1
|
Zhang ST, Li T, Deng SK, Spain JC, Zhou NY. A cytochrome P450 system initiates 4-nitroanisole degradation in Rhodococcus sp. strain JS3073. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131886. [PMID: 37348368 DOI: 10.1016/j.jhazmat.2023.131886] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Nitroanisoles are used widely as synthetic intermediates and explosives. Although bacteria have been reported to degrade 4-nitroanisole (4NA) under aerobic conditions, the key enzymes and the catalytic mechanism have remained elusive. Rhodococcus sp. strain JS3073 was isolated for its ability to grow on 4NA as the sole carbon and energy source. In this study, whole cell biotransformation experiments indicated that 4NA degradation is initiated by O-demethylation to form 4-nitrophenol (PNP), which undergoes subsequent degradation by a previously established pathway involving formation of 1,2,4-benzenetriol and release of nitrite. Based on comparative transcriptomics and heterologous expression, a novel three-component cytochrome P450 system encoded by pnaABC initiates the O-demethylation of 4NA to yield formaldehyde and PNP. The pnaABC genes encode a phthalate dioxygenase type reductase (PnaA), a cytochrome P450 monooxygenase (PnaB), and an EthD family protein (PnaC) with putative function similar to ferredoxins. This unusual P450 system also has a broad substrate specificity for nitroanisole derivatives. Sequence analysis of PnaAB revealed high identity with multiple self-sufficient P450s of the CYP116B subfamily. The findings revealed the molecular basis of the catabolic pathway for 4NA initiated by an unusual O-demethylase PnaABC and extends the understanding of the diversity among P450s and their electron transport chains.
Collapse
Affiliation(s)
- Shu-Ting Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shi-Kai Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jim C Spain
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514-5751, USA
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
2
|
Chánique AM, Polidori N, Sovic L, Kracher D, Assil-Companioni L, Galuska P, Parra LP, Gruber K, Kourist R. A Cold-Active Flavin-Dependent Monooxygenase from Janthinobacterium svalbardensis Unlocks Applications of Baeyer–Villiger Monooxygenases at Low Temperature. ACS Catal 2023; 13:3549-3562. [PMID: 36970468 PMCID: PMC10028610 DOI: 10.1021/acscatal.2c05160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/31/2023] [Indexed: 03/02/2023]
Abstract
Cold-active enzymes maintain a large part of their optimal activity at low temperatures. Therefore, they can be used to avoid side reactions and preserve heat-sensitive compounds. Baeyer-Villiger monooxygenases (BVMO) utilize molecular oxygen as a co-substrate to catalyze reactions widely employed for steroid, agrochemical, antibiotic, and pheromone production. Oxygen has been described as the rate-limiting factor for some BVMO applications, thereby hindering their efficient utilization. Considering that oxygen solubility in water increases by 40% when the temperature is decreased from 30 to 10 °C, we set out to identify and characterize a cold-active BVMO. Using genome mining in the Antarctic organism Janthinobacterium svalbardensis, a cold-active type II flavin-dependent monooxygenase (FMO) was discovered. The enzyme shows promiscuity toward NADH and NADPH and high activity between 5 and 25 °C. The enzyme catalyzes the monooxygenation and sulfoxidation of a wide range of ketones and thioesters. The high enantioselectivity in the oxidation of norcamphor (eeS = 56%, eeP > 99%, E > 200) demonstrates that the generally higher flexibility observed in the active sites of cold-active enzymes, which compensates for the lower motion at cold temperatures, does not necessarily reduce the selectivity of these enzymes. To gain a better understanding of the unique mechanistic features of type II FMOs, we determined the structure of the dimeric enzyme at 2.5 Å resolution. While the unusual N-terminal domain has been related to the catalytic properties of type II FMOs, the structure shows a SnoaL-like N-terminal domain that is not interacting directly with the active site. The active site of the enzyme is accessible only through a tunnel, with Tyr-458, Asp-217, and His-216 as catalytic residues, a combination not observed before in FMOs and BVMOs.
