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Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. CHEMOSPHERE 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
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Raj A, Dubey A, Malla MA, Kumar A. Pesticide pestilence: Global scenario and recent advances in detection and degradation methods. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 338:117680. [PMID: 37011532 DOI: 10.1016/j.jenvman.2023.117680] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/23/2023] [Accepted: 03/04/2023] [Indexed: 06/19/2023]
Abstract
Increased anthropogenic activities are confronted as the main cause for rising environmental and health concerns globally, presenting an indisputable threat to both environment and human well-being. Modern-day industrialization has given rise to a cascade of concurrent environmental and health challenges. The global human population is growing at an alarming rate, posing tremendous pressure on future food security, and healthy and environmentally sustainable diets for all. To feed all, the global food production needs to increase by 50% by 2050, but this increase has to occur from the limited arable land, and under the present-day climate variabilities. Pesticides have become an integral component of contemporary agricultural system, safeguarding crops from pests and diseases and their use must be reduce to fulfill the SDG (Sustainable Development Goals) agenda . However, their indiscriminate use, lengthy half-lives, and high persistence in soil and aquatic ecosystems have impacted global sustainability, overshot the planetary boundaries and damaged the pure sources of life with severe and negative impacts on environmental and human health. Here in this review, we have provided an overview of the background of pesticide use and pollution status and action strategies of top pesticide-using nations. Additionally, we have summarized biosensor-based methodologies for the rapid detection of pesticide residue. Finally, omics-based approaches and their role in pesticide mitigation and sustainable development have been discussed qualitatively. The main aim of this review is to provide the scientific facts for pesticide management and application and to provide a clean, green, and sustainable environment for future generations.
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Affiliation(s)
- Aman Raj
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, M.P., India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar, 470003, M.P, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar, 470003, M.P., India; Metagenomics and Secretomics Research Laboratory, Department of Botany, University of Allahabad (A Central University), Prayagraj, 211002, U.P., India.
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Fujihara H, Hirose J, Suenaga H. Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria. Front Microbiol 2023; 14:1168246. [PMID: 37350784 PMCID: PMC10282184 DOI: 10.3389/fmicb.2023.1168246] [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] [Received: 02/17/2023] [Accepted: 05/16/2023] [Indexed: 06/24/2023] Open
Abstract
A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.
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Affiliation(s)
- Hidehiko Fujihara
- Department of Food and Fermentation Sciences, Faculty of Food and Nutrition Sciences, Beppu University, Beppu, Japan
| | - Jun Hirose
- Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, Miyazaki, Japan
| | - Hikaru Suenaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Hassan S, Ganai BA. Deciphering the recent trends in pesticide bioremediation using genome editing and multi-omics approaches: a review. World J Microbiol Biotechnol 2023; 39:151. [PMID: 37029313 DOI: 10.1007/s11274-023-03603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Pesticide pollution in recent times has emerged as a grave environmental problem contaminating both aquatic and terrestrial ecosystems owing to their widespread use. Bioremediation using gene editing and system biology could be developed as an eco-friendly and proficient tool to remediate pesticide-contaminated sites due to its advantages and greater public acceptance over the physical and chemical methods. However, it is indispensable to understand the different aspects associated with microbial metabolism and their physiology for efficient pesticide remediation. Therefore, this review paper analyses the different gene editing tools and multi-omics methods in microbes to produce relevant evidence regarding genes, proteins and metabolites associated with pesticide remediation and the approaches to contend against pesticide-induced stress. We systematically discussed and analyzed the recent reports (2015-2022) on multi-omics methods for pesticide degradation to elucidate the mechanisms and the recent advances associated with the behaviour of microbes under diverse environmental conditions. This study envisages that CRISPR-Cas, ZFN and TALEN as gene editing tools utilizing Pseudomonas, Escherichia coli and Achromobacter sp. can be employed for remediation of chlorpyrifos, parathion-methyl, carbaryl, triphenyltin and triazophos by creating gRNA for expressing specific genes for the bioremediation. Similarly, systems biology accompanying multi-omics tactics revealed that microbial strains from Paenibacillus, Pseudomonas putida, Burkholderia cenocepacia, Rhodococcus sp. and Pencillium oxalicum are capable of degrading deltamethrin, p-nitrophenol, chlorimuron-ethyl and nicosulfuron. This review lends notable insights into the research gaps and provides potential solutions for pesticide remediation by using different microbe-assisted technologies. The inferences drawn from the current study will help researchers, ecologists, and decision-makers gain comprehensive knowledge of value and application of systems biology and gene editing in bioremediation assessments.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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Nanjani S, Patel Z, Sharma S, Pandita PR, Pandit R, Joshi MN, Patel AK, Joshi C. Transcriptome profiling reveals upregulation of benzoate degradation and related genes in Pseudomonas aeruginosa D6 during textile dye degradation. ENVIRONMENTAL RESEARCH 2022; 212:113288. [PMID: 35427588 DOI: 10.1016/j.envres.2022.113288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/10/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
