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Plasmid-Encoded Traits Vary across Environments. mBio 2023; 14:e0319122. [PMID: 36629415 PMCID: PMC9973032 DOI: 10.1128/mbio.03191-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host's taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.
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Bokade P, Gaur VK, Tripathi V, Bobate S, Manickam N, Bajaj A. Bacterial remediation of pesticide polluted soils: Exploring the feasibility of site restoration. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129906. [PMID: 36088882 DOI: 10.1016/j.jhazmat.2022.129906] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
For decades, reclamation of pesticide contaminated sites has been a challenging avenue. Due to increasing agricultural demand, the application of synthetic pesticides could not be controlled in its usage, and it has now adversely impacted the soil, water, and associated ecosystems posing adverse effects on human health. Agricultural soil and pesticide manufacturing sites, in particular, are one of the most contaminated due to direct exposure. Among various strategies for soil reclamation, ecofriendly microbial bioremediation suffers inherent challenges for large scale field application as interaction of microbes with the polluted soil varies greatly under climatic conditions. Methodically, starting from functional or genomic screening, enrichment isolation; functional pathway mapping, production of tensioactive metabolites for increasing the bioavailability and bio-accessibility, employing genetic engineering strategies for modifications in existing catabolic genes to enhance the degradation activity; each step-in degradation study has challenges and prospects which can be addressed for successful application. The present review critically examines the methodical challenges addressing the feasibility for restoring and reclaiming pesticide contaminated sites along with the ecotoxicological risk assessments. Overall, it highlights the need to fine-tune the available processes and employ interdisciplinary approaches to make microbe assisted bioremediation as the method of choice for reclamation of pesticide contaminated sites.
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Affiliation(s)
- Priyanka Bokade
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vivek Kumar Gaur
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; School of Energy and Chemical Engineering, UNIST, Ulsan 44919, South Korea
| | - Varsha Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Shishir Bobate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Natesan Manickam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India; Environmental Biotechnology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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Dellagnezze BM, Vasconcellos SP, Angelim AL, Melo VMM, Santisi S, Cappello S, Oliveira VM. Bioaugmentation strategy employing a microbial consortium immobilized in chitosan beads for oil degradation in mesocosm scale. MARINE POLLUTION BULLETIN 2016; 107:107-117. [PMID: 27158046 DOI: 10.1016/j.marpolbul.2016.04.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 05/22/2023]
Abstract
A bacterial consortium composed by four metagenomic clones and Bacillus subtilis strain CBMAI 707, all derived from petroleum reservoirs, was entrapped in chitosan beads and evaluated regarding hydrocarbon degradation capability. Experiments were carried out in mesocosm scale (3000L) with seawater artificially polluted with crude oil. At different time intervals, mesocosms were sampled and subjected to GC-FID and microbiological analyses, as total and heterotrophic culturable bacterial abundance (DAPI and CFU count), biological oxygen demand (BOD) and taxonomic diversity (massive sequencing of 16S rRNA genes). The results obtained showed that degradation of n-alkane hydrocarbons was similar between both treatments. However, aromatic compound degradation was more efficient in bioaugmentation treatment, with biodegradation percentages reaching up to 99% in 30days. Community dynamics was different between treatments and the consortium used in the bioaugmentation treatment contributed to a significant increase in aromatic hydrocarbon degradation.
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Affiliation(s)
- B M Dellagnezze
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil.
| | - S P Vasconcellos
- Federal University of São Paulo (UNIFESP), Rua Prof. Artur Riedel, 275, CEP 09972-270, Jd. Eldorado, Diadema, SP, Brazil
| | - A L Angelim
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - V M M Melo
- Lembiotech (UFC), Federal University of Ceará, Av. Humberto Monte, 2977, Campus do Pici, Bloco 909, 60455-000, Fortaleza, CE, Brazil
| | - S Santisi
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - S Cappello
- Institute for Coastal Marine Environment (IAMC), Consiglio Nazionale delle Ricerche (CNR) of Messina, Messina, Italy
| | - V M Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University - UNICAMP, CP 6171, CEP 13081-970 Campinas, SP, Brazil
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Silva-Rocha R, de Jong H, Tamames J, de Lorenzo V. The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC SYSTEMS BIOLOGY 2011; 5:191. [PMID: 22078029 PMCID: PMC3253710 DOI: 10.1186/1752-0509-5-191] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2011] [Accepted: 11/11/2011] [Indexed: 12/13/2022]
Abstract
Background The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Although nearly every metabolic and transcriptional component of this regulatory system is known to an extraordinary molecular detail, the complexity of its architecture is still perplexing. To gain an insight into the inner layout of this network a logic model of the TOL system was implemented, simulated and experimentally validated. This analysis made sense of the specific regulatory topology out on the basis of an unprecedented network motif around which the entire genetic circuit for m-xylene catabolism gravitates. Results The most salient feature of the whole TOL regulatory network is the control exerted by two distinct but still intertwined regulators (XylR and XylS) on expression of two separated catabolic operons (upper and lower) for catabolism of m-xylene. Following model reduction, a minimal modular circuit composed by five basic variables appeared to suffice for fully describing the operation of the entire system. In silico simulation of the effect of various perturbations were compared with experimental data in which specific portions of the network were activated with selected inducers: m-xylene, o-xylene, 3-methylbenzylalcohol and 3-methylbenzoate. The results accredited the ability of the model to faithfully describe network dynamics. This analysis revealed that the entire regulatory structure of the TOL system enables the action an unprecedented metabolic amplifier motif (MAM). This motif synchronizes expression of the upper and lower portions of a very long metabolic system when cells face the head pathway substrate, m-xylene. Conclusion Logic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium.
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Affiliation(s)
- Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología CSIC Cantoblanco-Madrid, 28049, Spain
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Shintani M, Takahashi Y, Yamane H, Nojiri H. The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microbes Environ 2011; 25:253-65. [PMID: 21576880 DOI: 10.1264/jsme2.me10155] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Over the past few decades, degradative plasmids have been isolated from bacteria capable of degrading a variety of both natural and man-made compounds. Degradative plasmids belonging to three incompatibility (Inc) groups in Pseudomonas (IncP-1, P-7, and P-9) have been well studied in terms of their replication, maintenance, and capacity for conjugative transfer. The host ranges of these plasmids are determined by replication or conjugative transfer systems. The host range of IncP-1 is broad, that of IncP-9 is intermediate, and that of IncP-7 is narrow. To understand the behavior of these plasmids and their hosts in various environments, the survivability of inocula, stability or transferability, and efficiency of biodegradation in environments and microcosms have been monitored. The biodegradation and plasmid transfer in various environments have been observed for all three groups, although the kinds of transconjugants differed with the Inc groups. In some cases, the deletion and amplification of catabolic genes acted to reduce the production of toxic catabolic intermediates, or to increase the activity on a particular catabolic pathway. The combination of degradative genes, the plasmid backbone of each Inc group, and the host of the plasmids is key to the degraders adapting to various hosts or to heterogeneous environments.