Collapse
Affiliation(s)
- Andrea M. Chánique
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Nakia Polidori
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Lucija Sovic
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Daniel Kracher
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
| | - Leen Assil-Companioni
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
| | - Philipp Galuska
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago 7810000, Chile
| | - Karl Gruber
- NAWI Graz, BioTechMed Graz, Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, Graz 8010, Austria
| | - Robert Kourist
- NAWI Graz, BioTechMed-Graz, Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, Graz 8010, Austria
- ACIB GmbH, Petersgasse 14/1, Graz 8010, Austria
| |
Collapse
|
3
|
Moriuchi R, Dohra H, Kanesaki Y, Ogawa N. Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate. Biosci Biotechnol Biochem 2021; 85:1546-1561. [PMID: 33720310 DOI: 10.1093/bbb/zbab044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/08/2021] [Indexed: 01/05/2023]
Abstract
RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.
Collapse
Affiliation(s)
- Ryota Moriuchi
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan
| | - Hideo Dohra
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| | - Naoto Ogawa
- The United Graduate School of Agricultural Science, Gifu University, Gifu-shi, Gifu, Japan.,Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka-shi, Shizuoka, Japan
| |
Collapse
|
4
|
Biodegradation of naphthenic acids: identification of Rhodococcus opacus R7 genes as molecular markers for environmental monitoring and their application in slurry microcosms. Appl Microbiol Biotechnol 2020; 104:2675-2689. [PMID: 31993702 DOI: 10.1007/s00253-020-10378-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 10/30/2019] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
Nowadays, the increase of the unconventional oil deposit exploitation and the amount of oil sands process-affected waters (OSPW) in tailing ponds emerges the importance of developing bio-monitoring strategies for the restoration of these habitats. The major constituents of such deposits are naphthenic acids (NAs), emerging contaminant mixtures with toxic and recalcitrant properties. With the aim of developing bio-monitoring strategies based on culture-independent approach, we identified genes coding for enzymes involved in NA degradation from Rhodococcus opacus R7 genome, after the evaluation of its ability to mineralize model NAs. R. opacus R7 whole-genome analysis unveiled the presence of pobA and chcpca gene clusters putatively involved in NAs degradation. Gene expression analysis demonstrated the specific induction of R7 aliA1 gene, encoding for a long-chain-fatty-acid-CoA ligase, in the presence of cyclohexanecarboxylic acid (CHCA) and hexanoic acid (HA), selected as representative compounds for alicyclic and linear NAs, respectively. Therefore, aliA1 gene was selected as a molecular marker to monitor the biodegradative potential of slurry-phase sand microcosms in different conditions: spiked with CHCA, in the presence of R. opacus R7, the autochthonous microbial community, and combining these factors. Results revealed that the aliA1-targeting culture-independent approach could be a useful method for bio-monitoring of NA degradation in a model laboratory system.
