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Feng JR, Ni HG. Effects of heavy metals and metalloids on the biodegradation of organic contaminants. ENVIRONMENTAL RESEARCH 2024; 246:118069. [PMID: 38160966 DOI: 10.1016/j.envres.2023.118069] [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: 09/03/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Heavy metals and metalloids (HMMs) inhibit the biodegradation of organic pollutants. The degree of inhibition depends not only on the concentration and bioavailability of HMMs but also on additional factors, such as environmental variables (e.g., inorganic components, organic matter, pH, and redox potential), the nature of the metals, and microbial species. Based on the degradation pattern and metal concentrations causing half biodegradation rate reductions (RC50s), the inhibition of biodegradation was: Hg2+, As2O3 > Cu2+, Cd2+, Pb2+, Cr3+ > Ni2+, Co2+ > Mn2+, Zn2+ > Fe3+. Four patterns were observed: inhibition increases with increasing metal concentration; low concentrations stimulate, while high concentrations inhibit; high concentrations inhibit less; and mild inhibition remains constant. In addition, metal ion mixtures have more complex inhibitory effects on the degradation of organic pollutants, which may be greater than, similar to, or less than that of individual HMMs. Finally, the inhibitory mechanism of HMMs on biodegradation is reviewed. HMMs generally have little impact on the biodegradation pathway of organic pollutants for bacterial strains. However, when pollutants are biodegraded by the community, HMMs may activate microbial populations harbouring different transformation pathways. HMMs can affect the biodegradation efficiency of organic pollutants by changing the surface properties of microbes, interfering with degradative enzymes, and interacting with general metabolism.
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Affiliation(s)
- Jin-Ru Feng
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China
| | - Hong-Gang Ni
- School of Urban Planning and Design, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
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2
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Eshghdoostkhatami Z, Cupples AM. Occurrence of Rhodococcus sp. RR1 prmA and Rhodococcus jostii RHA1 prmA across microbial communities and their enumeration during 1,4-dioxane biodegradation. J Microbiol Methods 2024; 219:106908. [PMID: 38403133 DOI: 10.1016/j.mimet.2024.106908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
1,4-Dioxane, a likely human carcinogen, is a co-contaminant at many chlorinated solvent contaminated sites. Conventional treatment technologies, such as carbon sorption or air stripping, are largely ineffective, and so many researchers have explored bioremediation for site clean-up. An important step towards this involves examining the occurrence of the functional genes associated with 1,4-dioxane biodegradation. The current research explored potential biomarkers for 1,4-dioxane in three mixed microbial communities (wetland sediment, agricultural soil, impacted site sediment) using monooxygenase targeted amplicon sequencing, followed by quantitative PCR (qPCR). A BLAST analysis of the sequencing data detected only two of the genes previously associated with 1,4-dioxane metabolism or co-metabolism, namely propane monooxygenase (prmA) from Rhodococcus jostii RHA1 and Rhodococcus sp. RR1. To investigate this further, qPCR primers and probes were designed, and the assays were used to enumerate prmA gene copies in the three communities. Gene copies of Rhodococcus RR1 prmA were detected in all three, while gene copies of Rhodococcus jostii RHA1 prmA were detected in two of the three sample types (except impacted site sediment). Further, there was a statistically significant increase in RR1 prmA gene copies in the microcosms inoculated with impacted site sediment following 1,4-dioxane biodegradation compared to the control microcosms (no 1,4-dioxane) or to the initial copy numbers before incubation. Overall, the results indicate the importance of Rhodococcus associated prmA, compared to other 1,4-dioxane degrading associated biomarkers, in three different microbial communities. Also, the newly designed qPCR assays provide a platform for others to investigate 1,4-dioxane biodegradation potential in mixed communities and should be of particular interest to those considering bioremediation as a potential 1,4-dioxane remediation approach.
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Affiliation(s)
- Zohre Eshghdoostkhatami
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA.
