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Soares-Castro P, Soares F, Reis F, Lino-Neto T, Santos PM. Bioprospection of the bacterial β-myrcene-biotransforming trait in the rhizosphere. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12650-w. [PMID: 37405434 PMCID: PMC10386936 DOI: 10.1007/s00253-023-12650-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023]
Abstract
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr+). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr+ isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr+-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr+ bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr+ trait is spread across different bacterial taxonomic classes. • The core-code for the Myr+ trait was detected in a novel ICE, only found in Pseudomonas spp.
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Affiliation(s)
- Pedro Soares-Castro
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisbon, Portugal
| | - Filipa Soares
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Francisca Reis
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Teresa Lino-Neto
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal
| | - Pedro M Santos
- CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal.
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He L, Huang X, Zhang G, Yuan L, Shen E, Zhang L, Zhang XH, Zhang T, Tao L, Ju F. Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. ENVIRONMENTAL MICROBIOME 2022; 17:19. [PMID: 35468809 PMCID: PMC9036809 DOI: 10.1186/s40793-022-00413-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench. RESULTS The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria. CONCLUSIONS This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.
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Affiliation(s)
- Liuqing He
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Xinyu Huang
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Ling Yuan
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Enhui Shen
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 Shandong China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China
| | - Liang Tao
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
| | - Feng Ju
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024 Zhejiang China
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 Zhejiang China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 Zhejiang China
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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Catabolism of the groundwater micropollutant 2,6-dichlorobenzamide beyond 2,6-dichlorobenzoate is plasmid encoded in Aminobacter sp. MSH1. Appl Microbiol Biotechnol 2018; 102:7963-7979. [PMID: 29984394 DOI: 10.1007/s00253-018-9189-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/19/2018] [Accepted: 06/20/2018] [Indexed: 01/01/2023]
Abstract
Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as sole source of carbon and energy. In the first step, MSH1 converts BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) by means of the BbdA amidase encoded on the IncP-1β plasmid pBAM1. Information about the genes and degradation steps involved in 2,6-DCBA metabolism in MSH1 or any other organism is currently lacking. Here, we show that the genes for 2,6-DCBA degradation in strain MSH1 reside on a second catabolic plasmid in MSH1, designated as pBAM2. The complete sequence of pBAM2 was determined revealing that it is a 53.9 kb repABC family plasmid. The 2,6-DCBA catabolic genes on pBAM2 are organized in two main clusters bordered by IS elements and integrase genes and encode putative functions like Rieske mono-/dioxygenase, meta-cleavage dioxygenase, and reductive dehalogenases. The putative mono-oxygenase encoded by the bbdD gene was shown to convert 2,6-DCBA to 3-hydroxy-2,6-dichlorobenzoate (3-OH-2,6-DCBA). 3-OH-DCBA was degraded by wild-type MSH1 and not by a pBAM2-free MSH1 variant indicating that it is a likely intermediate in the pBAM2-encoded DCBA catabolic pathway. Based on the activity of BbdD and the putative functions of the other catabolic genes on pBAM2, a metabolic pathway for BAM/2,6-DCBA in strain MSH1 was suggested.
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Sabir DK, Grosjean N, Rylott EL, Bruce NC. Investigating differences in the ability of XplA/B-containing bacteria to degrade the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). FEMS Microbiol Lett 2018; 364:3958792. [PMID: 28854671 DOI: 10.1093/femsle/fnx144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/11/2017] [Indexed: 11/13/2022] Open
Abstract
The xenobiotic hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a toxic explosive and environmental pollutant. This study examines three bacterial species that degrade RDX, using it as a sole source of nitrogen for growth. Although isolated from diverse geographical locations, the species contain near identical copies of genes encoding the RDX-metabolising cytochrome P450, XplA and accompanying reductase, XplB. Sequence analysis indicates a single evolutionary origin for xplA and xplB as part of a genomic island, which has been distributed around the world via horizontal gene transfer. Despite the fact that xplA and xplB are highly conserved between species, Gordonia sp. KTR9 and Microbacterium sp. MA1 degrade RDX more slowly than Rhodococcus rhodochrous 11Y. Both Gordonia sp. KTR9 and Microbacterium sp. MA1 were found to contain single base-pair mutations in xplB which, following expression and purification, were found to encode inactive XplB protein. Additionally, the Gordonia sp. KTR9 XplB was fused to glutamine synthetase, which would be likely to sterically inhibit XplB activity. Although the glutamine synthetase is fused to XplB and truncated by 71 residues, it was found to be active. Glutamine synthetase has been implicated in the regulation of nitrogen levels; controlling nitrogen availability will be important for effective bioremediation of RDX.