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Affiliation(s)
- Masaki Shintani
- Bioresource Center, Japan Collection of Microorganisms (BRC-JCM), Riken, 2–1 Hirosawa, Wako, Saitama 351–0198, Japan
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Richaume A, Smit E, Faurie G, Elsas JD. Influence of soil type on the transfer of plasmid RP4p from Pseudomonas fluorescens to introduced recipient and to indigenous bacteria. FEMS Microbiol Ecol 2011. [DOI: 10.1111/j.1574-6941.1992.tb01665.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Khomenkov VG, Shevelev AB, Zhukov VG, Zagustina NA, Bezborodov AM, Popov VO. Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808020014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Kuritz T. Cyanobacteria as agents for the control of pollution by pesticides and chlorinated organic compounds. J Appl Microbiol 2010; 85 Suppl 1:186S-192S. [DOI: 10.1111/j.1365-2672.1998.tb05298.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Matheson VG, Forney LJ, Suwa Y, Nakatsu CH, Sexstone AJ, Holben WE. Evidence for Acquisition in Nature of a Chromosomal 2,4-Dichlorophenoxyacetic Acid/(alpha)-Ketoglutarate Dioxygenase Gene by Different Burkholderia spp. Appl Environ Microbiol 2010; 62:2457-63. [PMID: 16535356 PMCID: PMC1388894 DOI: 10.1128/aem.62.7.2457-2463.1996] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the gene required to initiate the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by the soil bacterium Burkholderia sp. strain TFD6, which hybridized to the tfdA gene of the canonical 2,4-D catabolic plasmid pJP4 under low-stringency conditions. Cleavage of the ether bond of 2,4-D by cell extracts of TFD6 proceeded by an (alpha)-ketoglutarate-dependent reaction, characteristic of TfdA (F. Fukumori and R. P. Hausinger, J. Bacteriol. 175:2083-2086, 1993). The TFD6 tfdA gene was identified in a recombinant plasmid which complemented a tfdA transposon mutant of TFD6 created by chromosomal insertion of Tn5. The plasmid also expressed TfdA activity in Escherichia coli DH5(alpha), as evidenced by enzyme assays with cell extracts. Sequence analysis of the tfdA gene and flanking regions from strain TFD6 showed 99.5% similarity to a tfdA gene cloned from the chromosome of a different Burkholderia species (strain RASC) isolated from a widely separated geographical area. This chromosomal gene has 77.2% sequence identity to tfdA from plasmid pJP4 (Y. Suwa, W. E. Holben, and L. J. Forney, abstr. Q-403, in Abstracts of the 94th General Meeting of the American Society for Microbiology 1994.). The tfdA homologs cloned from strains TFD6 and RASC are the first chromosomally encoded 2,4-D catabolic genes to be reported. The occurrence of highly similar tfdA genes in different bacterial species suggests that this chromosomal gene can be horizontally transferred.
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Angles ML, Marshall KC, Goodman AE. Plasmid Transfer between Marine Bacteria in the Aqueous Phase and Biofilms in Reactor Microcosms. Appl Environ Microbiol 2010; 59:843-50. [PMID: 16348893 PMCID: PMC202198 DOI: 10.1128/aem.59.3.843-850.1993] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Plasmid transfer of broad-host-range plasmid RP1 from marine Vibrio sp. strain S14 to marine strain SW5 under optimum conditions on the surface of nutrient plates was improved 2 orders of magnitude by using the plasmid transfer process to select an SW5 recipient more efficient than the wild type in receiving and/or maintaining the plasmid. This recipient strain, SW5H, was used to form biofilms under flow conditions on the surfaces of glass beads in reactors. The S142(RP1) donor strain was introduced to the reactors after either 48 or 170 h of biofilm formation, and production of transconjugants in the aqueous phases and biofilms without selection pressure was assessed. Plasmid transfer to the recipient cells in the biofilm was detected for biofilms formed for 170 h but not in those formed for 48 h. The plasmid transfer frequency was significantly higher (P < 0.05) among cells attached to the bead surfaces in the biofilm than among cells in the aqueous phase.
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Affiliation(s)
- M L Angles
- School of Microbiology and Immunology, The University of New South Wales, Kensington, New South Wales 2033, Australia
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11
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Perelo LW. Review: In situ and bioremediation of organic pollutants in aquatic sediments. JOURNAL OF HAZARDOUS MATERIALS 2010; 177:81-9. [PMID: 20138425 DOI: 10.1016/j.jhazmat.2009.12.090] [Citation(s) in RCA: 225] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 12/01/2009] [Accepted: 12/18/2009] [Indexed: 05/24/2023]
Abstract
Organic pollutants in sediments are a worldwide problem because sediments act as sinks for hydrophobic, recalcitrant and hazardous compounds. Depending on biogeochemical processes these hydrocarbons are involved in adsorption, desorption and transformation processes and can be made available to benthic organisms as well as organisms in the water column through the sediment-water interface. Most of these recalcitrant hydrocarbons are toxic and carcinogenic, they may enter the food-chain and accumulate in biological tissue. Several approaches are being investigated or have been already used to remove organic hydrocarbons from sediments. This paper provides a review on types and sources of organic pollutants as well as their behavior in sediments. It presents the advantages and disadvantages of traditional sediment remediation techniques in use, such as dredging, capping and monitored natural attenuation. Furthermore, it describes new approaches with emphasis on bioremediation, like biostimulation, bioaugmentation and phytoremediation applied to sediments. These new techniques promise to be of lower impact and more cost efficient than traditional management strategies.
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Affiliation(s)
- Louisa Wessels Perelo
- Departamento de Engenharia Ambiental, Escola Politécnica, Universidade Federal da Bahia, Rua Prof. Aristides Novis, 02 - Federação, CEP 40210-910 Salvador, BA, Brazil.
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Miki T, Ueki M, Kawabata Z, Yamamura N. Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model. FEMS Microbiol Ecol 2007; 62:211-21. [PMID: 17627781 DOI: 10.1111/j.1574-6941.2007.00357.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.
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Affiliation(s)
- Takeshi Miki
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
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Providenti MA, Shaye RE, Lynes KD, McKenna NT, O'brien JM, Rosolen S, Wyndham RC, Lambert IB. The locus coding for the 3-nitrobenzoate dioxygenase of Comamonas sp. strain JS46 is flanked by IS1071 elements and is subject to deletion and inversion events. Appl Environ Microbiol 2006; 72:2651-60. [PMID: 16597970 PMCID: PMC1449074 DOI: 10.1128/aem.72.4.2651-2660.2006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Comamonas sp. strain JS46, 3-nitrobenzoate (3Nba) is initially oxidized at the 3,4 position by a dioxygenase, which results in release of nitrite and production of protocatechuate. The locus coding for the 3Nba dioxygenase (designated mnb, for m-nitrobenzoate) was mobilized from strain JS46 using a plasmid capture method, cloned, and sequenced. The 3Nba dioxygenase (MnbA) is a member of the phthalate family of aromatic oxygenases. An open reading frame designated mnbB that codes for an NAD(P)H-dependent class IA aromatic oxidoreductase is downstream of mnbA. MnbB is tentatively identified as the oxidoreductase that transfers reducing equivalents to MnbA in strain JS46. The mnb locus is flanked by IS1071 elements. The upstream element is interrupted by a novel insertion sequence designated ISCsp1, and the transposase genes of the flanking insertion elements are transcribed in the direction opposite the direction of mnbA transcription. Spontaneous deletion of mnb occurs because of homologous recombination between the directly repeated flanking IS1071 elements. In addition, in approximately 0.007 to 0.2% of any population of JS46 cells growing on 3Nba, alternative orientations of mnb relative to the flanking IS1071 elements are detected. These alternative forms are the result of inversions of mnb and the flanking IS1071 elements. Inversions appear to occur because of homologous recombination between the inverted repeats that flank the IS1071 elements.
