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Wu R, Xia H, Wu Y, Zhang S, Fang J, Wang Y, Wang H, Zhu Y, Liu L, Du S. Graphene oxide inhibits the transfer of ARGs in rice by reducing the root endophytic bacterial complexity. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 368:122241. [PMID: 39186855 DOI: 10.1016/j.jenvman.2024.122241] [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: 06/04/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/28/2024]
Abstract
Antibiotic resistance genes (ARGs) as an emerging contaminant have attracted much attention for their transfer in agricultural ecosystems. Meanwhile, graphene oxide (GO), due to its high adsorption capacity and antibacterial properties, poses potential environmental ecological risks to the occurrence of ARGs, bacteria, and plant physiological ecology. However, the impact and mechanism of GO on the transfer of ARGs in host plants remain unclear. Therefore, this study selected rice as the research object and inoculated Bacillus subtilis carrying ARGs to investigate the influence of GO on the migration of ARGs into rice and its microbiological mechanism. The study found that GO had a certain inhibitory effect on the transfer of ARGs in rice. Although GO reduced the rhizosphere pH in rice, leading to a transition in endophytic bacteria from dominance by Burkholderia to dominance by Gordonia, this process did not directly affect the transfer of ARGs in rice. Further analysis of bacterial interactions revealed that GO could inhibit the transfer of ARGs in rice by reducing the network complexity of endophytic bacteria. Additionally, GO inhibited the formation of endophytic bacterial biofilms and mobile elements, which might affect ARGs' migration in rice. This study elucidated the key microbiological ecological processes of GO on the transfer of ARGs in rice, providing fundamental information for the ecological risk assessment of GO.
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Affiliation(s)
- Ran Wu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hanche Xia
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Yue Wu
- Zhejiang Zhongyi Testing Research Institute Co., Ltd, Ningbo, 315040, China
| | - Siyu Zhang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Jin Fang
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yuying Wang
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Hua Wang
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yaxin Zhu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Lijuan Liu
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China
| | - Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou, 310015, China.
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Jansen Z, Alameri A, Wei Q, Kulhanek DL, Gilmour AR, Halper S, Schwalm ND, Thyer R. A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation. Appl Environ Microbiol 2024; 90:e0034024. [PMID: 39082821 PMCID: PMC11337820 DOI: 10.1128/aem.00340-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/29/2024] [Indexed: 08/22/2024] Open
Abstract
Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.
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Affiliation(s)
- Zachary Jansen
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Abdulaziz Alameri
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Qiyao Wei
- Department of Bioengineering, Rice University, Houston, Texas, USA
| | - Devon L. Kulhanek
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Andrew R. Gilmour
- Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas, USA
| | - Sean Halper
- DEVCOM Army Research Laboratory, Adelphi, Maryland, USA
| | | | - Ross Thyer
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
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Ngo ACR, Celebi B, Hermann Hadewig SN, Mügge C, Tischler D. Selective pressure leads to an improved synthetic consortium fit for dye degradation. CHEMOSPHERE 2024; 361:142489. [PMID: 38825247 DOI: 10.1016/j.chemosphere.2024.142489] [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: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
Microorganisms have great potential for bioremediation as they have powerful enzymes and machineries that can transform xenobiotics. The use of a microbial consortium provides more advantages in application point of view than pure cultures due to cross-feeding, adaptations, functional redundancies, and positive interactions among the organisms. In this study, we screened about 107 isolates for their ability to degrade dyes in aerobic conditions and without additional carbon source. From our screening results, we finally limited our synthetic consortium to Gordonia and Rhodococcus isolates. The synthetic consortium was trained and optimized for azo dye degradation using sequential treatment of small aromatic compounds such as phenols that act as selective pressure agents. After four rounds of optimization with different aims for each round, the consortium was able to decolorize and degrade various dyes after 48 h (80%-100% for brilliant black bn, methyl orange, and chromotrop 2b; 50-70% for orange II and reactive orange 16; 15-30% for chlorazol black e, reactive red 120, and allura red ac). Through rational approaches, we can show that treatment with phenolic compounds at micromolar dosages can significantly improve the degradation of bulky dyes and increase its substrate scope. Moreover, our selective pressure approach led to the production of various dye-degrading enzymes as azoreductase, laccase-like, and peroxidase-like activities were detected from the phenol-treated consortium. Evidence of degradation was also shown as metabolites arising from the degradation of methyl red and brilliant black bn were detected using HPLC and LC-MS analysis. Therefore, this study establishes the importance of rational and systematic screening and optimization of a consortium. Not only can this approach be applied to dye degradation, but this study also offers insights into how we can fully maximize microbial consortium activity for other applications, especially in biodegradation and biotransformation.
