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Sandhu M, Paul AT, Jha PN. Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil. PLoS One 2022; 17:e0266808. [PMID: 35486615 PMCID: PMC9053811 DOI: 10.1371/journal.pone.0266808] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/25/2022] [Indexed: 12/21/2022] Open
Abstract
Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.
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Affiliation(s)
- Monika Sandhu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Atish T. Paul
- Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
| | - Prabhat N. Jha
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
- * E-mail:
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Miri S, Rasooli A, Brar SK, Rouissi T, Martel R. Biodegradation of p-xylene-a comparison of three psychrophilic Pseudomonas strains through the lens of gene expression. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:21465-21479. [PMID: 34762239 DOI: 10.1007/s11356-021-17387-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 11/02/2021] [Indexed: 05/21/2023]
Abstract
p-Xylene is considered a recalcitrant compound despite showing a similar aromatic structure to other BTEXs (benzene, toluene, ethylbenzene, xylene isomers). This study evaluated the p-xylene biodegradation potential of three psychrophilic Pseudomonas strains (Pseudomonas putida S2TR-01, Pseudomonas synxantha S2TR-20, and Pseudomonas azotoformans S2TR-09). The p-xylene metabolism-related catabolic genes (xylM, xylA, and xylE) and the corresponding regulatory genes (xylR and xylS) of the selected strains were investigated. The biodegradation results showed that the P. azotoformans S2TR-09 strain was the only strain that was able to degrade 200 mg/L p-xylene after 60 h at 15 °C. The gene expression study indicated that the xylE (encoding catechol 2,3-dioxygenase) gene represents the bottleneck in p-xylene biodegradation. A lack of xylE expression leads to the accumulation of intermediates and the inhibition of biomass production and complete carbon recovery. The activity of xylene monooxygenase and catechol 2,3-dioxygenase was significantly increased in P. azotoformans S2TR-09 (0.5 and 0.08 U/mg, respectively) in the presence of p-xylene. The expression of the ring cleavage enzyme and its encoding gene (xylE) and activator (xylS) explained the differences in the p-xylene metabolism of the isolated bacteria and can be used as a novel biomarker of efficient p-xylene biodegradation at contaminated sites.
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Affiliation(s)
- Saba Miri
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Azadeh Rasooli
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, ON, M3J 1P3, Canada.
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada.
| | - Tarek Rouissi
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
| | - Richard Martel
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, G1K 9A9, Canada
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Meyer-Cifuentes I, Gruhl S, Haange SB, Lünsmann V, Jehmlich N, von Bergen M, Heipieper HJ, Müller JA. Benzylsuccinate Synthase is Post-Transcriptionally Regulated in the Toluene-Degrading Denitrifier Magnetospirillum sp. Strain 15-1. Microorganisms 2020; 8:microorganisms8050681. [PMID: 32392861 PMCID: PMC7285207 DOI: 10.3390/microorganisms8050681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 01/15/2023] Open
Abstract
The facultative denitrifying alphaproteobacterium Magnetospirillum sp. strain 15-1 had been isolated from the hypoxic rhizosphere of a constructed wetland model fed with toluene. This bacterium can catabolize toluene anaerobically but not aerobically. Here, we used strain 15-1 to investigate regulation of expression of the highly oxygen-sensitive glycyl radical enzyme benzylsuccinate synthase, which catalyzes the first step in anaerobic toluene degradation. In cells growing aerobically with benzoate, the addition of toluene resulted in a ~20-fold increased transcription of bssA, encoding for the catalytically active subunit of the enzyme. Under anoxic conditions, bssA mRNA copy numbers were up to 129-fold higher in cells growing with toluene as compared to cells growing with benzoate. Proteomics showed that abundance of benzylsuccinate synthase increased in cells growing anaerobically with toluene. In contrast, peptides of this enzyme were never detected in oxic conditions. These findings show that synthesis of benzylsuccinate synthase was under stringent post-transcriptional control in the presence of oxygen, which is a novel level of regulation for glycyl radical enzymes.