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Affiliation(s)
- Dana Khdr Sabir
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK.,Department of General Sciences, Charmo University, 46023 Chamchamal, Sulaimani, Kurdistan Region- IRAQ
| | - Nicolas Grosjean
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Elizabeth L Rylott
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
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Groundwater contamination with 2,6-dichlorobenzamide (BAM) and perspectives for its microbial removal. Appl Microbiol Biotechnol 2017; 101:5235-5245. [PMID: 28616645 DOI: 10.1007/s00253-017-8362-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 01/26/2023]
Abstract
The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water. Bioremediation is suggested as a valuable strategy for removing BAM from groundwater by deploying dedicated BAM-degrading bacteria in DWTP sand filters. Only a few bacterial strains with the capability to degrade BAM have been isolated, and of these, only three isolates belonging to the Aminobacter genus are able to mineralise BAM. Considerable effort has been made to elucidate degradation pathways, kinetics and degrader genes, and research has recently been presented on the application of strain Aminobacter sp. MSH1 for the purification of BAM-contaminated water. The aim of the present review was to provide insight into the issue of BAM contamination and to report on the current status and knowledge with regard to the application of microorganisms for purification of BAM-contaminated water resources. This paper discusses the prospects and challenges for bioaugmentation of DWTP sand filters with specific BAM-degrading bacteria and identifies relevant perspectives for future research.
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George KW, Hay AG. Bacterial strategies for growth on aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:1-33. [PMID: 21459192 DOI: 10.1016/b978-0-12-387022-3.00005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the biodegradation of aromatic compounds has been studied for over 40 years, there is still much to learn about the strategies bacteria employ for growth on novel substrates. Elucidation of these strategies is crucial for predicting the environmental fate of aromatic pollutants and will provide a framework for the development of engineered bacteria and degradation pathways. In this chapter, we provide an overview of studies that have advanced our knowledge of bacterial adaptation to aromatic compounds. We have divided these strategies into three broad categories: (1) recruitment of catabolic genes, (2) expression of "repair" or detoxification proteins, and (3) direct alteration of enzymatic properties. Specific examples from the literature are discussed, with an eye toward the molecular mechanisms that underlie each strategy.
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Affiliation(s)
- Kevin W George
- Field of Environmental Toxicology, Cornell University Ithaca, New York, USA; Department of Microbiology, Wing Hall, Cornell University Ithaca, New York, USA
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von Rozycki T, Nies DH, Saier MH. Genomic analyses of transport proteins in Ralstonia metallidurans. Comp Funct Genomics 2010; 6:17-56. [PMID: 18629293 PMCID: PMC2448597 DOI: 10.1002/cfg.454] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2004] [Revised: 12/14/2004] [Accepted: 12/15/2004] [Indexed: 11/06/2022] Open
Abstract
Ralstonia (Wautersia, Cupriavidus) metallidurans (Rme) is better able to withstand
high concentrations of heavy metals than any other well-studied organism. This fact
renders it a potential agent of bioremediation as well as an ideal model organism for
understanding metal resistance phenotypes. We have analysed the genome of Rme
for genes encoding homologues of established and putative transport proteins; 13%
of all genes in Rme encode such homologues. Nearly one-third of the transporters
identified (32%) appear to function in inorganic ion transport with three-quarters
of these acting on cations. Transporters specific for amino acids outnumber sugar
transporters nearly 3 : 1, and this fact plus the large number of uptake systems for
organic acids indicates the heterotrophic preferences of these bacteria. Putative drug
efflux pumps comprise 10% of the encoded transporters, but numerous efflux pumps
for heavy metals, metabolites and macromolecules were also identified. The results
presented should facilitate genetic manipulation and mechanistic studies of transport
in this remarkable bacterium.
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Affiliation(s)
- Torsten von Rozycki
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA
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Vanbroekhoven K, Ryngaert A, Wattiau P, Mot R, Springael D. Acinetobacter diversity in environmental samples assessed by 16S rRNA gene PCR-DGGE fingerprinting. FEMS Microbiol Ecol 2009; 50:37-50. [PMID: 19712375 DOI: 10.1016/j.femsec.2004.05.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
A primer pair was designed to selectively amplify a fragment of the Acinetobacter 16S rRNA gene from environmental samples by PCR. 16S rRNA gene products were only obtained in PCRs with DNA from members of the genus Acinetobacter and not with DNA from other bacterial species. Denaturing gradient gel electrophoresis (DGGE) of the Acinetobacter 16S rRNA gene amplicons enabled discrimination between different Acinetobacter species. PCR using the Acinetobacter primer pair allowed detection of Acinetobacter in soil with a detection limit of 10(4) cells g(-1) soil, but attachment of the GC-clamp to the forward primer resulted in a 100-fold decrease in sensitivity. Using a nested PCR approach, the detection limit could be lowered to at least 10 cells g(-1) of soil. The method was applied to assess Acinetobacter diversity in soil samples originating from different historically hydrocarbon-contaminated sites. In addition, for one oil-contaminated soil, the dynamics of the Acinetobacter community in response to different treatments was monitored over time in a laboratory biostimulation experimental set-up. In all cases, bands in the DGGE fingerprints were cloned and sequenced. Environmental samples taken from a mineral oil-contaminated site and from a kerosene-contaminated site demonstrated relatively simple Acinetobacter 16S rRNA gene fingerprints with A. lwoffii and A. johnsonii as dominant members. In contrast, soils derived from MTBE- and BTEX-contaminated sites did not harbor detectable Acinetobacter populations. Although Acinetobacter was detected in the soil employed for the biostimulation experiment prior to treatment, substantial changes in its populations were observed depending on the treatment.