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Affiliation(s)
| | - Beyzanur Celebi
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | | | - Carolin Mügge
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr Universität Bochum, Bochum, Germany
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Grimm D, Guy N, Lengyel G, Franks J, Maltman C. Gordonia metallireducens sp. nov., a tellurite- and selenite-resistant bacterium isolated from the sediment of an acid mine drainage stream. Int J Syst Evol Microbiol 2023; 73. [PMID: 37990983 DOI: 10.1099/ijsem.0.006176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
A polyphasic taxonomic study was carried out on strain TSed Te1T, isolated from sediment of a stream contaminated with acid drainage from a coal mine. The bacterium forms pink-pigmented colonies and has a rod-coccus growth cycle, which also includes some coryneform arrangements. This bacterium is capable of growing in the presence of up to 750 μg ml-1 tellurite and 5000 μg ml-1 selenite, reducing each to elemental form. Nearly complete 16S rRNA gene sequence analysis associated the strain with Gordonia, with 99.5 and 99.3 % similarity to Gordonia namibiensis and Gordonia rubripertincta, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization comparisons with the closest phylogenetic neighbour of TSed Te1T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids were C16 : 0, C18 : 1, C16 : 1 and tuberculostearic acid. The DNA G+C content was 67.6 mol%. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside, while MK-9(H2) was the only menaquinone found. Mycolic acids of C56-C60 were present. Whole-cell hydrolysates contained meso-diaminopimelic acid along with arabinose and galactose as the major cell-wall sugars. On the basis of the results obtained in this study, the bacterium was assigned to the genus Gordonia and represents a new species with the name Gordonia metallireducens sp. nov. The type strain is TSed Te1T (=NRRL B-65678T=DSM 114093T).
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Affiliation(s)
- David Grimm
- Department of Microbiology, Miami University College of Arts and Science, Oxford, Ohio 45056, USA
| | - Nathan Guy
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - George Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, Pennsylvania, USA
| | - Jonathan Franks
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, Pennsylvania 16057, USA
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5
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Frantsuzova E, Bogun A, Vetrova A, Delegan Y. Methods of Identifying Gordonia Strains in Clinical Samples. Pathogens 2022; 11:pathogens11121496. [PMID: 36558832 PMCID: PMC9786905 DOI: 10.3390/pathogens11121496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.
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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
| | - 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
| | - 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
- Correspondence:
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Sarkar B, Mandal S. Gordonia sp. BSTG01 isolated from Hevea brasiliensis plantation efficiently degrades polyisoprene (rubber). 3 Biotech 2021; 11:508. [PMID: 34881168 DOI: 10.1007/s13205-021-03063-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 12/17/2022] Open
Abstract
Polyisoprene is the principal constituent of rubber latex which has been estimated globally as one of the major solid wastes. Bacterial bioremediation of this solid waste remains a major point of interest for scientists. This study reports a Gram-positive, non-motile, non-spore-forming actinomycete Gordonia sp. BSTG01, isolated from the bark of Hevea brasiliensis of a rubber plantation garden can considerably degrade natural rubber (NR) and synthetic polyisoprene rubber (SR). Scanning electron microscopy showed adhesive colonization of strain BSTG01 on both natural and synthetic rubber surface, conflating into the rubber and forming a biofilm. Rubber-dependent growth of the strain was examined by the decrease of rubber mass and increase of its total protein content in a time-dependent manner. Degradation was also verified by Schiff's reagent which confirms the appearance of aldehydes in the culture media. Fourier transform infrared spectroscopy including the attenuated total reflectance with the NR and SR pieces overgrown by the isolate revealed variations of the overall chemicals arising on the polyisoprene backbone due to the degradation of rubber by the strain BSTG01. Isolate BSTG01 (MTCC 13159) is a strain of Gordonia and this is the first strain isolated from unexplored rubber plantation area with considerable rubber degradation properties. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03063-5.
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Affiliation(s)
- Biraj Sarkar
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019 India
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Oliveira AS, Amorim CL, Zlopasa J, van Loosdrecht M, Castro PML. Recovered granular sludge extracellular polymeric substances as carrier for bioaugmentation of granular sludge reactor. CHEMOSPHERE 2021; 275:130037. [PMID: 33667767 DOI: 10.1016/j.chemosphere.2021.130037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 06/12/2023]
Abstract
An increasing amount of industrial chemicals are being released into wastewater collection systems and indigenous microbial communities in treatment plants are not always effective for their removal. In this work, extracellular polymeric substances (EPS) recovered from aerobic granular sludge (AGS) were used as a natural carrier to immobilize a specific microbial strain, Rhodococcus sp. FP1, able to degrade 2-fluorophenol (2-FP). The produced EPS granules exhibited a 2-FP degrading ability of 100% in batch assays, retaining their original activity after up to 2-months storage. Furthermore, EPS granules were added to an AGS reactor intermittently fed with saline wastewater containing 2-FP. Degradation of 2-FP and stoichiometric fluorine release occurred 8 and 35 days after bioaugmentation, respectively. Chemical oxygen demand removal was not significantly impaired by 2-FP or salinity loads. Nutrients removal was impaired by 2-FP load, but after bioaugmentation, the phosphate and ammonium removal efficiency improved from 14 to 46% and from 25 to 42%, respectively. After 2-FP feeding ceased, at low/moderate salinity (0.6-6.0 g L-1 NaCl), ammonium removal was completely restored, and phosphate removal efficiency increased. After bioaugmentation, 11 bacteria isolated from AGS were able to degrade 2-FP, indicating that horizontal gene transfer could have occurred in the reactor. The improvement of bioreactor performance after bioaugmentation with EPS immobilized bacteria and the maintenance of cell viability through storage are the main advantages of the use of this natural microbial carrier for bioaugmentation, which can benefit wastewater treatment processes.