An upsurge in textile dye pollution has demanded immediate efforts to develop an optimum technology for their bioremediation. However, the molecular mechanism underpinning aerobic decolorization of dyes is still in its infancy. Thus, in the current work, the intricacies of aerobic remediation of textile dyes by Pseudomonas aeruginosa D6 were understood via a transcriptomic approach. The bacterium isolated from the sludge sample of a common effluent treatment plant was able to decolorize 54.42, 57.66, 50.84 and 65.86% of 100 mg L-1 of four different dyes i.e., TD01, TD04, TD05, and TD06, respectively. The maximum decolorization was achieved within six days and thus, the first and sixth day of incubation were selected for transcriptome analysis at the early and late phase of the decolorization, respectively. The expression profiles of all samples were compared to gain insight into the dye-specific response of bacterium and it was found that it behaved most uniquely in the presence of the dye TD01. Several genes critical to core metabolic processes like the TCA cycle, glycolysis, pentose phosphate pathway, translation, cell motility etc. Were found to be overexpressed in the presence of dyes. Interestingly, in response to dyes, the benzoate degradation pathway was significantly upregulated in the bacterium as compared to control (i.e., bacterium without dye). Thus, seven genes contributing to the induction of the same were further studied by RT-qPCR analysis. Overall, the involvement of the benzoate pathway implies the appearance of aromatic intermediates during decolorization, which in turn infers dye degradation.
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Affiliation(s)
- Sandhya Nanjani
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Zarna Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Shruti Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Priti Raj Pandita
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India.
| | - Amrutlal K Patel
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India.
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology (DST), 6th Floor, MS Building, Gandhinagar, Gujarat, 382011, India
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Comparative Genomic Analysis of Antarctic Pseudomonas Isolates with 2,4,6-Trinitrotoluene Transformation Capabilities Reveals Their Unique Features for Xenobiotics Degradation. Genes (Basel) 2022; 13:genes13081354. [PMID: 36011267 PMCID: PMC9407559 DOI: 10.3390/genes13081354] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
The nitroaromatic explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic and persistent environmental pollutant. Since physicochemical methods for remediation are poorly effective, the use of microorganisms has gained interest as an alternative to restore TNT-contaminated sites. We previously demonstrated the high TNT-transforming capability of three novel Pseudomonas spp. isolated from Deception Island, Antarctica, which exceeded that of the well-characterized TNT-degrading bacterium Pseudomonas putida KT2440. In this study, a comparative genomic analysis was performed to search for the metabolic functions encoded in the genomes of these isolates that might explain their TNT-transforming phenotype, and also to look for differences with 21 other selected pseudomonads, including xenobiotics-degrading species. Comparative analysis of xenobiotic degradation pathways revealed that our isolates have the highest abundance of key enzymes related to the degradation of fluorobenzoate, TNT, and bisphenol A. Further comparisons considering only TNT-transforming pseudomonads revealed the presence of unique genes in these isolates that would likely participate directly in TNT-transformation, and others involved in the β-ketoadipate pathway for aromatic compound degradation. Lastly, the phylogenomic analysis suggested that these Antarctic isolates likely represent novel species of the genus Pseudomonas, which emphasizes their relevance as potential agents for the bioremediation of TNT and other xenobiotics.
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Desmarais M, Fraraccio S, Dolinova I, Ridl J, Strnad H, Kubatova H, Sevcu A, Suman J, Strejcek M, Uhlik O. Genomic analysis of Acinetobacter pittii CEP14 reveals its extensive biodegradation capabilities, including cometabolic degradation of cis-1,2-dichloroethene. Antonie Van Leeuwenhoek 2022; 115:1041-1057. [PMID: 35701646 DOI: 10.1007/s10482-022-01752-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 11/27/2022]
Abstract
Halogenated organic compounds are naturally occurring in subsurface environments; however, accumulation of the degradative intermediate cis-1,2-dichloroethene (cDCE) at soil and groundwater sites contaminated with xenobiotic chlorinated ethenes is a global environmental and public health issue. Identifying microorganisms capable of cDCE degradation in these environments is of interest because of their potential application to bioremediation techniques. In this study, we sequenced, assembled, and analyzed the complete genome of Acinetobacter pittii CEP14, a strain isolated from chloroethene-contaminated groundwater, that has demonstrated the ability for aerobic cometabolic degradation of cDCE in the presence of n-hexane, phenol, and toluene. The A. pittii CEP14 genome consists of a 3.93 Mbp-long chromosome (GenBank accession no. CP084921) with a GC content of 38.9% and three plasmids (GenBank accession no. CP084922, CP084923, and CP084924). Gene function was assigned to 83.4% of the 3,930 coding DNA sequences. Functional annotation of the genome revealed that the CEP14 strain possessed all genetic elements to mediate the degradation of a range of aliphatic and aromatic compounds, including n-hexane and phenol. In addition, it harbors gene clusters involved in cytosol detoxification and oxidative stress resistance, which could play a role in the mitigation of toxic chemical intermediates that can arise during the degradation of cDCE. Gene clusters for heavy metal and antibiotic resistance were also identified in the genome of CEP14. These results suggest that CEP14 may be a versatile degrader of xenobiotic compounds and well-adapted to polluted environments, where a combination of heavy metal and organic compound pollution is often found.