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Affiliation(s)
- Miguel A Providenti
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6.
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Ashelford KE, Fry JC, Day MJ, Hill KE, Learner MA, Marchesi JR, Perkins CD, Weightman AJ. Using microcosms to study gene transfer in aquatic habitats. FEMS Microbiol Ecol 2006. [DOI: 10.1111/j.1574-6941.1997.tb00393.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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15
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De Gelder L, Vandecasteele FPJ, Brown CJ, Forney LJ, Top EM. Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community. Appl Environ Microbiol 2005; 71:5309-17. [PMID: 16151119 PMCID: PMC1214629 DOI: 10.1128/aem.71.9.5309-5317.2005] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.
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Affiliation(s)
- Leen De Gelder
- Department of Biological Sciences, 252 Life Sciences South, University of Idaho, Moscow, ID 83844-3051, USA
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16
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Thompson IP, van der Gast CJ, Ciric L, Singer AC. Bioaugmentation for bioremediation: the challenge of strain selection. Environ Microbiol 2005; 7:909-15. [PMID: 15946288 DOI: 10.1111/j.1462-2920.2005.00804.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite its long-term use in bioremediation, bioaugmentation of contaminated sites with microbial cells continues to be a source of controversy within environmental microbiology. This largely results from its notoriously unreliable performance record. In this article, we argue that the unpredictable nature of the approach comes from the initial strain selection step. Up until now, this has been dictated by the search for catabolically competent microorganisms, with little or no consideration given to other essential features that are required to be functionally active and persistent in target habitats. We describe how technical advances in molecular biology and analytical chemistry, now enable assessments of the functional diversity and spatial distribution of microbial communities to be made in situ. These advances now enable microbial populations, targeted for exploitation, to be differentiated to the cell level, an advance that is bound to improve microbial selection and exploitation. We argue that this information-based approach is already proving to be more effective than the traditional 'black-box' approach of strain selection. The future perspectives and opportunities for improving selection of effective microbial strains for bioaugmentation are also discussed.
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Affiliation(s)
- Ian P Thompson
- Environmental Biotechnology Section, NERC Centre for Ecology and Hydrology - Oxford, Mansfield Road, Oxford, OX1 3SR, UK.
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17
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Ueki M, Matsui K, Choi K, Kawabata Z. The enhancement of conjugal plasmid pBHR1 transfer between bacteria in the presence of extracellular metabolic products produced by Microcystis aeruginosa. FEMS Microbiol Ecol 2004; 51:1-8. [PMID: 16329851 DOI: 10.1016/j.femsec.2004.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 06/24/2004] [Accepted: 07/08/2004] [Indexed: 10/26/2022] Open
Abstract
Conjugal plasmid transfer from Escherichia coli S17-1 (pBHR1) to Pseudomonas stutzeri was investigated in the presence of a cyanophyta Microcystis aeruginosa. The plasmid transfer frequency increased with higher densities of M. aeruginosa. The extracellular metabolic products (EMPs) from M. aeruginosa were found to enhance the plasmid transfer between bacteria. Furthermore, the plasmid transfer frequency in medium containing EMPs was significantly higher than that in culture medium with or without glucose. These results suggest that M. aeruginosa enhances conjugal plasmid transfer between bacteria through its EMPs, and that identity of the carbon source is an important factor affecting conjugal plasmid transfer in aquatic environments.
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Affiliation(s)
- Masaya Ueki
- Center for Ecological Research, Kyoto University, Kamitanakami, Otsu, Shiga 520-2113, Japan.
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18
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Gilbride KA, Fulthorpe RR. A survey of the composition and diversity of bacterial populations in bleached kraft pulp-mill wastewater secondary treatment systems. Can J Microbiol 2004; 50:633-44. [PMID: 15467789 DOI: 10.1139/w04-031] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial community compositions from 10 pulp- and paper-mill treatment systems were compared using both traditional and molecular techniques. 16S-RFLP (Random Fragment Length Polymorphisms) analysis was used to examine the genotypic profiles of the whole bacterial community of each treatment system. Although all the communities shared approximately 60% of their DNA band pattern, as determined by computer-assisted cluster analysis, each community displayed a unique profile that was stable over time under normal operating parameters. Reverse Sample Genome Probing (RSGP) and 16S-RFLP were used to compare the culturable bacterial communities of several geographically separated pulp-mill biotreatment system communities. There was little overlap in the composition of the culturable community between mills at the genus level. Furthermore, RSGP variation was almost as high within a mill as between mills. Partial sequences of the 16S rRNA genes from culturable isolates identified Bacillus spp., Pseudomonas spp., and Xanthobacter as some of the dominant species. Finally, several 16S rRNA genes from two whole community 16S RNA gene libraries were partially sequenced and identified as similar to unknown α-, β-, and γ-Proteobacteria, Ralstonia, Alcaligenes, Nitrospira, Firmicutes, and clones representing the new Holophaga/Acidobacterium phylum. These findings suggest that although these pulp- and paper-mill biotreatment communities perform similar functions, they are populated by unique mixtures of species.Key words: biodiversity, 16S-RFLP, secondary treatment, pulp mills.
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Affiliation(s)
- Kimberley A Gilbride
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
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Gstalder ME, Faelen M, Mine N, Top EM, Mergeay M, Couturier M. Replication functions of new broad host range plasmids isolated from polluted soils. Res Microbiol 2003; 154:499-509. [PMID: 14499936 DOI: 10.1016/s0923-2508(03)00143-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The nucleotide sequencing of replicons isolated from three new broad host range plasmids, pMOL98, pEMT8, and pEMT3, originating from polluted soils, showed a typical organization of iteron replicons replicating by the theta mode. In the pMOL98 replicon, the origin region and the rep gene were identified in complementation experiments. Sequence comparisons showed that the regions bearing these features are highly identical to regions in pIP02T and pSB102 and that the Rep proteins (but not the origin regions) of these three plasmids show some identity to the Rep proteins of the IncW group of plasmids. This suggests that pMOL98, pIPO2T, and pSB102 constitute a new Inc/Rep family, distantly related to the IncW group, but having an incompatibility phenotype different from the IncW phenotype. The pEMT8 replicon displayed an orf whose conceptually translated product is related to the Rep proteins of four plasmids, pSD20, pSW500, pMLb, and pALC1, not yet classified into any known incompatibility group. The vegetative origins of these plasmids were not similar, suggesting that the five plasmids could belong to a new family with similar Rep proteins but different incompatibility phenotypes. The pEMT3 replicon is clearly related to IncP replicons (sequence similarities and incompatibility phenotype), although sequence comparisons revealed some divergence with respect to the two well-documented subgroups IncPalpha and IncPbeta. This suggests that in these plasmids, despite the existence of a powerful system of centralized control over replication, maintenance, and transfer functions, plasticity and evolution of these functions are at work. Our analysis confirms the extreme genetic flexibility of plasmids and the absolute necessity of using multiple techniques (PCR, DNA sequencing, DNA chips, and databases) to analyze the role of broad host range plasmids in the capture, recombination and spread of genetic traits among bacteria.