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Affiliation(s)
- Ana S Oliveira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Catarina L Amorim
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
| | - Jure Zlopasa
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Mark van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Paula M L Castro
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
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8
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Basik AA, Sanglier JJ, Yeo CT, Sudesh K. Microbial Degradation of Rubber: Actinobacteria. Polymers (Basel) 2021; 13:polym13121989. [PMID: 34204568 PMCID: PMC8235351 DOI: 10.3390/polym13121989] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
Rubber is an essential part of our daily lives with thousands of rubber-based products being made and used. Natural rubber undergoes chemical processes and structural modifications, while synthetic rubber, mainly synthetized from petroleum by-products are difficult to degrade safely and sustainably. The most prominent group of biological rubber degraders are Actinobacteria. Rubber degrading Actinobacteria contain rubber degrading genes or rubber oxygenase known as latex clearing protein (lcp). Rubber is a polymer consisting of isoprene, each containing one double bond. The degradation of rubber first takes place when lcp enzyme cleaves the isoprene double bond, breaking them down into the sole carbon and energy source to be utilized by the bacteria. Actinobacteria grow in diverse environments, and lcp gene containing strains have been detected from various sources including soil, water, human, animal, and plant samples. This review entails the occurrence, physiology, biochemistry, and molecular characteristics of Actinobacteria with respect to its rubber degrading ability, and discusses possible technological applications based on the activity of Actinobacteria for treating rubber waste in a more environmentally responsible manner.
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Affiliation(s)
- Ann Anni Basik
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Jean-Jacques Sanglier
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Chia Tiong Yeo
- Sarawak Biodiversity Centre, Km. 20 Jalan Borneo Heights, Semengoh, Kuching, Sarawak 93250, Malaysia; (J.-J.S.); (C.T.Y.)
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
- Correspondence: ; Tel.: +60-4-6534367; Fax: +60-4-6565125
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Larke-Mejía NL, Crombie AT, Pratscher J, McGenity TJ, Murrell JC. Novel Isoprene-Degrading Proteobacteria From Soil and Leaves Identified by Cultivation and Metagenomics Analysis of Stable Isotope Probing Experiments. Front Microbiol 2019; 10:2700. [PMID: 31866954 PMCID: PMC6908491 DOI: 10.3389/fmicb.2019.02700] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/07/2019] [Indexed: 02/01/2023] Open
Abstract
Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with 13C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the 13C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of 13C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the α-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.
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Affiliation(s)
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Terry J McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
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10
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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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11
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Kepenek ES, Gozen AG, Severcan F. Molecular characterization of acutely and gradually heavy metal acclimated aquatic bacteria by FTIR spectraoscopy. JOURNAL OF BIOPHOTONICS 2019; 12:e201800301. [PMID: 30578608 DOI: 10.1002/jbio.201800301] [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: 08/16/2018] [Revised: 11/11/2018] [Accepted: 12/19/2018] [Indexed: 05/28/2023]
Abstract
In the environment, bacteria can be exposed to the concentration gradient of toxic heavy metals (gradual) or sudden high concentration of them (acute). In both situations, bacteria get acclimated to toxic heavy metal concentrations. Acclimation causes metabolic and molecular changes in bacteria. In this study, we aimed to understand whether there are differences between molecular profiles of the bacteria (Brevundimonas, Gordonia and Microbacterium) which are under acute or gradual exposure to cadmium or lead by using ATR-FTIR spectroscopy. Our results revealed the differences between the acclimation groups in membrane dynamics including changes in the structure and composition of the membrane lipids and proteins. Furthermore, protein concentrations decreased in acclimated bacterial groups. Also, a remarkable increase in exopolymer production occurred in acclimated groups. Interestingly, bacteria under acute cadmium exposure produced the significantly higher amount of exopolymer than they did under gradual exposure. On the contrary, under lead exposure gradually acclimate strains produced significantly higher amounts of exopolymer than those of acutely acclimated ones. This information can be used in bioremediation studies to obtain bacterial strains producing a higher amount of exopolymer.
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Affiliation(s)
- Eda S Kepenek
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ayse G Gozen
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Istanbul Altınbas University, Istanbul, Turkey
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12
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Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2017; 44:393-413. [PMID: 29276839 DOI: 10.1080/1040841x.2017.1418286] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.
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Affiliation(s)
- Harshada Sowani
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Mohan Kulkarni
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Smita Zinjarde
- b Institute of Bioinformatics and Biotechnology , Savitribai Phule Pune University , Pune , India.,c Department of Microbiology , Savitribai Phule Pune University , Pune , India
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Sun S, Chen Y, Li L. Enhanced degradation of lignin by the strain fusion of Pseudomonas putida and Gordonia sp. BIOCATAL BIOTRANSFOR 2016. [DOI: 10.1080/10242422.2016.1247814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Shiying Sun
- Guangdong Testing Institute of Product Quality Supervision, Guangzhou, China,
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, State Key Laboratory of Pulp and Paper Engineering, College of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, PR
| | - Yuancai Chen
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, State Key Laboratory of Pulp and Paper Engineering, College of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, PR
| | - Lianghao Li
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, State Key Laboratory of Pulp and Paper Engineering, College of Environment and Energy, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, PR
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Silva TP, Paixão SM, Alves L. Ability of Gordonia alkanivorans strain 1B for high added value carotenoids production. RSC Adv 2016. [DOI: 10.1039/c6ra08126f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Currently, carotenoids are valuable bioactive molecules for several industries, such as chemical, pharmaceutical, food and cosmetics, due to their multiple benefits as natural colorants, antioxidants and vitamin precursors.
