G, La Rosa R, Scaloni A, Quatrini P, Puglia AM. Differential proteomic analysis of an engineered Streptomyces coelicolor strain reveals metabolic pathways supporting growth on n-hexadecane. Appl Microbiol Biotechnol 2012; 94:1289-301. [DOI: 10.1007/s00253-012-4046-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/16/2012] [Accepted: 03/19/2012] [Indexed: 12/12/2022]
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De Pasquale C, Palazzolo E, Lo Piccolo L, Quatrini P. Degradation of long-chain n-alkanes in soil microcosms by two actinobacteria. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2012; 47:374-381. [PMID: 22320689 DOI: 10.1080/10934529.2012.645786] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability of two recently isolated actinobacteria, that degrade medium and long chain n-alkanes in laboratory water medium, was investigated in soil microcosms using different standard soils that were artificially contaminated with n-alkanes of different length (C(12)- C(20)- C(24)- C(30)). The two strains, identified as Nocardia sp. SoB and Gordonia sp. SoCp, revealed a similar high HC degradation efficiency with an average of 75% alkane degraded after 28 days incubation. A selectivity of bacteria towards n-alkanes of different length was detected as well as a consistent effect of soil texture and other soil physical chemical characteristics on degradation. It was demonstrated the specific aptitude of these selected strains towards specific environmental conditions.
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Affiliation(s)
- Claudio De Pasquale
- Dipartimento dei Sistemi Agro-Ambientali (SAgA), Università degli Studi di Palermo, Palermo, Italy.
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Nie Y, Liang J, Fang H, Tang YQ, Wu XL. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl Environ Microbiol 2011; 77:7279-88. [PMID: 21873474 PMCID: PMC3194844 DOI: 10.1128/aem.00203-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.
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Affiliation(s)
- Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Jieliang Liang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
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