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Affiliation(s)
- Ingrid Meyer-Cifuentes
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (I.M.-C.); (S.G.); (J.A.M.)
- Junior Research Group of Microbial Biotechnology, Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany
| | - Sylvie Gruhl
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (I.M.-C.); (S.G.); (J.A.M.)
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (S.-B.H.); (V.L.); (N.J.); (M.v.B.)
| | - Vanessa Lünsmann
- Department of Molecular Systems Biology Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (S.-B.H.); (V.L.); (N.J.); (M.v.B.)
| | - Nico Jehmlich
- Department of Molecular Systems Biology Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (S.-B.H.); (V.L.); (N.J.); (M.v.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (S.-B.H.); (V.L.); (N.J.); (M.v.B.)
- Group of Functional Proteomics, Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology University of Leipzig, Talstrastr. 33, 04103 Leipzig, Germany
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (I.M.-C.); (S.G.); (J.A.M.)
- Correspondence: ; Tel.: +49-341-2351694
| | - Jochen A. Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, 04318 Leipzig, Germany; (I.M.-C.); (S.G.); (J.A.M.)
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Dziuba MV, Zwiener T, Uebe R, Schüler D. Single-step transfer of biosynthetic operons endows a non-magnetotactic Magnetospirillum strain from wetland with magnetosome biosynthesis. Environ Microbiol 2020; 22:1603-1618. [PMID: 32079043 DOI: 10.1111/1462-2920.14950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/03/2020] [Accepted: 02/18/2020] [Indexed: 11/28/2022]
Abstract
The magnetotactic lifestyle represents one of the most complex traits found in many bacteria from aquatic environments and depends on magnetic organelles, the magnetosomes. Genetic transfer of magnetosome biosynthesis operons to a non-magnetotactic bacterium has only been reported once so far, but it is unclear whether this may also occur in other recipients. Besides magnetotactic species from freshwater, the genus Magnetospirillum of the Alphaproteobacteria also comprises a number of strains lacking magnetosomes, which are abundant in diverse microbial communities. Their close phylogenetic interrelationships raise the question whether the non-magnetotactic magnetospirilla may have the potential to (re)gain a magnetotactic lifestyle upon acquisition of magnetosome gene clusters. Here, we studied the transfer of magnetosome gene operons into several non-magnetotactic environmental magnetospirilla. Single-step transfer of a compact vector harbouring >30 major magnetosome genes from M. gryphiswaldense induced magnetosome biosynthesis in a Magnetospirillum strain from a constructed wetland. However, the resulting magnetic cellular alignment was insufficient for efficient magnetotaxis under conditions mimicking the weak geomagnetic field. Our work provides insights into possible evolutionary scenarios and potential limitations for the dissemination of magnetotaxis by horizontal gene transfer and expands the range of foreign recipients that can be genetically magnetized.
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Affiliation(s)
- Marina V Dziuba
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Theresa Zwiener
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Rene Uebe
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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Okpala GN, Voordouw G. Comparison of Nitrate and Perchlorate in Controlling Sulfidogenesis in Heavy Oil-Containing Bioreactors. Front Microbiol 2018; 9:2423. [PMID: 30356844 PMCID: PMC6190851 DOI: 10.3389/fmicb.2018.02423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/21/2018] [Indexed: 11/21/2022] Open
Abstract
Control of microbial reduction of sulfate to sulfide in oil reservoirs (a process referred to as souring) with nitrate has been researched extensively. Nitrate is reduced to nitrite, which is a strong inhibitor of sulfate-reducing bacteria (SRB). Perchlorate has been proposed as an alternative souring control agent. It is reduced to chlorate (ClO3 -) and chlorite (ClO2 -), which is dismutated to chloride and O2. These can react with sulfide to form sulfur. Chlorite is also highly biocidal. Here we compared the effectiveness of perchlorate and nitrate in inhibiting SRB activity in medium containing heavy oil from the Medicine Hat Glauconitic C (MHGC) field, which has a low reservoir temperature and is injected with nitrate to control souring. Using acetate, propionate and butyrate as electron donors, perchlorate-reducing bacteria (PRB) were obtained in enrichment culture and perchlorate-reducing Magnetospirillum spp. were isolated from MHGC produced waters. In batch experiments with MHGC oil as the electron donor, nitrate was reduced to nitrite and inhibited sulfate reduction. However, perchlorate was not reduced and did not inhibit sulfate reduction in these incubations. Bioreactor experiments were conducted with sand-packed glass columns, containing MHGC oil and inoculated with an oil-grown mesophilic SRB enrichment. Once active souring (reduction of 2 mM sulfate to sulfide) was observed, these were treated with nitrate and/or perchlorate. As in the batch experiments, 4 mM nitrate completely inhibited sulfide production, while partial inhibition occurred with 1 and 2 mM nitrate, but injection of 4 mM perchlorate did not inhibit sulfate reduction and perchlorate was not reduced. The enriched and isolated PRB were unable to use heavy oil components, like alkylbenzenes, which were readily used by nitrate-reducing bacteria. Hence perchlorate, injected into a low temperature heavy oil reservoir like the MHGC, may not be reduced to toxic intermediates making nitrate a preferable souring control agent.