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Affiliation(s)
- Tiago P. Silva
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - Susana M. Paixão
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
| | - Luís Alves
- LNEG – Laboratório Nacional de Energia e Geologia, IP
- Unidade de Bioenergia
- 1649-038 Lisboa
- Portugal
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Hesham AEL, Mohamed NH, Ismail MA, Shoreit AAM. Degradation of natural rubber latex by new Streptomyces labedae strain ASU-03 isolated from Egyptian soil. Microbiology (Reading) 2015; 84:351-358. [DOI: 10.1134/s0026261715030078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
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16
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Vázquez-Boland JA, Giguère S, Hapeshi A, MacArthur I, Anastasi E, Valero-Rello A. Rhodococcus equi: the many facets of a pathogenic actinomycete. Vet Microbiol 2013; 167:9-33. [PMID: 23993705 DOI: 10.1016/j.vetmic.2013.06.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 06/27/2013] [Indexed: 12/20/2022]
Abstract
Rhodococcus equi is a soil-dwelling pathogenic actinomycete that causes pulmonary and extrapulmonary pyogranulomatous infections in a variety of animal species and people. Young foals are particularly susceptible and develop a life-threatening pneumonic disease that is endemic at many horse-breeding farms worldwide. R. equi is a facultative intracellular parasite of macrophages that replicates within a modified phagocytic vacuole. Its pathogenicity depends on a virulence plasmid that promotes intracellular survival by preventing phagosome-lysosome fusion. Species-specific tropism of R. equi for horses, pigs and cattle appears to be determined by host-adapted virulence plasmid types. Molecular epidemiological studies of these plasmids suggest that human R. equi infection is zoonotic. Analysis of the recently determined R. equi genome sequence has identified additional virulence determinants on the bacterial chromosome. This review summarizes our current understanding of the clinical aspects, biology, pathogenesis and immunity of this fascinating microbe with plasmid-governed infectivity.
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Affiliation(s)
- José A Vázquez-Boland
- Microbial Pathogenesis Unit, School of Biomedical Sciences and Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH9 3JT, UK; Grupo de Patogenómica Bacteriana, Facultad de Veterinaria, Universidad de León, 24071 León, Spain.
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Microbial gutta-percha degradation shares common steps with rubber degradation by Nocardia nova SH22a. Appl Environ Microbiol 2012; 79:1140-9. [PMID: 23220954 DOI: 10.1128/aem.03016-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocardia nova SH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 × 10(7) CFU per μg of plasmid DNA was achieved. By applying this optimized protocol to N. nova SH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an α-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, β-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP.
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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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Involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of Gordonia polyisoprenivorans strain VH2. Appl Environ Microbiol 2012; 78:2874-87. [PMID: 22327575 DOI: 10.1128/aem.07969-11] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search.
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Functional characterization of pGKT2, a 182-kilobase plasmid containing the xplAB genes, which are involved in the degradation of hexahydro-1,3,5-trinitro-1,3,5-triazine by Gordonia sp. strain KTR9. Appl Environ Microbiol 2010; 76:6329-37. [PMID: 20709853 DOI: 10.1128/aem.01217-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several microorganisms have been isolated that can transform hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a cyclic nitramine explosive. To better characterize the microbial genes that facilitate this transformation, we sequenced and annotated a 182-kb plasmid, pGKT2, from the RDX-degrading strain Gordonia sp. KTR9. This plasmid carries xplA, encoding a protein sharing up to 99% amino acid sequence identity with characterized RDX-degrading cytochromes P450. Other genes that cluster with xplA are predicted to encode a glutamine synthase-XplB fusion protein, a second cytochrome P450, Cyp151C, and XplR, a GntR-type regulator. Rhodococcus jostii RHA1 expressing xplA from KTR9 degraded RDX but did not utilize RDX as a nitrogen source. Moreover, an Escherichia coli strain producing XplA degraded RDX but a strain producing Cyp151C did not. KTR9 strains cured of pGKT2 did not transform RDX. Physiological studies examining the effects of exogenous nitrogen sources on RDX degradation in strain KTR9 revealed that ammonium, nitrite, and nitrate each inhibited RDX degradation by up to 79%. Quantitative real-time PCR analysis of glnA-xplB, xplA, and xplR showed that transcript levels were 3.7-fold higher during growth on RDX than during growth on ammonium and that this upregulation was repressed in the presence of various inorganic nitrogen sources. Overall, the results indicate that RDX degradation by KTR9 is integrated with central nitrogen metabolism and that the uptake of RDX by bacterial cells does not require a dedicated transporter.