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Affiliation(s)
- Miguel Desmarais
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Iva Dolinova
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
- Department of Genetics and Molecular Diagnostics, Regional Hospital Liberec, Liberec, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hynek Strnad
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Kubatova
- State Office for Nuclear Safety, Prague, Czech Republic
| | - Alena Sevcu
- Department of Applied Biology, Advanced Technologies and Innovation Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Institute for Nanomaterials, Technical University of Liberec, Liberec, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Prague, Czech Republic.
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A New ICE clc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716. Microorganisms 2021; 9:microorganisms9122462. [PMID: 34946064 PMCID: PMC8704644 DOI: 10.3390/microorganisms9122462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/23/2022] Open
Abstract
Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICEbph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICEXTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICEbph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICEbph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICEbph-salKF716 compared to other catabolic ICEs.
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Suman J, Strejcek M, Zubrova A, Capek J, Wald J, Michalikova K, Hradilova M, Sredlova K, Semerad J, Cajthaml T, Uhlik O. Predominant Biphenyl Dioxygenase From Legacy Polychlorinated Biphenyl (PCB)-Contaminated Soil Is a Part of Unusual Gene Cluster and Transforms Flavone and Flavanone. Front Microbiol 2021; 12:644708. [PMID: 34721309 PMCID: PMC8552027 DOI: 10.3389/fmicb.2021.644708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, the diversity of bphA genes was assessed in a 13C-enriched metagenome upon stable isotope probing (SIP) of microbial populations in legacy PCB-contaminated soil with 13C-biphenyl (BP). In total, 13 bphA sequence variants (SVs) were identified in the final amplicon dataset. Of these, one SV comprised 59% of all sequences, and when it was translated into a protein sequence, it exhibited 87, 77.4, and 76.7% identity to its homologs from Pseudomonas furukawaii KF707, Cupriavidus sp. WS, and Pseudomonas alcaliphila B-367, respectively. This same BphA sequence also contained unusual amino acid residues, Alanine, Valine, and Serine in region III, which had been reported to be crucial for the substrate specificity of the corresponding biphenyl dioxygenase (BPDO), and was accordingly designated BphA_AVS. The DNA locus of 18 kbp containing the BphA_AVS-coding sequence retrieved from the metagenome was comprised of 16 ORFs and was most likely borne by Paraburkholderia sp. The BPDO corresponding to bphAE_AVS was cloned and heterologously expressed in E. coli, and its substrate specificity toward PCBs and a spectrum of flavonoids was assessed. Although depleting a rather narrow spectrum of PCB congeners, the efficient transformation of flavone and flavanone was demonstrated through dihydroxylation of the B-ring of the molecules. The homology-based functional assignment of the putative proteins encoded by the rest of ORFs in the AVS region suggests their potential involvement in the transformation of aromatic compounds, such as flavonoids. In conclusion, this study contributes to the body of information on the involvement of soil-borne BPDOs in the metabolism of flavonoid compounds, and our paper provides a more advanced context for understanding the interactions between plants, microbes and anthropogenic compounds in the soil.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jan Capek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Wald
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Klara Michalikova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Miluse Hradilova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Kamila Sredlova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Jaroslav Semerad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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Lopez Marin MA, Strejcek M, Junkova P, Suman J, Santrucek J, Uhlik O. Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil Bacteria. Front Microbiol 2021; 12:685263. [PMID: 34267737 PMCID: PMC8276245 DOI: 10.3389/fmicb.2021.685263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
A bacterial species is best characterized after its isolation in a pure culture. This is an arduous endeavor for many soil microorganisms, but it can be simplified by several techniques for improving culturability: for example, by using growth-promoting factors. We investigated the potential of a Micrococcus luteus culture supernatant containing resuscitation-promoting factor (SRpf) to increase the number and diversity of cultured bacterial taxa from a nutrient-rich compost soil. Phosphate-buffered saline and inactivated SRpf were included as controls. After agitation with SRpf at 28°C for 1 day, the soil suspension was diluted and plated on two different solid, oligotrophic media: tenfold diluted Reasoner’s 2A agar (R2A) and soil extract-based agar (SA). Colonies were collected from the plates to assess the differences in diversity between different treatments and cultivation media. The diversity on both R2A and SA was higher in the SRpf-amended extracts than the controls, but the differences on R2A were higher. Importantly, 51 potentially novel bacterial species were isolated on R2A and SA after SRpf treatment. Diversity in the soil extracts was also determined by high-throughput 16S rRNA amplicon sequencing, which showed an increase in the abundance of specific taxa before their successful cultivation. Conclusively, SRpf can effectively enhance the growth of soil bacterial species, including those hitherto uncultured.