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3
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Yang SNN, Haritos V, Kertesz MA, Coleman NV. A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli. Environ Microbiol 2024; 26:e16567. [PMID: 38233213 DOI: 10.1111/1462-2920.16567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.
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Affiliation(s)
- Sui Nin Nicholas Yang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Victoria Haritos
- Department of Chemical and Biological Engineering, Monash University, Melbourne, Victoria, Australia
| | - Michael A Kertesz
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
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4
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Wang Z, Qiu H, Chen Y, Chen X, Fu C, Yu L. Microbial metabolism of diosgenin by a novel isolated Mycolicibacterium sp. HK-90: A promising biosynthetic platform to produce 19-carbon and 21-carbon steroids. Microb Biotechnol 2024; 17:e14415. [PMID: 38381074 PMCID: PMC10880577 DOI: 10.1111/1751-7915.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/13/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK-90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK-90 involves the selective removal of 5,6-spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG-1 and SCG-2, in the genome of strain HK-90. SCG-1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m-∆kstD1 converting phytosterols to intermediate 9α-hydroxyandrostenedione (9-OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG-2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG-2 resulted in the conversion of diosgenin to 9-OHAD and 9,16-dihydroxy-pregn-4-ene-3,20-dione (9,16-(OH)2 -PG) in mutant m-ΔkstD2. Moreover, the engineered strain mHust-ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9-OHAD by metabolizing phytosterols, and accumulate 9-OHAD and 9,16-(OH)2 -PG from diosgenin. Diosgenin catabolism in strain mHust-ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16-(OH)2 -PG, and 9-OHAD to 9α-hydroxytestosterone (9-OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21-carbon and 19-carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism.
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Affiliation(s)
- Zhikuan Wang
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Hailiang Qiu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Yulong Chen
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Xuemin Chen
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Chunhua Fu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of BiotechnologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
- Key Laboratory of Molecular BiophysicsMinistry of EducationWuhanChina
- Hubei Engineering Research Center for Both Edible and Medicinal ResourcesWuhanChina
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5
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Cupples AM, Li Z, Wilson FP, Ramalingam V, Kelly A. In silico analysis of soil, sediment and groundwater microbial communities to predict biodegradation potential. J Microbiol Methods 2022; 202:106595. [DOI: 10.1016/j.mimet.2022.106595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 12/27/2022]
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Inoue D, Hisada K, Ike M. Effectiveness of tetrahydrofuran at enhancing the 1,4-dioxane degradation ability of activated sludge lacking prior exposure to 1,4-dioxane. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:1707-1718. [PMID: 36240306 DOI: 10.2166/wst.2022.296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
1,4-dioxane (DX) is a contaminant of emerging concern in water environments. The enrichment of DX-degrading bacteria indigenous to activated sludge is key for the efficient biological removal of DX in wastewater. To identify an effective substrate, which enables the selective enrichment of DX-degrading bacteria and has lower toxicity and persistence than DX, this study explored the effectiveness of tetrahydrofuran (THF) at enhancing the DX degradation ability of activated sludge without historical exposure to DX. Although the activated sludge initially exhibited negligible ability to degrade DX (100 mg-C/L) as the sole carbon source, the repeated batch cultivation on THF could enrich bacterial populations capable of degrading DX, inducing the DX degradation ability in activated sludge as effectively as DX did. The THF-enrichment culture after 4 weeks degraded 100 mg-C/L DX almost completely within 21 d. Sequencing analyses revealed that soluble di-iron monooxygenase group 5C, including THF/DX monooxygenase, would play a dominant role in the initial oxidation of DX in THF-enrichment culture, which completely differed from the enrichment culture cultivated on DX. The results indicate that THF can be applied as an effective substrate to enhance the DX degradation ability of microbial consortia, irrespective of the intrinsic ability.