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Intapun J, Sainte-Beuve J, Bonfils F, Tanrattanakul V, Dubreucq E, Vaysse L. Effect of microorganisms during the initial coagulum maturation of Hevea natural rubber. J Appl Polym Sci 2010. [DOI: 10.1002/app.32331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Shavandi M, Sadeghizadeh M, Zomorodipour A, Khajeh K. Biodesulfurization of dibenzothiophene by recombinant Gordonia alkanivorans RIPI90A. BIORESOURCE TECHNOLOGY 2009; 100:475-479. [PMID: 18653330 DOI: 10.1016/j.biortech.2008.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 06/09/2008] [Accepted: 06/10/2008] [Indexed: 05/26/2023]
Abstract
The dszABC genes from newly reported dibenzothiophene biodesulfurizing bacterium, Gordonia alkanivorans RIPI90A were cloned and sequenced. The overall nucleotide sequence similarity between the dszABC genes of G. alkanivorans RIPI90A and those of Rhodococcus erythropolis IGTS8 and Gordonia nitida were 83.1% and 83.2%, respectively. A gene transfer system for G. alkanivorans RIPI90A was established employing the Escherichia coli-Rhodococcus shuttle vector pRSG43 as suitable cloning vector, resulting in transformation efficiencies up to 1.6 x 10(5)CFUs microg(-1) plasmid DNA. This stable vector was applied to cloning and efficient expression of the dsz genes under the control of lac promoter. The recombinant strain was able to desulfurize dibenzothiophene in the presence of inorganic sulfate and sulfur-containing amino acids. The maximum desulfurization activity by recombinant resting cells (131.8 microM2-hydroxybiphenylg(dry cell weight)(-1)h(-1)) was increased 2.67-fold in comparison to the highest desulfurization activity of native resting cells.
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Affiliation(s)
- Mahmoud Shavandi
- Department of Genetics, Faculty of Science, Tarbiat Modares University, Tehran, Iran
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Arenskötter Q, Heller J, Dietz D, Arenskötter M, Steinbüchel A. Cloning and characterization of alpha-methylacyl coenzyme A racemase from Gordonia polyisoprenivorans VH2. Appl Environ Microbiol 2008; 74:7085-9. [PMID: 18820059 PMCID: PMC2583472 DOI: 10.1128/aem.01491-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 09/18/2008] [Indexed: 11/20/2022] Open
Abstract
The mcr gene of Gordonia polyisoprenivorans VH2 is not clustered with genes required for rubber degradation. Its disruption by insertion of a kanamycin resistance cassette impaired growth on methyl-branched isoprenoids but not on linear hydrocarbons. Intact mcr from this bacterium or from Nocardia farcinica IFM 10152 complemented the mutant. Reverse transcription analysis showed similar mcr(VH2) expression results during cultivation with poly(cis-1,4-isoprene) and propionate. Additional genes coding for a putative cytochrome P450 monooxygenase and a short-chain dehydrogenase/reductase involved in beta-oxidation and poly(cis-1,4-isoprene) degradation were also characterized.
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Affiliation(s)
- Quyen Arenskötter
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Correnstrasse 3, D-48149 Münster, Germany
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Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids. J Bacteriol 2008; 190:5797-805. [PMID: 18606735 DOI: 10.1128/jb.00468-08] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The pathogenic actinomycete Rhodococcus equi harbors different types of virulence plasmids associated with specific nonhuman hosts. We determined the complete DNA sequence of a vapB(+) plasmid, typically associated with pig isolates, and compared it with that of the horse-specific vapA(+) plasmid type. pVAPB1593, a circular 79,251-bp element, had the same housekeeping backbone as the vapA(+) plasmid but differed over an approximately 22-kb region. This variable region encompassed the vap pathogenicity island (PAI), was clearly subject to selective pressures different from those affecting the backbone, and showed major genetic rearrangements involving the vap genes. The pVAPB1593 PAI harbored five different vap genes (vapB and vapJ to -M, with vapK present in two copies), which encoded products differing by 24 to 84% in amino acid sequence from the six full-length vapA(+) plasmid-encoded Vap proteins, consistent with a role for the specific vap gene complement in R. equi host tropism. Sequence analyses, including interpolated variable-order motifs for detection of alien DNA and reconstruction of Vap family phylogenetic relationships, suggested that the vap PAI was acquired by an ancestor plasmid via lateral gene transfer, subsequently evolving by vap gene duplication and sequence diversification to give different (host-adapted) plasmids. The R. equi virulence plasmids belong to a new family of actinobacterial circular replicons characterized by an ancient conjugative backbone and a horizontally acquired niche-adaptive plasticity region.