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Affiliation(s)
- Marco Antonio Lopez Marin
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Michal Strejcek
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Petra Junkova
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Jachym Suman
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Jiri Santrucek
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
| | - Ondrej Uhlik
- Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czechia
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Rolli E, Vergani L, Ghitti E, Patania G, Mapelli F, Borin S. 'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions. Environ Microbiol 2021; 23:5690-5703. [PMID: 34139059 PMCID: PMC8596516 DOI: 10.1111/1462-2920.15647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the ‘cry‐for‐help’ hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto‐extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by‐products with a higher toxicity. We propose that the ‘cry‐for‐help’ mechanism could drive the exudation‐mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.
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Affiliation(s)
- Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Lorenzo Vergani
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Elisa Ghitti
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Giovanni Patania
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
| | - Sara Borin
- Department of Food, Environmental and Nutritional Sciences, DeFENS, University of Milan, Via Celoria 2, Milan, 20133, Italy
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12
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Singh AK, Bilal M, Iqbal HMN, Raj A. Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlook. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:144561. [PMID: 33736422 DOI: 10.1016/j.scitotenv.2020.144561] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 02/05/2023]
Abstract
The feasibility of in-silico techniques, together with the computational framework, has been applied to predictive bioremediation aiming to clean-up contaminants, toxicity evaluation, and possibilities for the degradation of complex recalcitrant compounds. Emerging contaminants from different industries have posed a significant hazard to the environment and public health. Given current bioremediation strategies, it is often a failure or inadequate for sustainable mitigation of hazardous pollutants. However, clear-cut vital information about biodegradation is quite incomplete from a conventional remediation techniques perspective. Lacking complete information on bio-transformed compounds leads to seeking alternative methods. Only scarce information about the transformed products and toxicity profile is available in the published literature. To fulfill this literature gap, various computational or in-silico technologies have emerged as alternating techniques, which are being recognized as in-silico approaches for bioremediation. Molecular docking, molecular dynamics simulation, and biodegradation pathways predictions are the vital part of predictive biodegradation, including the Quantitative Structure-Activity Relationship (QSAR), Quantitative structure-biodegradation relationship (QSBR) model system. Furthermore, machine learning (ML), artificial neural network (ANN), genetic algorithm (GA) based programs offer simultaneous biodegradation prediction along with toxicity and environmental fate prediction. Herein, we spotlight the feasibility of in-silico remediation approaches for various persistent, recalcitrant contaminants while traditional bioremediation fails to mitigate such pollutants. Such could be addressed by exploiting described model systems and algorithm-based programs. Furthermore, recent advances in QSAR modeling, algorithm, and dedicated biodegradation prediction system have been summarized with unique attributes.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico.
| | - Abhay Raj
- Environmental Microbiology Laboratory, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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13
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Zubrova A, Michalikova K, Semerad J, Strejcek M, Cajthaml T, Suman J, Uhlik O. Biphenyl 2,3-Dioxygenase in Pseudomonas alcaliphila JAB1 Is Both Induced by Phenolics and Monoterpenes and Involved in Their Transformation. Front Microbiol 2021; 12:657311. [PMID: 33995321 PMCID: PMC8119895 DOI: 10.3389/fmicb.2021.657311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/29/2021] [Indexed: 01/09/2023] Open
Abstract
The involvement of bacterial aromatic ring-hydroxylating dioxygenases (ARHDs) in the degradation of aromatic pollutants, such as polychlorinated biphenyls (PCBs), has been well studied. However, there is considerable speculation as to the origin of this ability. One hypothesis is centered on a connection between the ability to degrade aromatic pollutants and the necessity of soil bacteria to cope with and/or utilize secondary plant metabolites (SPMs). To investigate this connection, we researched the involvement of biphenyl 2,3-dioxygenase (BPDO), an ARHD essential for the degradation of PCBs, in the metabolism of SPMs in the soil bacterium Pseudomonas alcaliphila JAB1, a versatile degrader of PCBs. We demonstrated the ability of the strain JAB1 to transform a variety of SPMs, namely the flavonoids apigenin, flavone, flavanone, naringenin, fisetin, quercetin, morin, and catechin, caffeic acid, trans-cinnamic acid, and the monoterpenes (S)-limonene and (R)-carvone. Of those, the transformation of flavone, flavanone, and (S)-limonene was conditioned by the activity of JAB1-borne BPDO and thus was researched in more detail, and we found evidence for the limonene monooxygenase activity of the BPDO. Furthermore, the bphA gene in the strain JAB1 was demonstrated to be induced by a wide range of SPMs, with monoterpenes being the strongest inducers of the SPMs tested. Thus, our findings contribute to the growing body of evidence that ARHDs not only play a role in the catabolism of aromatic pollutants, but also of natural plant-derived aromatics, and this study supports the hypothesis that ARHDs participate in ecological processes mediated by SPMs.