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Affiliation(s)
- Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan E-mail:
| | - Kazuki Hisada
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan E-mail:
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan E-mail:
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Allenby A, Cunningham MR, Hillebrand-Voiculescu A, Comte JC, Doherty R, Kumaresan D. Occurrence of methane-oxidizing bacteria and methanogenic archaea in earth’s cave systems—A metagenomic analysis. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.909865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Karst ecosystems represent up to 25% of the land surface and recent studies highlight their potential role as a sink for atmospheric methane. Despite this, there is limited knowledge of the diversity and distribution of methane-oxidizing bacteria (MOB) or methanogens in karst caves and the sub-surface environment in general. Here, we performed a survey of 14 shotgun metagenomes from cave ecosystems covering a broad set of environmental conditions, to compare the relative abundance and phylogenetic diversity of MOB and methanogens, targeting biomarker genes for methane monooxygenase (pmoA and mmoX) and methyl-coenzyme M reductase (mcrA). Taxonomic analysis of metagenomes showed 0.02–1.28% of classified reads were related to known MOB, of which Gammaproteobacterial MOB were the most abundant making up on average 70% of the surveyed caves’ MOB community. Potential for biogenic methane production in caves was also observed, with 0.008–0.39% of reads classified to methanogens and was dominated by sequences related to Methanosarcina. We have also generated a cave ecosystems protein database (CEPD) based on protein level assembly of cave metagenomes that can be used to profile genes of interest.
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8
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Richards PM, Ewald JM, Zhao W, Rectanus H, Fan D, Durant N, Pound M, Mattes TE. Natural Biodegradation of Vinyl Chloride and cis-Dichloroethene in Aerobic and Suboxic Conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:56154-56167. [PMID: 35322370 DOI: 10.1007/s11356-022-19755-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Chlorinated ethene (CE) groundwater contamination is commonly treated through anaerobic biodegradation (i.e., reductive dechlorination) either as part of an engineered system or through natural attenuation. Aerobic biodegradation has also been recognized as a potentially significant pathway for the removal of the lower CEs cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). However, the role of aerobic biodegradation under low oxygen conditions typical of contaminated groundwater is unclear. Bacteria capable of aerobic VC biodegradation appear to be common in the environment, while aerobic biodegradation of cDCE is less common and little is known regarding the organisms responsible. In this study, we investigate the role of aerobic cDCE and VC biodegradation in a mixed contaminant plume (including CEs, BTEX, and ketones) at Naval Air Station North Island, Installation Restoration Site 9. Sediment and groundwater collected from the plume source area, mid-plume, and shoreline were used to prepare microcosms under fully aerobic (8 mg/L dissolved oxygen (DO)) and suboxic (< 1 mg/L DO) conditions. In the shoreline microcosms, VC and cDCE were rapidly degraded under suboxic conditions (100% and 77% removal in < 62 days). In the suboxic VC microcosms, biodegradation was associated with a > 5 order of magnitude increase in the abundance of functional gene etnE, part of the aerobic VC utilization pathway. VC and cDCE were degraded more slowly under fully aerobic conditions (74% and 30% removal) in 110 days. High-throughput 16S rRNA and etnE sequencing suggest the presence of novel VC- and cDCE-degrading bacteria. These results suggest that natural aerobic biodegradation of cDCE and VC is occurring at the site and provide new evidence that low (< 1 mg/L) DO levels play a significant role in natural attenuation of cDCE and VC.
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Affiliation(s)
- Patrick M Richards
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Jessica M Ewald
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Weilun Zhao
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA
| | - Heather Rectanus
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Dimin Fan
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Neal Durant
- Geosyntec Consultants, Inc, 10211 Wincopin Circle, 4th Floor, Columbia, MD, 21044, USA
| | - Michael Pound
- Naval Facilities Engineering Systems Command (NAVFAC) Southwest, 750 Pacific Hwy, San Diego, CA, 92132, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, The University of Iowa, Iowa City, IA, 52242, USA.