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Bröker D, Dietz D, Arenskötter M, Steinbüchel A. The genomes of the non-clearing-zone-forming and natural-rubber- degrading species Gordonia polyisoprenivorans and Gordonia westfalica harbor genes expressing Lcp activity in Streptomyces strains. Appl Environ Microbiol 2008; 74:2288-97. [PMID: 18296529 PMCID: PMC2293141 DOI: 10.1128/aem.02145-07] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 02/14/2008] [Indexed: 11/20/2022] Open
Abstract
The latex-clearing protein (Lcp(K30)) from the rubber-degrading bacterium Streptomyces sp. strain K30 is involved in the cleavage of poly(cis-1,4-isoprene), yielding isoprenoid aldehydes and ketones. Lcp homologues have so far been detected in all investigated clearing-zone-forming rubber-degrading bacteria. Internal degenerated oligonucleotides derived from lcp genes of Streptomyces sp. strain K30 (lcp(K30)), Streptomyces coelicolor strain A3(2), and Nocardia farcinica strains IFM10152 and E1 were applied in PCR to investigate whether lcp homologues occur also in the non-clearing-zone-forming rubber-utilizing bacteria Gordonia polyisoprenivorans strains VH2 and Y2K, Gordonia alkanivorans strain 44187, and Gordonia westfalica strain Kb1, which grow adhesively on rubber. The 1,230- and 1,224-bp lcp-homologous genes from G. polyisoprenivorans strain VH2 (lcp(VH2)) and G. westfalica strain Kb1 (lcp(Kb1)) were obtained after screening genomic libraries by degenerated PCR amplification, and their translational products exhibited 50 and 52% amino acid identity, respectively, to Lcp(K30). Recombinant lcp(VH2) and lcp(Kb1) harboring cells of the non-rubber-degrading Streptomyces lividans strain TK23 were able to form clearing zones and aldehydes on latex overlay-agar plates, thus indicating that lcp(VH2) and lcp(Kb1) encode functionally active proteins. Analysis by gel permeation chromatography demonstrated lower polymer concentrations and molecular weights of the remaining polyisoprenoid molecules after incubation with these recombinant S. lividans strains. Reverse transcription-PCR analysis demonstrated that lcp(VH2) was transcribed in cells of G. polyisoprenivorans strain VH2 cultivated in the presence of poly(cis-1,4-isoprene) but not in the presence of sodium acetate. Anti-Lcp(K30) immunoglobulin Gs, which were raised in this study, were rather specific for Lcp(K30) and did not cross-react with Lcp(VH2) and Lcp(Kb1). A lcp(VH2) disruption mutant was still able to grow with poly(cis-1,4-isoprene) as sole carbon source; therefore, lcp(VH2) seems not to be essential for rubber degradation in G. polyisoprenivorans.
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Affiliation(s)
- Daniel Bröker
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Bröker D, Arenskötter M, Steinbüchel A. Transfer of megaplasmid pKB1 from the rubber-degrading bacterium Gordonia westfalica strain Kb1 to related bacteria and its modification. Appl Microbiol Biotechnol 2007; 77:1317-27. [PMID: 18034340 DOI: 10.1007/s00253-007-1262-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 10/17/2007] [Accepted: 10/22/2007] [Indexed: 11/28/2022]
Abstract
Because engineering of the 101.016-bp megaplasmid pKB1 of Gordonia westfalica Kb1 failed due to the absence of an effective transfer system, pKB1 was transferred by conjugation from G. westfalica Kb1 to a kanamycin-resistant mutant of Rhodococcus opacus PD630 at a frequency of about 6.2 x 10(-8) events per recipient cell. Furthermore, pKB1 was transferred to G. polyisoprenivorans strains VH2 and Y2K and to Mycobacterium smegmatis by electroporation at frequencies of 5.5 x 10(3), 1.9 x 10(3), and 8.3 x 10(2) transformants per microgram plasmid DNA. The pKB1-encoded cadmium resistance gene cadA was used for selection in these experiments. Recombinant pKB1-containing G. polyisoprenivorans VH2 and M. smegmatis were then used to engineer pKB1. A kanamycin resistance cassette was inserted into the pKB1-encoded cadA gene, ligated to suicide plasmid pBBR1MCS-5, and the resulting plasmid was electroporated into plasmid-harboring strains. Homologous recombination between cadA on suicide plasmid and the respective sequence in pKB1 led to its integration into pKB1. Thus, two selection markers were accommodated in pKB1 to monitor plasmid transfer into Gordonia and related taxa for analysis of genes essential for rubber degradation and others. In this study, two transfer methods for large plasmids and strategies for engineering of pKB1 were successfully applied, thereby, extending the tool box for Gordonia.
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Affiliation(s)
- Daniel Bröker
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149, Münster, Germany
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Yang JC, Lessard PA, Sengupta N, Windsor SD, O'brien XM, Bramucci M, Tomb JF, Nagarajan V, Sinskey AJ. TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12. Plasmid 2006; 57:55-70. [PMID: 16997374 DOI: 10.1016/j.plasmid.2006.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/01/2006] [Accepted: 08/04/2006] [Indexed: 11/13/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) revealed three previously uncharacterized megaplasmids in the genome of Rhodococcus erythropolis AN12. These megaplasmids, pREA400, pREA250, and pREA100, are approximately 400, 250, and 100kb, respectively, based on their migration in pulsed-field gels. Genetic screening of an AN12 transposon insertion library showed that two megaplasmids, pREA400, and pREA250, are conjugative. Mobilization frequencies of these AN12 megaplasmids to recipient R. erythropolis SQ1 were determined to be approximately 7x10(-4) and 5x10(-4) events per recipient cell, respectively. It is known for other bacterial systems that a relaxase encoded by the traA gene is required to initiate DNA transfer during plasmid conjugation. Sequences adjacent to the transposon insertion in megaplasmid pREA400 revealed a putative traA-like open reading frame. A targeted gene disruption method was developed to generate a traA mutation in AN12, which allowed us to address the role of the traA gene product for Rhodococcus megaplasmid conjugation. We found that the AN12 traA mutant is no longer capable of transferring the pREA400 megaplasmid to SQ1. Furthermore, we confirmed that the conjugation defect was specifically due to the disruption of the traA gene, as pREA400 megaplasmid conjugation defect is restored with a complementing copy of the traA gene.