Collapse
|
5
|
Watahiki S, Kimura N, Yamazoe A, Miura T, Sekiguchi Y, Noda N, Matsukura S, Kasai D, Takahata Y, Nojiri H, Fukuda M. Ecological impact assessment of a bioaugmentation site on remediation of chlorinated ethylenes by multi-omics analysis. J GEN APPL MICROBIOL 2019; 65:225-233. [PMID: 30853704 DOI: 10.2323/jgam.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bioremediation may affect the ecological system around bioremediation sites. However, little is known about how microbial community structures change over time after the initial injection of degraders. In this study, we have assessed the ecological impact of bioaugmentation using metagenomic and metatranscriptomic approaches to remove trichlorinated ethylene/cis-dichloroethylene (TCE/cDCE) by Rhodococcus jostii strain RHA1 as an aerobic chemical compound degrader. Metagenomic analysis showed that the number of organisms belonging to the genus Rhodococcus, including strain RHA1, increased from 0.1% to 76.6% of the total microbial community on day 0 at the injection site. Subsequently, the populations of strain RHA1 and other TCE/cDCE-degrading bacteria gradually decreased over time, whereas the populations of the anaerobic dechlorinators Geobacter and Dehalococcoides increased at later stages. Metatranscriptomic analysis revealed a high expression of aromatic compound-degrading genes (bphA1-A4) in strain RHA1 after RHA1 injection. From these results, we concluded that the key dechlorinators of TCE/cDCE were mainly aerobic bacteria, such as RHA1, until day 1, after which the key dechlorinators changed to anaerobic bacteria, such as Geobacter and Dehalococcocides, after day 6 at the injection well. Based on the α-diversity, the richness levels of the microbial community were increased after injection of strain RHA1, and the microbial community composition had not been restored to that of the original composition during the 19 days after treatment. These results provide insights into the assessment of the ecological impact and bioaugmentation process of RHA1 at bioremediation sites.
Collapse
Affiliation(s)
- Saori Watahiki
- Life Sciences and Bioengineering, Graduate School of Life and Environmental Science, University of Tsukuba.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Nobutada Kimura
- Life Sciences and Bioengineering, Graduate School of Life and Environmental Science, University of Tsukuba.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | | | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Satoko Matsukura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology
| | | | | | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology
| |
Collapse
|
6
|
Di Canito A, Zampolli J, Orro A, D’Ursi P, Milanesi L, Sello G, Steinbüchel A, Di Gennaro P. Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7. BMC Genomics 2018; 19:587. [PMID: 30081830 PMCID: PMC6080516 DOI: 10.1186/s12864-018-4965-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. The present study aimed to identify genes involved in the o-xylene degradation in R. opacus strain R7 through a genome-based approach. RESULTS Using genome-based analysis we identified all the sequences in the R7 genome annotated as dioxygenases or monooxygenases/hydroxylases and clustered them into two different trees. The akb, phe and prm sequences were selected as genes encoding respectively for dioxygenases, phenol hydroxylases and monooxygenases and their putative involvement in o-xylene oxidation was evaluated. The involvement of the akb genes in o-xylene oxidation was demonstrated by RT-PCR/qPCR experiments after growth on o-xylene and by the selection of the R7-50 leaky mutant. Although the akb genes are specifically activated for o-xylene degradation, metabolic intermediates of the pathway suggested potential alternative oxidation steps, possibly through monooxygenation. This led us to further investigate the role of the prm and the phe genes. Results showed that these genes were transcribed in a constitutive manner, and that the activity of the Prm monooxygenase was able to transform o-xylene slowly in intermediates as 3,4-dimethylphenol and 2-methylbenzylalcohol. Moreover, the expression level of phe genes, homologous to the phe genes of Rhodococcus spp. 1CP and UPV-1 with a 90% identity, could explain their role in the further oxidation of o-xylene and R7 growth on dimethylphenols. CONCLUSIONS These results suggest that R7 strain is able to degrade o-xylene by the Akb dioxygenase system leading to the production of the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for several monooxygenases/phenol hydroxylases, supports the involvement of other oxygenases converging in the o-xylene degradation pathway in R7 strain.