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Identification of active gaseous-alkane degraders at natural gas seeps. THE ISME JOURNAL 2022; 16:1705-1716. [PMID: 35319019 PMCID: PMC9213486 DOI: 10.1038/s41396-022-01211-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/30/2022] [Accepted: 02/04/2022] [Indexed: 11/29/2022]
Abstract
Natural gas seeps release significant amounts of methane and other gases including ethane and propane contributing to global climate change. In this study, bacterial actively consuming short-chain alkanes were identified by cultivation, whole-genome sequencing, and stable-isotope probing (SIP)-metagenomics using 13C-propane and 13C-ethane from two different natural gas seeps, Pipe Creek and Andreiasu Everlasting Fire. Nearly 100 metagenome-assembled genomes (MAGs) (completeness 70–99%) were recovered from both sites. Among these, 16 MAGs had genes encoding the soluble di-iron monooxygenase (SDIMO). The MAGs were affiliated to Actinobacteria (two MAGs), Alphaproteobacteria (ten MAGs), and Gammaproteobacteria (four MAGs). Additionally, three gaseous-alkane degraders were isolated in pure culture, all of which could grow on ethane, propane, and butane and possessed SDIMO-related genes. Two Rhodoblastus strains (PC2 and PC3) were from Pipe Creek and a Mycolicibacterium strain (ANDR5) from Andreiasu. Strains PC2 and PC3 encoded putative butane monooxygenases (MOs) and strain ANDR5 contained a propane MO. Mycolicibacterium strain ANDR5 and MAG19a, highly abundant in incubations with 13C-ethane, share an amino acid identity (AAI) of 99.3%. We show using a combination of enrichment and isolation, and cultivation-independent techniques, that these natural gas seeps contain a diverse community of active bacteria oxidising gaseous-alkanes, which play an important role in biogeochemical cycling of natural gas.
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Environmental Potential for Microbial 1,4-Dioxane Degradation Is Sparse despite Mobile Elements Playing a Role in Trait Distribution. Appl Environ Microbiol 2022; 88:e0209121. [PMID: 35297726 DOI: 10.1128/aem.02091-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1,4-Dioxane (dioxane) is an emerging contaminant of concern for which bioremediation is seen as a promising solution. To date, eight distinct gene families have been implicated in dioxane degradation, though only dioxane monooxygenase (DXMO) from Pseudonocardia dioxanivorans is routinely used as a biomarker in environmental surveys. In order to assess the functional and taxonomic diversity of bacteria capable of dioxane degradation, we collated existing, poorly-organized information on known biodegraders to create a curated suite of biomarkers with confidence levels for assessing 1,4-dioxane degradation potential. The characterized enzyme systems for dioxane degradation are frequently found on mobile elements, and we identified that many of the curated biomarkers are associated with other hallmarks of genomic rearrangements, indicating lateral gene transfer plays a role in dissemination of this trait. This is contrasted by the extremely limited phylogenetic distribution of known dioxane degraders, where all representatives belong to four classes within three bacterial phyla. Based on the curated set of expanded biomarkers, a search of more than 11,000 publicly available metagenomes identified a sparse and taxonomically limited distribution of potential dioxane degradation proteins. Our work provides an important and necessary structure to the current knowledge base for dioxane degradation and clarifies the potential for natural attenuation of dioxane across different environments. It further highlights a disconnect between the apparent mobility of these gene families and their limited distributions, indicating dioxane degradation may be difficult to integrate into a microorganism's metabolism. IMPORTANCE New regulatory limits for 1,4-dioxane in groundwater have been proposed or adopted in many countries, including the United States and Canada, generating a direct need for remediation options as well as better tools for assessing the fate of dioxane in an environment. A comprehensive suite of biomarkers associated with dioxane degradation was identified and then leveraged to examine the global potential for dioxane degradation in natural and engineered environments. We identified consistent differences in the dioxane-degrading gene families associated with terrestrial, aquatic, and wetland environments, indicating reliance on a single biomarker for assessing natural attenuation of dioxane is likely to miss key players. Most environments do not currently host the capacity for dioxane degradation-the sparse distribution of dioxane degradation potential highlights the need for bioaugmentation approaches over biostimulation of naturally occurring microbial communities.