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Affiliation(s)
- Joyce C Yang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Tahkoniemi H, Helmja K, Menert A, Kaljurand M. Fermentation reactor coupled with capillary electrophoresis for on-line bioprocess monitoring. J Pharm Biomed Anal 2006; 41:1585-91. [PMID: 16495032 DOI: 10.1016/j.jpba.2006.01.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 01/17/2006] [Accepted: 01/19/2006] [Indexed: 11/21/2022]
Abstract
In this paper, a filter probe integrated into a computerized pneumatic sampler for capillary electroseparations was developed for an on-line monitoring of bioprocesses. The optimization of the performance of the coupled system was done by using a response surface modeling and three-level two-factor design. The resolution was found to be the most important parameter influencing the performance of an on-line analysis of the microbial metabolism. For the on-line analysis the migration time and detection limit were also found to be important parameters. Different parameters were combined by using an overall desirability function to find optimum conditions for all parameters. The equipment with an optimized separation protocol was used to monitor the bioaccumulation of Cu, Zn, Co and Cd (with detection limits 0.46, 0.37, 1.2, 0.84 mM correspondingly) by the Rhodococcus sp. bacteria isolated from the highly polluted technogenic soil of northeastern Estonia during a 2-week experiment.
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Affiliation(s)
- H Tahkoniemi
- Department of Chemistry, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
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Veiga-Crespo P, Feijoo-Siota L, de Miguel T, Poza M, Villa TG. Proposal of a method for the genetic transformation of Gordonia jacobaea. J Appl Microbiol 2006; 100:608-14. [PMID: 16478500 DOI: 10.1111/j.1365-2672.2005.02806.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Gordonia jacobaea is a recently isolated bacterial species with potential industrial application on account of its ability to store large quantities of trans-canthaxanthin. Its genetic manipulation is, however, difficult and cumbersome owing to the presence of mycolic acids in the cell wall and, especially, because of current lack of knowledge about its basic genetics. The present work describes a method for the genetic transformation of G. jacobaea. METHODS AND RESULTS Gordonia jacobaea was grown in media supplemented with different glycine, penicillin G and isoniazid concentrations. The temperature, carbon source, growth phase and ultrasounds were analyzed for improving the method efficiency. The cells were finally transformed by electroporation. Finally, the method was applied to Brevibacteriumlactofermentum and Gordonia bronchialis. CONCLUSIONS The growth of G. jacobaea in the presence of glycine and isoniazid is essential for obtaining electrocompetents cells. The temperature, growth phase and ultrasounds appeared as the main factors for increasing the transformation efficiency. The use of shuttle plasmids became necessary. The method described can be used with other Corynebacteria species. SIGNIFICANCE AND IMPACT OF THE STUDY Because of the importance of the CNM group (Corynebacteria, Nocardia and Mycobacteria genera) in different areas such as industry, bioremediation improve the knowledge of their molecular mechanisms are becoming essential. The method described here improves the genetic manipulation of this group of bacteria.
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Affiliation(s)
- P Veiga-Crespo
- Department of Microbiology, Faculty of Pharmacy, University of Santiago de Compostela, A Coruña, Spain
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Roy RV, Das M, Banerjee R, Bhowmick AK. Comparative studies on rubber biodegradation through solid-state and submerged fermentation. Process Biochem 2006. [DOI: 10.1016/j.procbio.2005.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Banh Q, Arenskötter M, Steinbüchel A. Establishment of Tn5096-based transposon mutagenesis in Gordonia polyisoprenivorans. Appl Environ Microbiol 2005; 71:5077-84. [PMID: 16151089 PMCID: PMC1214614 DOI: 10.1128/aem.71.9.5077-5084.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transposons Tn5, Tn10, Tn611, and Tn5096 were characterized regarding transposition in Gordonia polyisoprenivorans strain VH2. No insertional mutants were obtained employing Tn5 or Tn10. The thermosensitive plasmid pCG79 harboring Tn611 integrated into the chromosome of G. polyisoprenivorans; however, the insertional mutants were fairly unstable und reverted frequently to the wild-type phenotype. In contrast, various stable mutants were obtained employing Tn5096-mediated transposon mutagenesis. Auxotrophic mutants, mutants defective or deregulated in carotenoid biosynthesis, and mutants defective in utilization of rubber and/or highly branched isoprenoid hydrocarbons were obtained by integration of plasmid pMA5096 harboring Tn5096 as a whole into the genome. From about 25,000 isolated mutants, the insertion loci of pMA5096 were subsequently mapped in 20 independent mutants in genes which could be related to the above-mentioned metabolic pathways or to putative regulation proteins. Analyses of the genotypes of pMA5096-mediated mutants defective in biodegradation of poly(cis-1,4-isoprene) did not reveal homologues to recently identified genes coding for enzymes catalyzing the initial cleavage of poly(cis-1,4-isoprene). One rubber-negative mutant was disrupted in mcr, encoding an alpha-methylacyl-coenzyme A racemase. This mutant was defective in degradation of poly(cis-1,4-isoprene) and also of highly branched isoprenoid hydrocarbons.