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Affiliation(s)
- Marie-Eve Gstalder
- Laboratoire de Génétique des Procaryotes, IBMM, Université Libre de Bruxelles, rue des Prof. Jeener et Brachet, 12, 6104 Gosselies, Belgium.
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Hill KE, Weightman AJ. Horizontal transfer of dehalogenase genes on IncP1beta plasmids during bacterial adaptation to degrade alpha-halocarboxylic acids. FEMS Microbiol Ecol 2003; 45:273-82. [PMID: 19719596 DOI: 10.1016/s0168-6496(03)00158-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The diversity of bacterial alpha-halocarboxylic acid (alphaHA) dehalogenases from a polluted soil was investigated. Polymerase chain reaction (PCR) primers designed to amplify group I and group II dehalogenase (deh) gene sequences were used to screen bacterial isolates, nine beta-Proteobacteria and one gamma-Proteobacterium, from soil enrichments. Primers successfully amplified deh sequences from all 10 alphaHA-utilising isolates. Bacteria isolated at 15 or 30 degrees C on chloroacetic acid or 2-chloropropionic acid from the same polluted soil were shown to contain up to four plasmids, some of these common between isolates. Analysis of deletion mutants and Southern hybridisation showed that each isolate contained an apparently identical IncP1beta plasmid c. 80 kb in size, carrying group I deh genes in addition to an associated insertion sequence element. Moreover, an identical conjugative catabolic plasmid was isolated exogenously in several transconjugants independently selected from biparental matings between Ralstonia eutropha JMP222 and enrichment samples. PCR cloning and sequencing of deh genes directly from enrichment cultures inoculated with the same soil revealed that an identical deh gene was present in both primary, secondary and tertiary enrichment cultures, although this deh could not be amplified directly from soil. Two alphaHA-utilising bacteria isolated at lower temperature were found also to contain group II deh genes. Transfer of the deh catabolic phenotype to R. eutropha strain JMP222 occurred at high frequencies for four strains tested, a result that was consistent with assignment of the plasmids to the IncP1 incompatibility group. The promiscuous nature and broad host range of IncP plasmids make them likely to be involved in horizontal gene transfer during adaptation of bacteria to degrade organohalogens.
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Affiliation(s)
- Katja E Hill
- School of Biosciences, Cardiff University, P.O. Box 915, Cardiff CF10 3TL, UK.
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Top EM, Springael D. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 2003; 14:262-9. [PMID: 12849778 DOI: 10.1016/s0958-1669(03)00066-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Retrospective studies clearly indicate that mobile genetic elements (MGEs) play a major role in the in situ spread and even de novo construction of catabolic pathways in bacteria, allowing bacterial communities to rapidly adapt to new xenobiotics. The construction of novel pathways seems to occur by an assembly process that involves horizontal gene transfer: different appropriate genes or gene modules that encode different parts of the novel pathway are recruited from phylogenetically related or distant hosts into one single host. Direct evidence for the importance of catabolic MGEs in bacterial adaptation to xenobiotics stems from observed correlations between catabolic gene transfer and accelerated biodegradation in several habitats and from studies that monitor catabolic MGEs in polluted sites.
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Affiliation(s)
- Eva M Top
- Department of Biological Sciences, 347 Life Sciences Building South, University of Idaho, Moscow, ID 83844-3051, USA.
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Dennis P, Edwards EA, Liss SN, Fulthorpe R. Monitoring gene expression in mixed microbial communities by using DNA microarrays. Appl Environ Microbiol 2003; 69:769-78. [PMID: 12570994 PMCID: PMC143597 DOI: 10.1128/aem.69.2.769-778.2003] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A DNA microarray to monitor the expression of bacterial metabolic genes within mixed microbial communities was designed and tested. Total RNA was extracted from pure and mixed cultures containing the 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Ralstonia eutropha JMP134, and the inducing agent 2,4-D. Induction of the 2,4-D catabolic genes present in this organism was readily detected 4, 7, and 24 h after the addition of 2,4-D. This strain was diluted into a constructed mixed microbial community derived from a laboratory scale sequencing batch reactor. Induction of two of five 2,4-D catabolic genes (tfdA and tfdC) from populations of JMP134 as low as 10(5) cells/ml was clearly detected against a background of 10(8) cells/ml. Induction of two others (tfdB and tfdE) was detected from populations of 10(6) cells/ml in the same background; however, the last gene, tfdF, showed no significant induction due to high variability. In another experiment, the induction of resin acid degradative genes was statistically detectable in sludge-fed pulp mill effluent exposed to dehydroabietic acid in batch experiments. We conclude that microarrays will be useful tools for the detection of bacterial gene expression in wastewaters and other complex systems.
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Affiliation(s)
- Philip Dennis
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
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Fukui R. Suppression of Soilborne Plant Pathogens through Community Evolution of Soil Microorganisms. Microbes Environ 2003. [DOI: 10.1264/jsme2.18.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ryo Fukui
- Department of Bio-productive Science, Faculty of Agriculture, Utsunomiya University
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Top EM, Springael D, Boon N. Catabolic mobile genetic elements and their potential use in bioaugmentation of polluted soils and waters. FEMS Microbiol Ecol 2002; 42:199-208. [DOI: 10.1111/j.1574-6941.2002.tb01009.x] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Hickey WJ, Sabat G, Yuroff AS, Arment AR, Pérez-Lesher J. Cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2. Appl Environ Microbiol 2001; 67:4603-9. [PMID: 11571162 PMCID: PMC93209 DOI: 10.1128/aem.67.10.4603-4609.2001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2001] [Accepted: 07/31/2001] [Indexed: 11/20/2022] Open
Abstract
We have identified in Pseudomonas aeruginosa strain JB2 a novel cluster of mobile genes encoding degradation of hydroxy- and halo-aromatic compounds. Nineteen open reading frames were located and, based on sequence similarities, were putatively identified as encoding a ring hydroxylating oxygenase (hybABCD), an ATP-binding cassette-type transporter, an extradiol ring-cleavage dioxygenase, transcriptional regulatory proteins, enzymes mediating chlorocatechol degradation, and transposition functions. Expression of hybABCD in Escherichia coli cells effected stoichiometric transformation of 2-hydroxybenzoate (salicylate) to 2,5-dihydroxybenzoate (gentisate). This activity was predicted from sequence similarity to functionally characterized genes, nagAaGHAb from Ralstonia sp. strain U2 (S. L. Fuenmayor, M. Wild, A. L. Boyes, and P. A. Williams, J. Bacteriol. 180:2522-2530, 1998), and is the second confirmed example of salicylate 5-hydroxylase activity effected by an oxygenase outside the flavoprotein group. Growth of strain JB2 or Pseudomonas huttiensis strain D1 (an organism that had acquired the 2-chlorobenzoate degradation phenotype from strain JB2) on benzoate yielded mutants that were unable to grow on salicylate or 2-chlorobenzoate and that had a deletion encompassing hybABCD and the region cloned downstream. The mutants' inability to grow on 2-chlorobenzoate suggested the loss of additional genes outside of, but contiguous with, the characterized region. Pulsed-field gel electrophoresis revealed a plasmid of >300 kb in strain D1, but no plasmids were detected in strain JB2. Hybridization analyses confirmed that the entire 26-kb region characterized here was acquired by strain D1 from strain JB2 and was located in the chromosome of both organisms. Further studies to delineate the element's boundaries and functional characteristics could provide new insights into the mechanisms underlying evolution of bacterial genomes in general and of catabolic pathways for anthropogenic pollutants in particular.