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Affiliation(s)
- Andrea Zubrova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Klara Michalikova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Jaroslav Semerad
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Tomas Cajthaml
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czechia.,Faculty of Science, Institute for Environmental Studies, Charles University, Prague, Czechia
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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14
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Mahjoubi M, Aliyu H, Neifar M, Cappello S, Chouchane H, Souissi Y, Masmoudi AS, Cowan DA, Cherif A. Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14. Sci Rep 2021; 11:8124. [PMID: 33854112 PMCID: PMC8046798 DOI: 10.1038/s41598-021-87487-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 02/12/2021] [Indexed: 02/02/2023] Open
Abstract
Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.
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Affiliation(s)
- Mouna Mahjoubi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Habibu Aliyu
- grid.7892.40000 0001 0075 5874Institute of Process Engineering in Life Science 2: Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Mohamed Neifar
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Simone Cappello
- Istituto per le Risorse Biologiche e le Biotecnologie Marine (IRBIM)-CNR of Messina, Sp. San Raineri, 86, 98122 Messina, Italy
| | - Habib Chouchane
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Yasmine Souissi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Ahmed Salaheddine Masmoudi
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
| | - Don A. Cowan
- grid.49697.350000 0001 2107 2298Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002 South Africa
| | - Ameur Cherif
- grid.424444.60000 0001 1103 8547University of Manouba, ISBST, BVBGR-LR11ES31, Biotechpole SidiThabet, 2020 Ariana, Tunisia
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15
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Lopez-Echartea E, Suman J, Smrhova T, Ridl J, Pajer P, Strejcek M, Uhlik O. Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility. G3-GENES GENOMES GENETICS 2021; 11:6029021. [PMID: 33693598 PMCID: PMC8022969 DOI: 10.1093/g3journal/jkaa030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/30/2020] [Indexed: 11/30/2022]
Abstract
Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution. One such bacterial strain, designated Pvy, was isolated from sediment samples from a lagoon in Romania located near an oil refinery due to its capacity to degrade dibenzofuran (DF). The genome sequence of the Pvy strain was obtained using an Oxford Nanopore MiniION platform. According to the consensus 16S rRNA gene sequence that was compiled from six 16S rRNA gene copies contained in the genome and orthologous average nucleotide identity (OrthoANI) calculation, the Pvy strain was identified as Pseudomonas veronii, which confirmed the identification obtained with the aid of MALDI-TOF mass spectrometry and MALDI BioTyper. The genome was analyzed with respect to enzymes responsible for the overall biodegradative versatility of the strain. The Pvy strain was able to derive carbon from naphthalene (NP) and several aromatic compounds of natural origin, including salicylic, protocatechuic, p-hydroxybenzoic, trans-cinnamic, vanillic, and indoleacetic acids or vanillin, and was shown to degrade but not utilize DF. In total seven loci were found in the Pvy genome, which enables the strain to participate in the degradation of these aromatic compounds. Our experimental data also indicate that the transcription of the NP-dioxygenase α-subunit gene (ndoB), carried by the plasmid of the Pvy strain, is inducible by DF. These features make the Pvy strain a potential candidate for various bioremediation applications.