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Affiliation(s)
- Quyen Banh
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Stinear TP, Pryor MJ, Porter JL, Cole ST. Functional analysis and annotation of the virulence plasmid pMUM001 from Mycobacterium ulcerans. MICROBIOLOGY-SGM 2005; 151:683-692. [PMID: 15758215 DOI: 10.1099/mic.0.27674-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The presence of a 174 kb plasmid called pMUM001 in Mycobacterium ulcerans, the first example of a mycobacterial plasmid encoding a virulence determinant, was recently reported. Over half of pMUM001 is devoted to six genes, three of which encode giant polyketide synthases (PKS) that produce mycolactone, an unusual cytotoxic lipid produced by M. ulcerans. In this present study the remaining 75 non-PKS-associated protein-coding sequences (CDS) are analysed and it is shown that pMUM001 is a low-copy-number element with a functional ori that supports replication in Mycobacterium marinum but not in the fast-growing mycobacteria Mycobacterium smegmatis and Mycobacterium fortuitum. Sequence analyses revealed a highly mosaic plasmid gene structure that is reminiscent of other large plasmids. Insertion sequences (IS) and fragments of IS, some previously unreported, are interspersed among functional gene clusters, such as those genes involved in plasmid replication, the synthesis of mycolactone, and a potential phosphorelay signal transduction system. Among the IS present on pMUM001 were multiple copies of the high-copy-number M. ulcerans elements IS2404 and IS2606. No plasmid transfer systems were identified, suggesting that trans-acting factors are required for mobilization. The results presented here provide important insights into this unusual virulence plasmid from an emerging but neglected human pathogen.
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Affiliation(s)
- Timothy P Stinear
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue du Docteur Roux, 75725 Paris Cedex 15, France
| | - Melinda J Pryor
- Plate-Forme 4 - Intégration et analyse génomiques, Génopole, Institut Pasteur, 28 Rue du Docteur Roux, 75725 Paris Cedex 15, France
| | - Jessica L Porter
- Australian Bacterial Pathogenesis Program, Department of Microbiology, Monash University, Clayton, 3800, Australia
| | - Stewart T Cole
- Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 Rue du Docteur Roux, 75725 Paris Cedex 15, France
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Rose K, Steinbüchel A. Biodegradation of natural rubber and related compounds: recent insights into a hardly understood catabolic capability of microorganisms. Appl Environ Microbiol 2005; 71:2803-12. [PMID: 15932971 PMCID: PMC1151847 DOI: 10.1128/aem.71.6.2803-2812.2005] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Karsten Rose
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Mattes TE, Coleman NV, Spain JC, Gossett JM. Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614. Arch Microbiol 2004; 183:95-106. [PMID: 15599705 DOI: 10.1007/s00203-004-0749-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Revised: 10/25/2004] [Accepted: 11/04/2004] [Indexed: 10/26/2022]
Abstract
Nocardioides sp. strain JS614 utilizes vinyl chloride and ethene as carbon and energy sources. JS614 could be influential in natural attenuation and biogeochemical ethene cycling, and useful for bioremediation, biocatalysis and metabolic engineering, but a fundamental understanding of the physiological and genetic basis of vinyl chloride and ethene assimilation in strain JS614 is required. Alkene monooxygenase (AkMO) activity was demonstrated in whole-cell assays and epoxyalkane:coenzyme M transferase (EaCoMT) activity was detected in JS614 cell-free extracts. Pulsed-field gel electrophoresis revealed a 290-kb plasmid (pNoc614) in JS614. Curing experiments and PCR indicated that pNoc614 encodes vinyl chloride/ethene-degradation genes. JS614 vinyl chloride/ethene catabolic genes and flanking DNA (34.8 kb) were retrieved from a fosmid clone. AkMO and EaCoMT genes were found in a putative operon that included CoA transferase, acyl-CoA synthetase, dehydrogenase, and reductase genes. Adjacent to this gene cluster was a divergently transcribed gene cluster that encoded possible coenzyme M biosynthesis enzymes. Reverse transcription-PCR demonstrated the vinyl chloride- and ethene-inducible nature of several genes. Genes encoding possible plasmid conjugation, integration, and partitioning functions were also discovered on the fosmid clone.
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Affiliation(s)
- Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA 52242, USA.
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Arenskötter M, Bröker D, Steinbüchel A. Biology of the metabolically diverse genus Gordonia. Appl Environ Microbiol 2004; 70:3195-204. [PMID: 15184112 PMCID: PMC427784 DOI: 10.1128/aem.70.6.3195-3204.2004] [Citation(s) in RCA: 231] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Matthias Arenskötter
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Muenster, Germany
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