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Affiliation(s)
- W J Hickey
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin 53706-1299, USA.
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Providenti MA, Wyndham RC. Identification and functional characterization of CbaR, a MarR-like modulator of the cbaABC-encoded chlorobenzoate catabolism pathway. Appl Environ Microbiol 2001; 67:3530-41. [PMID: 11472929 PMCID: PMC93053 DOI: 10.1128/aem.67.8.3530-3541.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Comamonas testosteroni BR60 (formerly Alcaligenes sp. strain BR60), catabolism of the pollutant 3-chlorobenzoate (3CBA) is initiated by enzymes encoded by cbaABC, an operon found on composite transposon Tn5271 of plasmid pBRC60. The cbaABC gene product CbaABC converts 3CBA to protocatechuate (PCA) and 5-Cl-PCA, which are then metabolized by the chromosomal PCA meta (extradiol) ring fission pathway. In this study, cbaA was found to possess a sigma(70) type promoter. O(2) uptake experiments with whole cells and expression studies with cbaA-lacZ constructs showed that cbaABC was induced by 3CBA. Benzoate, which is not a substrate of the 3CBA pathway, was a gratuitous inducer, and CbaR, a MarR family repressor coded for by a divergently transcribed gene upstream of cbaABC, could modulate induction mediated by benzoate. Purified CbaR bound specifically to two regions of the cbaA promoter (P(cbaA)); site I, a high-affinity site, is between the transcriptional start point (position +1) and the start codon of cbaA, while site II, a lower-affinity site, overlaps position +1. 3CBA at concentrations as low as 40 microM interfered with binding to P(cbaA). PCA also interfered with binding, while benzoate only weakly disrupted binding. Unexpectedly, benzoate with a hydroxyl or carboxyl at position 3 improved CbaR binding. Data are also presented that suggest that an unidentified regulator is encoded on the chromosome that induces cbaABC in response to benzoate and 3CBA.
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Affiliation(s)
- M A Providenti
- Institute of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6
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Abstract
Nucleotide sequence analysis, and more recently whole genome analysis, shows that bacterial evolution has often proceeded by horizontal gene flow between different species and genera. In bacteria, gene transfer takes place by transformation, transduction, or conjugation and this review examines the roles of these gene transfer processes, between different bacteria, in a wide variety of ecological niches in the natural environment. This knowledge is necessary for our understanding of plasmid evolution and ecology, as well as for risk assessment. The rise and spread of multiple antibiotic resistance plasmids in medically important bacteria are consequences of intergeneric gene transfer coupled to the selective pressures posed by the increasing use and misuse of antibiotics in medicine and animal feedstuffs. Similarly, the evolution of degradative plasmids is a response to the increasing presence of xenobiotic pollutants in soil and water. Finally, our understanding of the role of horizontal gene transfer in the environment is essential for the evaluation of the possible consequences of the deliberate environmental release of natural or recombinant bacteria for agricultural and bioremediation purposes.
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Affiliation(s)
- J Davison
- Institut National de la Recherche Agronomique, Route de Saint Cyr, Versailles, F-78026, France.
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McGowan C, Fulthorpe R, Wright A, Tiedje JM. Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders. Appl Environ Microbiol 1998; 64:4089-92. [PMID: 9758850 PMCID: PMC106609 DOI: 10.1128/aem.64.10.4089-4092.1998] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class Proteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the alpha-Proteobacteria yielded tfdA PCR products. A comparison of the dendrogram of the tfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains with tfdA sequences highly similar to the tfdA sequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to a Burkholderia cepacia recipient.
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Affiliation(s)
- C McGowan
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48823-1101, USA
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Plasmids responsible for horizontal transfer of naphthalene catabolism genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from pseudomonas putida NCIB 9816-4. Appl Environ Microbiol 1998; 64:3633-40. [PMID: 9758778 PMCID: PMC106482 DOI: 10.1128/aem.64.10.3633-3640.1998] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The presence of a highly conserved nahAc allele among phylogenetically diverse bacteria carrying naphthalene-catabolic plasmids provided evidence for in situ horizontal gene transfer at a coal tar-contaminated site (J. B. Herrick, K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen, Appl. Environ. Microbiol. 63:2330-2337, 1997). The objective of the present study was to identify and characterize the different-sized naphthalene-catabolic plasmids in order to determine the probable mechanism of horizontal transfer of the nahAc gene in situ. Filter matings between naphthalene-degrading bacterial isolates and their cured progeny revealed that the naphthalene-catabolic plasmids were self-transmissible. Limited interstrain transfer was also found. Analysis of the restriction fragment length polymorphism (RFLP) patterns indicated that catabolic plasmids from 12 site-derived isolates were closely related to each other and to the naphthalene-catabolic plasmid (pDTG1) of Pseudomonas putida NCIB 9816-4, which was isolated decades ago in Bangor, Wales. The similarity among all site-derived naphthalene-catabolic plasmids and pDTG1 was confirmed by using the entire pDTG1 plasmid as a probe in Southern hybridizations. Two distinct but similar naphthalene-catabolic plasmids were retrieved directly from the microbial community indigenous to the contaminated site in a filter mating by using a cured, rifampin-resistant site-derived isolate as the recipient. RFLP patterns and Southern hybridization showed that both of these newly retrieved plasmids, like the isolate-derived plasmids, were closely related to pDTG1. These data indicate that a pDTG1-like plasmid is the mobile genetic element responsible for transferring naphthalene-catabolic genes among bacteria in situ. The pervasiveness and persistence of this naphthalene-catabolic plasmid suggest that it may have played a role in the adaptation of this microbial community to the coal tar contamination at our study site.