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Affiliation(s)
| | - Gerrit Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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Blázquez B, Carmona M, Díaz E. Transcriptional Regulation of the Peripheral Pathway for the Anaerobic Catabolism of Toluene and m-Xylene in Azoarcus sp. CIB. Front Microbiol 2018; 9:506. [PMID: 29623071 PMCID: PMC5874301 DOI: 10.3389/fmicb.2018.00506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/06/2018] [Indexed: 11/17/2022] Open
Abstract
Alkylbenzenes, such as toluene and m-xylene, are an important class of contaminant hydrocarbons that are widespread and tend to accumulate in subsurface anoxic environments. The peripheral pathway for the anaerobic oxidation of toluene in bacteria consists of an initial activation catalyzed by a benzylsuccinate synthase (encoded by bss genes), and a subsequent modified β-oxidation of benzylsuccinate to benzoyl-CoA and succinyl-CoA (encoded by bbs genes). We have shown here that the bss and bbs genes, which are located within an integrative and conjugative element, are essential for anaerobic degradation of toluene but also for m-xylene oxidation in the denitrifying beta-proteobacterium Azoarcus sp. CIB. New insights into the transcriptional organization and regulation of a complete gene cluster for anaerobic catabolism of toluene/m-xylene in a single bacterial strain are presented. The bss and bbs genes are transcriptionally coupled into two large convergent catabolic operons driven by the PbssD and PbbsA promoters, respectively, whose expression is inducible when cells grow anaerobically in toluene or m-xylene. An adjacent tdiSR operon driven by the PtdiS promoter encodes a putative two-component regulatory system. TdiR behaves as a transcriptional activator of the PbssD, PbbsA, and PtdiS promoters, being benzylsuccinate/(3-methyl)benzylsuccinate, rather than toluene/m-xylene, the inducers that may trigger the TdiS-mediated activation of TdiR. In addition to the TdiSR-based specific control, the expression of the bss and bbs genes in Azoarcus sp. CIB is under an overimposed regulation that depends on certain environmental factors, such as the presence/absence of oxygen or the availability of preferred carbon sources (catabolite repression). This work paves the way for future strategies toward the reliable assessment of microbial activity in toluene/m-xylene contaminated environments.
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Affiliation(s)
- Blas Blázquez
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Manuel Carmona
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
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Draft Genome Sequence of Magnetospirillum sp. Strain 15-1, a Denitrifying Toluene Degrader Isolated from a Planted Fixed-Bed Reactor. GENOME ANNOUNCEMENTS 2017; 5:5/32/e00764-17. [PMID: 28798176 PMCID: PMC5552985 DOI: 10.1128/genomea.00764-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Magnetospirillum sp. 15-1. This strain was isolated from a planted fixed-bed reactor based on its ability to degrade toluene under anaerobic conditions. The genome assembly consists of 5.4 Mb in 28 contigs and 5,095 coding sequences containing the genes involved in anaerobic toluene degradation.
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