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Affiliation(s)
- Eglantina Lopez-Echartea
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Tereza Smrhova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Jakub Ridl
- Department of Genomics and Bioinformatics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 40 Prague, Czech Republic.,Division of Animal Evolutionary Biology, Department of Zoology, Faculty of Science, Charles University in Prague, Vinicna 7, 128 44 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske nemocnice 1200, 169 02 Prague 6, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Technicka 3, 166 28 Prague 6, Czech Republic
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16
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Ferreira LC, Maul JE, Viana MVC, de Sousa TJ, de Carvalho Azevedo VA, Roberts DP, de Souza JT. Complete genome sequence of the biocontrol agent Serratia marcescens strain N4-5 uncovers an assembly artefact. Braz J Microbiol 2020; 52:245-250. [PMID: 32965626 DOI: 10.1007/s42770-020-00382-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/15/2020] [Indexed: 10/23/2022] Open
Abstract
Serratia marcescens are gram-negative bacteria found in several environmental niches, including the plant rhizosphere and patients in hospitals. Here, we present the genome of Serratia marcescens strain N4-5 (=NRRL B-65519), which has a size of 5,074,473 bp (664-fold coverage) and contains 4840 protein coding genes, 21 RNA genes, and an average G + C content of 59.7%. N4-5 harbours a plasmid of 11,089 bp and 43.5% G + C content that encodes six unique CDS repeated 2.5× times totalling 13 CDS. Our genome assembly and manual curation uncovered the insertion of two extra copies of the 5S rRNA gene in the assembled sequence, which was confirmed by PCR and Sanger sequencing to be a misassembly. This artefact was subsequently removed from the final assembly. The occurrence of extra copies of the 5S rRNA gene was also observed in most complete genomes of Serratia spp. deposited in public databases in our comparative analysis. These elements, which also occur naturally, can easily be confused with true genetic variation. Efforts to discover and correct assembly artefacts should be made in order to generate genome sequences that represent the biological truth underlying the studied organism. We present the genome of N4-5 and discuss genes potentially involved in biological control activity against plant pathogens and also the possible mechanisms responsible for the artefact we observed in our initial assembly. This report raises awareness about the extra copies of the 5S rRNA gene in sequenced bacterial genomes as they may represent misassemblies and therefore should be verified experimentally.
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Affiliation(s)
- Larissa Carvalho Ferreira
- Plant Pathology Department, Federal University of Lavras, Lavras, MG, 37200-000, Brazil.,Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | | | - Thiago Jesus de Sousa
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Jorge Teodoro de Souza
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, UK.
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17
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Wang X, Li D, Gao P, Gu W, He X, Yang W, Tang W. Analysis of biosorption and biotransformation mechanism of Pseudomonas chengduensis strain MBR under Cd(II) stress from genomic perspective. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110655. [PMID: 32361136 DOI: 10.1016/j.ecoenv.2020.110655] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Microbial treatment of heavy metal-polluted sites is considered an environmentally friendly bioremediation technology with high potential. This study shows that Pseudomonas chengduensis strain MBR, a bacterium that can potentially be applied in the treatment of heavy metal pollution, is most affected by Cd(II) stress at the beginning of its growth. Up to 100% of total Cd(II) adsorption occurs in the first 48 h after treatment of stationary phase cells with Cd(II). A biofilm forms on the cell surface, Cd(II) adsorbs, and is reduced to Cd (0) in the form of nanoscale particles. The genome of strain MBR was sequenced, annotated and analyzed. We identified various genes potentially related to cadmium resistance, transport and metabolism. Analysis of the strain MBR genome is helpful to explore the mechanism of Cd(II) resistance, and can provide new ideas for cadmium pollution control.
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Affiliation(s)
- Xu Wang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; College of Life Sciences, Sichuan University, Chengdu, 610064, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Daping Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ping Gao
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Wenzhi Gu
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohong He
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, 610041, China
| | - Wenyi Yang
- College of Environmental Sciences, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenzhong Tang
- State Key Laboratory on Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 10085, China
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18
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Firuzi P, Asl Hashemi A, Samadi Kafil H, Gholizadeh P, Aslani H. Comparative study on the microbial quality in the swimming pools disinfected by the ozone-chlorine and chlorine processes in Tabriz, Iran. ENVIRONMENTAL MONITORING AND ASSESSMENT 2020; 192:516. [PMID: 32666262 DOI: 10.1007/s10661-020-08470-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Applying a desirable disinfestation process is necessary to control the pathogenic microorganisms in the swimming pools and prevent both dermal and intestinal effects. Therefore, the present study was conducted to compare the bacterial community and diversity in the two swimming pools disinfected by the chlorine and ozone (O3)-chlorine processes. A total of 24 samples were taken from the two swimming pools in three distinct seasons to analyze the bacterial and physico-chemical indicators. Culture and molecular methods were used to evaluate the microbial quality. Two sets of sample taken from the pools with the maximum swimmer load in the summer were investigated by the next-generation sequencing (NGS) technique. In total, 410 and 406 bacterial species were identified in the chlorine- and ozone-chlorine-disinfected pools, respectively. Among the eight dominant bacterial species in each swimming pool, Pseudomonas alcaliphila, Pseudomonas stutzeri, and Pseudomonas acnes were common species between the two studied pools. Oleomonas sagaranensis (350 reads/18593), Staphylococcus caprae (302 reads /18593), and Anaerococcus octavius (110 reads/18593) were among the dominant bacteria in the chlorine-disinfected pool. Bacterial diversity was lower in the ozone-chlorine-disinfected pool than the other one, and the highest bacterial sequencing belonged to the genus Pseudomonas (85.79%). Results showed that water quality of in O3-chlorine-disinfected pool was more desirable than the chlorine-disinfected pool. Molecular methods along with conventional culture methods would be advantageous for microbial assessment in the swimming pools.