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Ravatn R, Studer S, Springael D, Zehnder AJ, van der Meer JR. Chromosomal integration, tandem amplification, and deamplification in Pseudomonas putida F1 of a 105-kilobase genetic element containing the chlorocatechol degradative genes from Pseudomonas sp. Strain B13. J Bacteriol 1998; 180:4360-9. [PMID: 9721270 PMCID: PMC107442 DOI: 10.1128/jb.180.17.4360-4369.1998] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of chlorobenzene-degrading transconjugants of Pseudomonas putida F1 which had acquired the genes for chlorocatechol degradation (clc) from Pseudomonas sp. strain B13 revealed that the clc gene cluster was present on a 105-kb amplifiable genetic element (named the clc element). In one such transconjugant, P. putida RR22, a total of seven or eight chromosomal copies of the entire genetic element were present when the strain was cultivated on chlorobenzene. Chromosomal integrations of the 105-kb clc element occurred in two different loci, and the target sites were located within the 3' end of glycine tRNA structural genes. Tandem amplification of the clc element was preferentially detected in one locus on the F1 chromosome. After prolonged growth on nonselective medium, transconjugant strain RR22 gradually diverged into subpopulations with lower copy numbers of the clc element. Two nonadjacent copies of the clc element in different loci always remained after deamplification, but strains with only two copies could no longer use chlorobenzene as a sole substrate. This result suggests that the presence of multiple copies of the clc gene cluster was a prerequisite for the growth of P. putida RR22 on chlorobenzene and that amplification of the element was positively selected for in the presence of chlorobenzene.
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Affiliation(s)
- R Ravatn
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), CH-8600 Dübendorf, Switzerland
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de Souza ML, Wackett LP, Sadowsky MJ. The atzABC genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl Environ Microbiol 1998; 64:2323-6. [PMID: 9603862 PMCID: PMC106326 DOI: 10.1128/aem.64.6.2323-2326.1998] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas sp. strain ADP initiates atrazine catabolism via three enzymatic steps, encoded by atzA, -B, and -C, which yield cyanuric acid, a nitrogen source for many bacteria. In-well lysis, Southern hybridization, and plasmid transfer studies indicated that the atzA, -B, and -C genes are localized on a 96-kb self-transmissible plasmid, pADP-1, in Pseudomonas sp. strain ADP. High-performance liquid chromatography analyses showed that cyanuric acid degradation was not encoded by pADP-1. pADP-1 was transferred to Escherichia coli strains at a frequency of 4.7 x 10(-2). This suggests a potential molecular mechanism for the dispersion of the atzABC genes to other soil bacteria.
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Affiliation(s)
- M L de Souza
- Department of Biochemistry, University of Minnesota, St. Paul, Minnesota 55108, USA
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Christensen BB, Sternberg C, Andersen JB, Eberl L, Moller S, Givskov M, Molin S. Establishment of new genetic traits in a microbial biofilm community. Appl Environ Microbiol 1998; 64:2247-55. [PMID: 9603843 PMCID: PMC106307 DOI: 10.1128/aem.64.6.2247-2255.1998] [Citation(s) in RCA: 194] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Conjugational transfer of the TOL plasmid (pWWO) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. The community consisted of three species, Pseudomonas putida RI, Acinetobacter sp. strain C6, and an unidentified isolate, D8. Only P. putida RI could act as a recipient for the TOL plasmid. Cells carrying a chromosomally integrated lacIq gene and a lacp-gfp-tagged version of the TOL plasmid were introduced as donor strains in the biofilm community after its formation. The occurrence of plasmid-carrying cells was analyzed by viable-count-based enumeration of donors and transconjugants. Upon transfer of the plasmids to the recipient cells, expression of green fluorescence was activated as a result of zygotic induction of the gfp gene. This allowed a direct in situ identification of cells receiving the gfp-tagged version of the TOL plasmid. Our data suggest that the frequency of horizontal plasmid transfer was low, and growth (vertical transfer) of the recipient strain was the major cause of plasmid establishment in the biofilm community. Employment of scanning confocal laser microscopy on fixed biofilms, combined with simultaneous identification of P. putida cells and transconjugants by 16S rRNA hybridization and expression of green fluorescence, showed that transconjugants were always associated with noninfected P. putida RI recipient microcolonies. Pure colonies of transconjugants were never observed, indicating that proliferation of transconjugant cells preferentially took place on preexisting P. putida RI microcolonies in the biofilm.
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Affiliation(s)
- B B Christensen
- Department of Microbiology, The Technical University of Denmark, DK-2800 Lyngby, Denmark
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Focht DD, Searles DB, Koh SC. Genetic exchange in soil between introduced chlorobenzoate degraders and indigenous biphenyl degraders. Appl Environ Microbiol 1996; 62:3910-3. [PMID: 8837452 PMCID: PMC168206 DOI: 10.1128/aem.62.10.3910-3913.1996] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pseudomonas aeruginosa JB2, a chlorobenzoate degrader, was inoculated into soil having indigenous biphenyl degraders but no identifiable 2-chlorobenzoate (2CBa) or 2,5-dichlorobenzoate (2,5DCBa) degraders. The absence of any indigenous chlorobenzoate degraders was noted by the failure to obtain enrichment cultures with the addition of 2CBa, 3CBa, or 2,5DCBa and by the failure of soil DNA to hybridize to the tfdC gene, which encodes ortho fission of chlorocatechols. In contrast, DNA extracted from inoculated soils hybridized to this probe. Bacteria able to utilize both biphenyl and 2CBa as growth substrates were absent in uninoculated soil, but their presence increased with time in the inoculated soils. This increase was related kinetically to the growth of biphenyl degraders. Pseudomonas sp. strain AW, a dominant biphenyl degrader, was selected as a possible parental strain. Eight of nine recombinant strains, chosen at random, had high phenotypic similarity (90% or more) to the inoculant; the other, strain JB2-M, had 78% similarity. Two hybrid strains, P. aeruginosa JB2-3 and Pseudomonas sp. JB2-M, were the most effective of all strains, including strain AW, in metabolizing polychlorinated biphenyls (Aroclor 1242). Repetitive extragenic palindromic-PCR analysis of putative parental strains JB2 and AW and the two recombinant strains JB2-3 and JB2-M showed similar fragments among the recombinants and JB2 but not AW. These results indicate that the bph genes were transferred to the chlorobenzoate-degrading inoculant from indigenous biphenyl degraders.
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Affiliation(s)
- D D Focht
- Department of Soil and Environmental Sciences, University of California, Riverside 92521, USA.