Collapse
Affiliation(s)
- Alessandra Di Canito
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Jessica Zampolli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Alessandro Orro
- ITB, CNR, via Fratelli Cervi 19, 20133 Segrate, Milan, Italy
| | | | | | - Guido Sello
- Department of Chemistry, University of Milano, via Golgi 19, 20133 Milan, Italy
| | - Alexander Steinbüchel
- Department of Molecular Microbiology and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Environmental Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| |
Collapse
|
7
|
Hernández MA, Lara J, Gago G, Gramajo H, Alvarez HM. The pleiotropic transcriptional regulator NlpR contributes to the modulation of nitrogen metabolism, lipogenesis and triacylglycerol accumulation in oleaginous rhodococci. Mol Microbiol 2016; 103:366-385. [DOI: 10.1111/mmi.13564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Martín A. Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
| | - Julia Lara
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Gabriela Gago
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Hugo Gramajo
- IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario; Ocampo y Esmeralda 2000 Rosario Santa Fe Argentina
| | - Héctor M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Ruta Provincial N° 1, Km 4-Ciudad Universitaria 9000 Comodoro Rivadavia Chubut Argentina
| |
Collapse
|
8
|
Jin HM, Jeong HI, Kim KH, Hahn Y, Madsen EL, Jeon CO. Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment. Sci Rep 2016; 6:21796. [PMID: 26887987 PMCID: PMC4757865 DOI: 10.1038/srep21796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
A genome-wide transcriptional analysis of Alteromonas naphthalenivorans SN2 was performed to investigate its ecophysiological behavior in contaminated tidal flats and seawater. The experimental design mimicked these habitats that either added naphthalene or pyruvate; tidal flat-naphthalene (TF-N), tidal flat-pyruvate (TF-P), seawater-naphthalene (SW-N), and seawater-pyruvate (SW-P). The transcriptional profiles clustered by habitat (TF-N/TF-P and SW-N/SW-P), rather than carbon source, suggesting that the former may exert a greater influence on genome-wide expression in strain SN2 than the latter. Metabolic mapping of cDNA reads from strain SN2 based on KEGG pathway showed that metabolic and regulatory genes associated with energy metabolism, translation, and cell motility were highly expressed in all four test conditions, probably highlighting the copiotrophic properties of strain SN2 as an opportunistic marine r-strategist. Differential gene expression analysis revealed that strain SN2 displayed specific cellular responses to environmental variables (tidal flat, seawater, naphthalene, and pyruvate) and exhibited certain ecological fitness traits -- its notable PAH degradation capability in seasonally cold tidal flat might be reflected in elevated expression of stress response and chaperone proteins, while fast growth in nitrogen-deficient and aerobic seawater probably correlated with high expression of glutamine synthetase, enzymes utilizing nitrite/nitrate, and those involved in the removal of reactive oxygen species.
Collapse
Affiliation(s)
- Hyun Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.,Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Gyeongsangbuk-do 37242, Republic of Korea
| | - Hye Im Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyung Hyun Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Eugene L Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| |
Collapse
|
9
|
Coronado E, Valtat A, van der Meer JR. Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:480-488. [PMID: 25683238 DOI: 10.1111/1758-2229.12276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/31/2015] [Indexed: 06/04/2023]
Abstract
In order to better understand the fate and activity of bacteria introduced into contaminated material for the purpose of enhancing biodegradation rates, we constructed Sphingomonas wittichii RW1 variants with gene reporters interrogating dibenzofuran metabolic activity. Three potential promoters from the dibenzofuran metabolic network were selected and fused to the gene for enhanced green fluorescent protein (EGFP). The stability of the resulting genetic constructions in RW1 was examined, with plasmids based on the broad-host range vector pME6012 being the most reliable. One of the selected promoters, upstream of the gene Swit_4925 for a putative 2-hydroxy-2,4-pentadienoate hydratase, was inducible by growth on dibenzofuran. Sphingomonas wittichii RW1 equipped with the Swit_4925 promoter egfp fusion grew in a variety of non-sterile sandy microcosms contaminated with dibenzofuran and material from a former gasification site. The strain also grew in microcosms without added dibenzofuran but to a very limited extent, and EGFP expression indicated the formation of consistent small subpopulations of cells with an active inferred dibenzofuran metabolic network. Evidence was obtained for competition for dibenzofuran metabolites scavenged by resident bacteria in the gasification site material, which resulted in a more rapid decline of the RW1 population. Our results show the importance of low inoculation densities in order to observe the population development of the introduced bacteria and further illustrate that the limited availability of unique carbon substrate may be the most important factor impinging growth.