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Affiliation(s)
- Parisa Firuzi
- Department of Environmental Health Engineering, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Asl Hashemi
- Department of Environmental Health Engineering, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Aslani
- Health and Environment Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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19
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Garrido-Sanz D, Sansegundo-Lobato P, Redondo-Nieto M, Suman J, Cajthaml T, Blanco-Romero E, Martin M, Uhlik O, Rivilla R. Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence. Microb Genom 2020; 6. [PMID: 32238227 PMCID: PMC7276702 DOI: 10.1099/mgen.0.000363] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The complete genome sequence of Rhodococcus sp. WAY2 (WAY2) consists of a circular chromosome, three linear replicons and a small circular plasmid. The linear replicons contain typical actinobacterial invertron-type telomeres with the central CGTXCGC motif. Comparative phylogenetic analysis of the 16S rRNA gene along with phylogenomic analysis based on the genome-to-genome blast distance phylogeny (GBDP) algorithm and digital DNA–DNA hybridization (dDDH) with other Rhodococcus type strains resulted in a clear differentiation of WAY2, which is likely a new species. The genome of WAY2 contains five distinct clusters of bph, etb and nah genes, putatively involved in the degradation of several aromatic compounds. These clusters are distributed throughout the linear plasmids. The high sequence homology of the ring-hydroxylating subunits of these systems with other known enzymes has allowed us to model the range of aromatic substrates they could degrade. Further functional characterization revealed that WAY2 was able to grow with biphenyl, naphthalene and xylene as sole carbon and energy sources, and could oxidize multiple aromatic compounds, including ethylbenzene, phenanthrene, dibenzofuran and toluene. In addition, WAY2 was able to co-metabolize 23 polychlorinated biphenyl congeners, consistent with the five different ring-hydroxylating systems encoded by its genome. WAY2 could also use n-alkanes of various chain-lengths as a sole carbon source, probably due to the presence of alkB and ladA gene copies, which are only found in its chromosome. These results show that WAY2 has a potential to be used for the biodegradation of multiple organic compounds.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Paula Sansegundo-Lobato
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Tomas Cajthaml
- Laboratory of Environmental Biotechnology, Institute of Microbiology, Czech Academy of Sciences v.v.i., Vídeňská 1083, 14200 Prague, Czech Republic
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technika 3, 16628 Prague, Czech Republic
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, C/ Darwin 2, 28049 Madrid, Spain
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20
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Steliga T, Wojtowicz K, Kapusta P, Brzeszcz J. Assessment of Biodegradation Efficiency of Polychlorinated Biphenyls (PCBs) and Petroleum Hydrocarbons (TPH) in Soil Using Three Individual Bacterial Strains and Their Mixed Culture. Molecules 2020; 25:E709. [PMID: 32041368 PMCID: PMC7036857 DOI: 10.3390/molecules25030709] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 01/31/2023] Open
Abstract
Biodegradation is one of the most effective and profitable methods for the elimination of toxic polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPH) from the environment. In this study, aerobic degradation of the mentioned pollutants by bacterial strains Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN129, and Rhodococcus sp. IN306 and mixed culture M1 developed based on those strains at 1:1:1 ratio was analyzed. The effectiveness of individual strains and of the mixed culture was assessed based on carried out respirometric tests and chromatographic analyses. The Rhodococcus sp. IN306 turned out most effective in terms of 18 PCB congeners biodegradation (54.4%). The biodegradation index was decreasing with an increasing number of chlorine atoms in a molecule. Instead, the Mycolicobacterium frederiksbergense IN53 was the best TPH degrader (37.2%). In a sterile soil, contaminated with PCBs and TPH, the highest biodegradation effectiveness was obtained using inoculation with mixed culture M1, which allowed to reduce both the PCBs (51.8%) and TPH (34.6%) content. The PCBs and TPH biodegradation capacity of the defined mixed culture M1 was verified ex-situ with prism method in a non-sterile soil polluted with aged petroleum hydrocarbons (TPH) and spent transformer oil (PCBs). After inoculation with mixed culture M1, the PCBs were reduced during 6 months by 84.5% and TPH by 70.8% as well as soil toxicity was decreased.