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DiGiovanni GD, Neilson JW, Pepper IL, Sinclair NA. Gene transfer of Alcaligenes eutrophus JMP134 plasmid pJP4 to indigenous soil recipients. Appl Environ Microbiol 1996; 62:2521-6. [PMID: 8779592 PMCID: PMC168035 DOI: 10.1128/aem.62.7.2521-2526.1996] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
This study evaluated the potential for gene transfer of a large catabolic plasmid from an introduced organism to indigenous soil recipients. The donor organism Alcaligenes eutrophus JMP134 contained the 80-kb plasmid pJP4, which contains genes that code for mercury resistance. Genes on this plasmid plus chromosomal genes also allow degradation of 2,4-dichloruphenoxyacetic acid (2,4-D). When JMP134 was inoculated into a nonsterile soil microcosm amended with 1,000 micrograms of 2,4-D g-1, significant (10(6) g of soil-1) populations of indigenous recipients or transconjugants arose. These transconjugants all contained an 80-kb plasmid similar in size to pJP4, and all degraded 2,4-D. In addition, all transconjugants were resistant to mercury and contained the tfdB gene of pJP4 as detected by PCR. No mercury-resistant, 2,4-D-degrading organisms with large plasmids or the tfdB gene were found in the 2,4-D-amended but uninoculated control microcosm. These data clearly show that the plasmid pJP4 was transferred to indigenous soil recipients. Even more striking is the fact that not only did the indigenous transconjugant population survive and proliferate but also enhanced rates of 2,4-D degradation occurred relative to microcosms in which no such gene transfer occurred. Overall, these data indicate that gene transfer from introduced organisms is an effective means of bioaugmentation and that survival of the introduced organism is not a prerequisite for biodegradation that utilizes introduced biodegradative genes.
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Affiliation(s)
- G D DiGiovanni
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson 85721, USA
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38
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Nakatsu CH, Fulthorpe RR, Holland BA, Peel MC, Wyndham RC. The phylogenetic distribution of a transposable dioxygenase from the Niagara River watershed. Mol Ecol 1995; 4:593-603. [PMID: 7582167 DOI: 10.1111/j.1365-294x.1995.tb00259.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Horizontal gene transfer in the Bacteria has been demonstrated to occur under natural conditions. The ecological impact of gene transfer events depends on the new genetic material being expressed in recipient organisms, and on natural selection processes operating on these recipients. The phylogenetic distribution of cbaAB genes for chlorobenzoate 3,4-(4,5)-dioxygenase, which are carried within Tn5271 on the IncP beta plasmid pBRC60, was investigated using isolates from freshwater microcosms and from the Niagara River watershed. The latter included isolates from surface water, groundwater and bioremediation reactor samples. The cbaAB genes have become integrated, through interspecific transfer, primarily into species of the beta Proteobacteria (44/48 isolates). Only four isolates, identified as Pseudomonas fluorescens (3/48) and Xanthomonas maltophilia (1/48), belonged to the gamma Proteobacteria, despite the observation that pBRC60 was capable of mobilizing these genes into a wide range of beta and gamma Proteobacteria in the laboratory. The natural host range correlated with the distribution of the meta-ring-fission pathway for metabolism of protocatechuates formed when the cbaAB genes were expressed (45/48 isolates). We proposed the hypothesis that natural selection has favoured recipients that successfully integrate the activity of the transferred dioxygenase with the conserved meta ring-fission pathway. The hypothesis was tested by transferring a plasmid construct containing the cbaAB genes into type strains representative of the beta and gamma Proteobacteria. The concept of applying mobile catabolic genes to probe the phylogenetic distribution of compatible degradative pathways is discussed.
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Affiliation(s)
- C H Nakatsu
- Institute of Biology, Carleton University, Ottawa, ON, Canada
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Doyle JD, Stotzky G, McClung G, Hendricks CW. Effects of genetically engineered microorganisms on microbial populations and processes in natural habitats. ADVANCES IN APPLIED MICROBIOLOGY 1995; 40:237-87. [PMID: 7604738 DOI: 10.1016/s0065-2164(08)70366-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- J D Doyle
- ManTech Environmental Technology, Inc., Corvallis, Oregon 97333, USA
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Abstract
The structure and function of transposable elements that code for catabolic pathways involved in the biodegradation of organic compounds are reviewed. Seven of these catabolic transposons have structural features that place them in the Class I (composite) or Class II (Tn3-family) bacterial elements. One is a conjugative transposon. Another three have been found to have properties of transposable elements but have not been characterized sufficiently to assign to a known class. Structural features of the toluene (Tn4651/Tn4653) and naphthalene (Tn4655) elements that illustrate the enormous potential for acquisition, deletion and rearrangement of DNA within catabolic transposons are discussed. The recently characterized chlorobenzoate (Tn5271) and chlorobenzene (Tn5280) catabolic transposons encode different aromatic ring dioxygenases, however they both illustrate the constraints that must be overcome when recipients of catabolic transposons assemble and regulate complete metabolic pathways for environmental pollutants. The structures of the chlorobenzoate catabolic transposon Tn5271 and the related haloacetate dehalogenase catabolic element of plasmid pUO1 are compared and a hypothesis for their formation is discussed. The structures and activities of catabolic transposons of unknown class coding for the catabolism of halogenated alkanoic acids (DEH) and chlorobiphenyl (Tn4371) are also reviewed.
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Affiliation(s)
- R C Wyndham
- Ottawa-Carleton Institute of Biology, Carleton University, ON Canada
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43
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Fetzner S, Lingens F. Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol Rev 1994; 58:641-85. [PMID: 7854251 PMCID: PMC372986 DOI: 10.1128/mr.58.4.641-685.1994] [Citation(s) in RCA: 148] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail.
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Affiliation(s)
- S Fetzner
- Institut für Mikrobiologie der Universität Hohenheim, Stuttgart, Germany
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44
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Springael D, Diels L, Mergeay M. Transfer and expression of PCB-degradative genes into heavy metal resistant Alcaligenes eutrophus strains. Biodegradation 1994; 5:343-57. [PMID: 7765842 DOI: 10.1007/bf00696469] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Sites polluted with organic compounds frequently contain inorganic pollutants such as heavy metals. The latter might inhibit the biodegradation of the organics and impair bioremediation. Chromosomally located polychlorinated biphenyl (PCB) catabolic genes of Alcaligenes eutrophus A5, Achromobacter sp. LBS1C1 and Alcaligenes denitrificans JB1 were introduced into the heavy metal resistant Alcaligenes eutrophus strain CH34 and related strains by means of natural conjugation. Mobile elements containing the PCB catabolic genes were transferred from A. eutrophus A5 and Achromobacter sp. LB51C1 into A. eutrophus CH34 after transposition onto their endogenous IncP plasmids pSS50 and pSS60, respectively. The PCB catabolic genes of A. denitrificans JB1 were transferred into A. eutrophus CH34 by means of RP4::Mu3A mediated prime plasmid formation. The A. eutrophus CH34 transconjugant strains expressed both catabolic and metal resistance markers. Such constructs may be useful for the decontamination of sites polluted by both organics and heavy metals.