Collapse
Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Annabelle Valtat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| |
Collapse
|
10
|
Uchida Y, Wang Y, Akiyama H, Nakajima Y, Hayatsu M. Expression of denitrification genes in response to a waterlogging event in a Fluvisol and its relationship with large nitrous oxide pulses. FEMS Microbiol Ecol 2014; 88:407-23. [PMID: 24592962 DOI: 10.1111/1574-6941.12309] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/11/2014] [Accepted: 02/18/2014] [Indexed: 11/30/2022] Open
Abstract
The contributions of large N2 O pulses following waterlogging to the annual cumulative N2 O productions were significant in a Fluvisol. To uncover the mechanisms underlying these large N2 O pulses, a Fluvisol sampled from an agricultural field in Japan was subjected to waterlogging during incubation. Larger N2 O emissions were observed in intact soil cores when compared to emissions from sieved soils, indicating the importance of soil properties. The most important factor controlling the magnitude of the N2 O pulses after waterlogging was the soil moisture prior to waterlogging. The major pathway for N2 O production was denitrification. Quantitative PCR and quantitative RT-PCR analyses showed that the denitrification genes (nirS, nirK, and nosZ) correlated with N2 O emissions at the mRNA level but not at the DNA level. The change in denitrification gene mRNA levels was more prominent in the 0- to 1-cm soil compared with the 1- to 3-cm soil. Water-soluble and hot-water-soluble carbon contents also showed the highest amount in the 0- to 1-cm soil. These indicate that there was a strong variation in soil microbial properties over very small changes in soil depth, and this variation is important in determining the magnitude of N2 O emissions.
Collapse
Affiliation(s)
- Yoshitaka Uchida
- Task Force for Innovation in Life, Resources and Environment Sciences, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | | | | | | | | |
Collapse
|
11
|
Iino T, Miyauchi K, Kasai D, Masai E, Fukuda M. Characterization of nitrate and nitrite utilization system in Rhodococcus jostii RHA1. J Biosci Bioeng 2013; 115:600-6. [PMID: 23294576 DOI: 10.1016/j.jbiosc.2012.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/29/2012] [Accepted: 12/04/2012] [Indexed: 01/01/2023]
Abstract
A polychlorinated-biphenyl degrader, Rhodococcus jostii RHA1, has the potential to be used in soil for the remediation of environmental contamination. It has been found that RHA1 genes, ro06365 (narK) and ro06366, encoding a nitrate/nitrite transporter and nitrite reductase, respectively, were highly upregulated during the growth in sterile soil. In this study, these genes and ro00862, a paralog of ro06366 were characterized to reveal the nitrate and nitrite utilization systems of RHA1. The transcriptional induction of ro06366 (nirB1) and ro00862 (nirB2) by either nitrate or nitrite was revealed by qRT-PCR. Deletion mutants for each gene exhibited retarded growth on either nitrate or nitrite as a sole nitrogen source. Furthermore, their double mutant, Dnit, grew on and consumed neither nitrate nor nitrite as a sole nitrogen source, suggesting that both nirB1 and nirB2 are involved in the utilization of nitrite and nitrate. A narK mutant, DnarK, exhibited no growth on nitrate and retarded growth on nitrite as the sole nitrogen source. DnarK showed no consumption of nitrate and reduced consumption of nitrite, suggesting that narK is essential for nitrate uptake and is partially involved in nitrite uptake. The induced transcription of nirB1, nirB2, and narK was repressed in the presence of 3 mM ammonium or more. The upregulation of nirB1 and narK in sterilized soil containing ammonium and nitrate suggests that the ammonium concentration of the sterilized soil is equivalent to less than 3 mM. The unique nitrogen metabolism system of RHA1 and its importance for the growth in soil are discussed.
Collapse
Affiliation(s)
- Toju Iino
- Department of Bioengineering, Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | | | | | | | | |
Collapse
|