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Affiliation(s)
- Teresa Steliga
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Katarzyna Wojtowicz
- Department of Reservoir Fluid Production Technology, Oil and Gas Institute–National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland;
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
| | - Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute-National Research Institute, ul. Lubicz 25 A, 31-503 Krakow, Poland; (P.K.); (J.B.)
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Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils. PLoS One 2019; 14:e0221253. [PMID: 31437185 PMCID: PMC6705854 DOI: 10.1371/journal.pone.0221253] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/04/2019] [Indexed: 12/28/2022] Open
Abstract
Extended soil contamination by polychlorinated biphenyls (PCBs) represents a global environmental issue that can hardly be addressed with the conventional remediation treatments. Rhizoremediation is a sustainable alternative, exploiting plants to stimulate in situ the degradative bacterial communities naturally occurring in historically polluted areas. This approach can be enhanced by the use of bacterial strains that combine PCB degradation potential with the ability to promote plant and root development. With this aim, we established a collection of aerobic bacteria isolated from the soil of the highly PCB-polluted site “SIN Brescia-Caffaro” (Italy) biostimulated by the plant Phalaris arundinacea. The strains, selected on biphenyl and plant secondary metabolites provided as unique carbon source, were largely dominated by Actinobacteria and a significant number showed traits of interest for remediation, harbouring genes homologous to bphA, involved in the PCB oxidation pathway, and displaying 2,3-catechol dioxygenase activity and emulsification properties. Several strains also showed the potential to alleviate plant stress through 1-aminocyclopropane-1-carboxylate deaminase activity. In particular, we identified three Rhodococcus strains able to degrade in vitro several PCB congeners and to promote lateral root emergence in the model plant Arabidopsis thaliana in vivo. In addition, these strains showed the capacity to colonize the root system and to increase the plant biomass in PCB contaminated soil, making them ideal candidates to sustain microbial-assisted PCB rhizoremediation through a bioaugmentation approach.
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Crognale S, Stazi SR, Firrincieli A, Pesciaroli L, Fedi S, Petruccioli M, D'Annibale A. Time-Dependent Changes in Morphostructural Properties and Relative Abundances of Contributors in Pleurotus ostreatus/ Pseudomonas alcaliphila Mixed Biofilms. Front Microbiol 2019; 10:1819. [PMID: 31447819 PMCID: PMC6695841 DOI: 10.3389/fmicb.2019.01819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
Pleurotus ostreatus dual biofilms with bacteria are known to be involved in rock phosphate solubilization, endophytic colonization, and even in nitrogen fixation. Despite these relevant implications, no information is currently available on the architecture of P. ostreatus-based dual biofilms. In addition to this, there is a limited amount of information regarding the estimation of the temporal changes in the relative abundances of the partners in such binary systems. To address these issues, a dual biofilm model system with this fungus was prepared by using Pseudomonas alcaliphila 34 as the bacterial partner due to its very fast biofilm-forming ability. The application of the bacterial inoculum to already settled fungal biofilm on a polystyrene surface coated with hydroxyapatite was the most efficient approach to the production of the mixed system the ultrastructure of which was investigated by a multi-microscopy approach. Transmission electron microscopy analysis showed that the adhesion of bacterial cells onto the mycelial cell wall appeared to be mediated by the presence of an abundant layer of extracellular matrix (ECM). Scanning electron microscopy analysis showed that ECM filaments of bacterial origin formed initially a reticular structure that assumed a tabular semblance after 72 h, thus overshadowing the underlying mycelial network. Across the thickness of the mixed biofilms, the presence of an extensive network of channels with large aggregates of viable bacteria located on the edges of their lumina was found by confocal laser scanning microscopy; on the outermost biofilm layer, a significant fraction of dead bacterial cells was evident. Albeit with tangible differences, similar results regarding the estimation of the temporal shifts in the relative abundances of the two partners were obtained by two independent methods, the former relying on qPCR targeting of 16S and 18S rRNA genes and the latter on ester-linked fatty acid methyl esters analysis.
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Affiliation(s)
- Silvia Crognale
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Silvia Rita Stazi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Lorena Pesciaroli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Alessandro D'Annibale
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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Voronina AO, Egorova DO, Korsakova ES, Plotnikova EG. Diversity of the bphA1 Genes in a Microbial Community from Anthropogenically Contaminated Soil and Isolation of New Pseudomonads Degrading Biphenyl/Chlorinated Biphenyls. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Dangi AK, Sharma B, Hill RT, Shukla P. Bioremediation through microbes: systems biology and metabolic engineering approach. Crit Rev Biotechnol 2018; 39:79-98. [DOI: 10.1080/07388551.2018.1500997] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Arun Kumar Dangi
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Babita Sharma
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Russell T. Hill
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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