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Affiliation(s)
- D Springael
- Laboratory of Genetics and Biotechnology, Flemish Institute for Technological Research (VITO), Mol, Belgium
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45
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Rore H, Demolder K, Wilde K, Top E, Houwen F, Verstraete W. Transfer of the catabolic plasmid RP4::Tn4371 to indigenous soil bacteria and its effect on respiration and biphenyl breakdown. FEMS Microbiol Ecol 1994. [DOI: 10.1111/j.1574-6941.1994.tb00231.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Neilson JW, Josephson KL, Pepper IL, Arnold RB, Di Giovanni GD, Sinclair NA. Frequency of horizontal gene transfer of a large catabolic plasmid (pJP4) in soil. Appl Environ Microbiol 1994; 60:4053-8. [PMID: 7993092 PMCID: PMC201935 DOI: 10.1128/aem.60.11.4053-4058.1994] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Limited work has been done to assess the bioremediation potential of transfer of plasmid-borne degradative genes from introduced to indigenous organisms in the environment. Here we demonstrate the transfer by conjugation of the catabolic plasmid pJP4, using a model system with donor and recipient organisms. The donor organism was Alcaligenes eutrophus JMP134 and the recipient organism was Variovorax paradoxus isolated from a toxic waste site. Plasmid pJP4 contains genes for mercury resistance and 2,4-dichlorophenoxyacetic (2,4-D) acid degradation. A transfer frequency of approximately 1/10(3) donor and recipient cells (parent cells) was observed on solid agar media, decreasing to 1/10(5) parent cells in sterile soil and finally 1/10(6) parent cells in 2,4-D-amended, nonsterile soil. Presumptive transconjugants were confirmed to be resistant to Hg, to be capable of degrading 2,4-D, and to contain a plasmid of size comparable to that of pJP4. In addition, we confirmed the transfer through PCR amplifications of the tfdB gene. Although transfer of pJP4 did occur at a high frequency in pure culture, the rate was significantly decreased by the introduction of abiotic (sterile soil) and biotic (nonsterile soil) stresses. An evaluation of the data from this model system implies that the reliance on plasmid transfer from a donor organism as a remediative strategy has limited potential.
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Affiliation(s)
- J W Neilson
- Department of Soil and Water Science, University of Arizona, Tucson 85721
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Wyndham RC, Nakatsu C, Peel M, Cashore A, Ng J, Szilagyi F. Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system. Appl Environ Microbiol 1994; 60:86-93. [PMID: 8117095 PMCID: PMC201273 DOI: 10.1128/aem.60.1.86-93.1994] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The distribution of Tn5271-related DNA sequences in samples of groundwater and a groundwater bioremediation system at the Hyde Park (Niagara Falls, N.Y.) chemical landfill site was investigated. PCR amplification of target sequences within the cha genes of Tn5271 revealed similar sequences in the groundwater community and in samples from the sequencing batch reactors treating that groundwater. Cell dilution combined with PCR amplification indicated that cha sequences were carried in about 1 of 10 culturable bacteria from the treatment system. Characterization of isolates involved in chlorobenzoate and toluene biodegradation in the treatment system indicated that two phenotypic clusters, Alcaligenes faecalis type 2 and CDC group IVC-2, contained all of the Tn5271 probe-positive isolates from the community. These two groups differed phenotypically from recipient groups isolated following horizontal transfer of pBRC60 (Tn5271) in pristine freshwater microcosms. A genetic rearrangement in Tn5271 attributable to the intramolecular transposition of the flanking element IS1071R was detected in an isolate from the treatment system. Comparison of the structure of the intramolecular transposition derivative from groundwater isolate OCC13(pBRC13) with a laboratory-derived intramolecular transposition derivative of pBRC60 revealed similarities. The rearrangement was shown to increase the stability of the plasmid under starvation conditions.
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Affiliation(s)
- R C Wyndham
- Institute of Biology, Carleton University, Ottawa, Ontario, Canada
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48
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Nakatsu CH, Wyndham RC. Cloning and expression of the transposable chlorobenzoate-3,4-dioxygenase genes of Alcaligenes sp. strain BR60. Appl Environ Microbiol 1993; 59:3625-33. [PMID: 8285670 PMCID: PMC182508 DOI: 10.1128/aem.59.11.3625-3633.1993] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Growth on 3-chlorobenzoate was found to induce the enzymes of the protocatechuate meta ring fission pathway in Alcaligenes sp. strain BR60. The chlorobenzoate catabolic genes, designated cba, were localized to a 3.7-kb NotI-EcoRI fragment within the nonrepeated region of the composite transposon Tn5271. The cba genes were cloned onto two broad-host-range vectors and expressed in Escherichia coli and Alcaligenes sp. strain BR6024. In E. coli, expression of the cba genes with the IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible tac promoter of the IncQ vector pMMB66HE resulted in the production of protocatechuate and chlorodihydroxybenzoate metabolites of 3-chlorobenzoate. Expression of this construct in one orientation resulted in the formation of two polypeptides 51 and 42 kDa in size. This result was confirmed by subcloning into pGEM3Zf and then incorporating L-35S-methionine into newly synthesized proteins, using the thermally regulated T7 polymerase-promoter system. Introduction of the NotI-EcoRI fragment into Alcaligenes sp. strain BR6024 (Cba-P), using the IncP broad-host-range, mobilizable plasmid pBW13, restored the 3-chlorobenzoate-degradative phenotype and resulted in the accumulation of protocatechuate and chlorodihydroxybenzoate intermediates. The data indicate that a two-component dioxygenase specified by Tn5271 oxidizes 3-chlorobenzoate at the 3,4- or 4,5-positions. This activity extends the range of pathways for chloroaromatic compounds known to be functional in the environment. The new pathway avoids the toxicity attributed to the accumulation of chlorocatechol metabolites in bacteria degrading chlorobenzoates.
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Affiliation(s)
- C H Nakatsu
- Institute of Biology, Carleton University, Ottawa, Ontario, Canada
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van der Meer JR, de Vos WM, Harayama S, Zehnder AJ. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev 1992; 56:677-94. [PMID: 1480115 PMCID: PMC372894 DOI: 10.1128/mr.56.4.677-694.1992] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microorganisms in the environment can often adapt to use xenobiotic chemicals as novel growth and energy substrates. Specialized enzyme systems and metabolic pathways for the degradation of man-made compounds such as chlorobiphenyls and chlorobenzenes have been found in microorganisms isolated from geographically separated areas of the world. The genetic characterization of an increasing number of aerobic pathways for degradation of (substituted) aromatic compounds in different bacteria has made it possible to compare the similarities in genetic organization and in sequence which exist between genes and proteins of these specialized catabolic routes and more common pathways. These data suggest that discrete modules containing clusters of genes have been combined in different ways in the various catabolic pathways. Sequence information further suggests divergence of catabolic genes coding for specialized enzymes in the degradation of xenobiotic chemicals. An important question will be to find whether these specialized enzymes evolved from more common isozymes only after the introduction of xenobiotic chemicals into the environment. Evidence is presented that a range of genetic mechanisms, such as gene transfer, mutational drift, and genetic recombination and transposition, can accelerate the evolution of catabolic pathways in bacteria. However, there is virtually no information concerning the rates at which these mechanisms are operating in bacteria living in nature and the response of such rates to the presence of potential (xenobiotic) substrates. Quantitative data on the genetic processes in the natural environment and on the effect of environmental parameters on the rate of evolution are needed.
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Affiliation(s)
- J R van der Meer
- Department of Microbiology, Wageningen Agricultural University, The Netherlands
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50
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Richaume A, Smit E, Faurie G, Elsas JD. Influence of soil type on the transfer of plasmid RP4p fromPseudomonas fluorescensto introduced recipient and to indigenous bacteria. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05785.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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