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Affiliation(s)
- Karolien Vanbroekhoven
- Environmental and Process Technology, Vlaamse Instelling voor Technologisch Onderzoek, Boeretang 200, B-2400 Mol, Belgium
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Furukawa K, Fujihara H. Microbial degradation of polychlorinated biphenyls: Biochemical and molecular features. J Biosci Bioeng 2008; 105:433-49. [PMID: 18558332 DOI: 10.1263/jbb.105.433] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/04/2008] [Indexed: 11/17/2022]
Affiliation(s)
- Kensuke Furukawa
- Depatment of Food and Bioscience, Faculty of Food and Nutrition, Beppu University, Beppu, Ohita 874-8501, Japan.
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Zhu C, Zhang L, Zhao L. Molecular cloning, genetic organization of gene cluster encoding phenol hydroxylase and catechol 2,3-dioxygenase in Alcaligenes faecalis IS-46. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9660-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Phale PS, Basu A, Majhi PD, Deveryshetty J, Vamsee-Krishna C, Shrivastava R. Metabolic Diversity in Bacterial Degradation of Aromatic Compounds. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2007; 11:252-79. [PMID: 17883338 DOI: 10.1089/omi.2007.0004] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.
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Affiliation(s)
- Prashant S Phale
- Biotechnology Group, School of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, India.
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Plotnikova EG, Rybkina DO, Anan’ina LN, Yastrebova OV, Demakov VA. Characteristics of microorganisms isolated from technogenic soils of the Kama region. RUSS J ECOL+ 2006. [DOI: 10.1134/s1067413606040035] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Springael D, Top EM. Horizontal gene transfer and microbial adaptation to xenobiotics: new types of mobile genetic elements and lessons from ecological studies. Trends Microbiol 2004; 12:53-8. [PMID: 15040322 DOI: 10.1016/j.tim.2003.12.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The characterization of bacteria that degrade organic xenobiotics has revealed that they can adapt to these compounds by expressing 'novel' catabolic pathways. At least some of them appear to have evolved by patchwork assembly of horizontally transmitted genes and subsequent mutations and gene rearrangements. Recent studies have revealed the existence of new types of xenobiotic catabolic mobile genetic elements, such as catabolic genomic islands, which integrate into the chromosome after transfer. The significance of horizontal gene transfer and patchwork assembly for bacterial adaptation to pollutants under real environmental conditions remains uncertain, but recent publications suggest that these processes do occur in a polluted environment.
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Affiliation(s)
- Dirk Springael
- Department of Land Management, Faculty of Agriculture and Applied Biological Sciences, Catholic University of Leuven, Belgium.
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Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D. The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol 2003; 69:4837-45. [PMID: 12902278 PMCID: PMC169086 DOI: 10.1128/aem.69.8.4837-4845.2003] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the biphenyl catabolic transposon Tn4371 has been completed and analyzed. It confirmed that the element has a mosaic structure made of several building blocks. In addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of Achromobacter georgiopolitanum KKS102, Tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, plasmid functions. One gene cluster contains most of the genes required to express a type IV secretion-mating pair formation apparatus coupled with a TraG ATPase, all of which are related to those found on IncP and Ti plasmids. Orthologues of all Tn4371 plasmid-related genes and of the tyrosine recombinase gene were found, with a very similar organization, in the chromosome of Ralstonia solanacearum and on the yet-to-be-determined genomic sequences of Erwinia chrysanthemi and Azotobacter vinelandii. In each of these chromosomal segments, conserved segments were separated by different groups of genes, which also differed from the Tn4371 bph genes. The conserved blocks of genes were also identified, in at least two copies, in the chromosome of Ralstonia metallidurans CH34. Tn4371 thus appears to represent a new family of potentially mobile genomic islands with a broad host range since they reside in a wide range of soil proteobacteria, including plant pathogens.
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van der Meer JR, Sentchilo V. Genomic islands and the evolution of catabolic pathways in bacteria. Curr Opin Biotechnol 2003; 14:248-54. [PMID: 12849776 DOI: 10.1016/s0958-1669(03)00058-2] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Genes for the degradation of organic pollutants have usually been allocated to plasmid DNAs in bacteria or considered non-mobile when detected in the chromosome. New discoveries have shown that catabolic genes can also be part of so-called integrative and conjugative elements (ICElands), a group of mobile DNA elements also known as genomic islands and conjugative transposons. One such ICEland is the clc element for chlorobenzoate and chlorocatechol degradation in Pseudomonas sp. strain B13. Genome comparisons and genetic data on integrase functioning reveal that the clc element and several other unclassified ICElands belong to a group of elements with conserved features. The clc element is unique among them in carrying the genetic information for several degradation pathways, whereas the others give evidence for pathogenicity functions. Many more such elements may exist, bridging the gap between pathogenicity and degradation functions.
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Affiliation(s)
- Jan Roelof van der Meer
- Swiss Federal Institute for Environmental Science and Technology, EAWAG, Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland.
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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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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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