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A multicomponent THF hydroxylase initiates tetrahydrofuran degradation in Cupriavidus metallidurans ZM02. Appl Environ Microbiol 2022; 88:e0188021. [PMID: 35108100 DOI: 10.1128/aem.01880-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tetrahydrofuran (THF) has been recognized as a water contaminant because of its human carcinogenicity, extensive use, and widespread distribution. Previously reported multicomponent monooxygenases (MOs) involved in THF degradation were highly conserved, and all of them were from Gram-positive bacteria. In this study, a novel THF-degrading gene cluster (dmpKLMNOP) encoding THF hydroxylase was identified on the chromosome of a newly isolated Gram-negative THF-degrading bacterium, Cupriavidus metallidurans ZM02, and functionally characterized. Transcriptome sequencing and RT-qPCR demonstrated that the expression of dmpKLMNOP was upregulated during the growth of strain ZM02 on THF or phenol. The deletion of oxygenase alpha or beta subunit or the reductase component disrupted the degradation of THF but did not affect the utilization of its hydroxylated product 2-hydroxytetrahydrofuran. Cupriavidus pinatubonensis JMP134 heterologously expressing dmpKLMNOP from strain ZM02 could grow on THF, indicating that the THF hydroxylase DmpZM02KLMNOP is responsible for the initial degradation of THF. Furthermore, the THF and phenol oxidation activities of crude enzyme extracts were detected, and the highest THF and phenol catalytic activities were 1.38±0.24 μmol min-1 mg-1 and 1.77±0.37 μmol min-1 mg-1, respectively, with the addition of NADPH and Fe2+. The characterization of THF hydroxylase associated with THF degradation enriches our understanding of THF-degrading gene diversity and provides a novel potential enzyme for the bioremediation of THF-containing pollutants. IMPORTANCE Multicomponent MOs catalyzing the initial hydroxylation of THF are vital rate-limiting enzymes in the THF degradation pathway. Previous studies of THF degradation gene clusters have focused on Gram-positive bacteria, and the molecular mechanism of THF degradation in Gram-negative bacteria has rarely been reported. In this study, a novel THF hydroxylase encoded by dmpKLMNOP in strain ZM02 was identified to be involved in both THF and phenol degradation. Our findings provide new insights into the THF-degrading gene cluster and enzymes in Gram-negative bacteria.
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Moratti CF, Scott C, Coleman NV. Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review. Front Bioeng Biotechnol 2022; 9:804234. [PMID: 35083206 PMCID: PMC8784404 DOI: 10.3389/fbioe.2021.804234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.
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Affiliation(s)
- Claudia F. Moratti
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, Australia
| | - Nicholas V. Coleman
- School of Life and Environmental Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia
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Cortés-Albayay C, Sangal V, Klenk HP, Nouioui I. Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov. Front Microbiol 2021; 12:767895. [PMID: 35003006 PMCID: PMC8727900 DOI: 10.3389/fmicb.2021.767895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022] Open
Abstract
Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1T (CECT 8761T = DSM 6695T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027T. Phenotypic, chemotaxonomic and genomic data considering strain L1T (CECT 8761T = DSM 6695T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.
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Affiliation(s)
- Carlos Cortés-Albayay
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vartul Sangal
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Hans-Peter Klenk
- Faculty of Science, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Imen Nouioui
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- *Correspondence: Imen Nouioui,
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Inoue D, Yoshikawa T, Okumura T, Yabuki Y, Ike M. Treatment of 1,4-dioxane-containing water using carriers immobilized with indigenous microorganisms in landfill leachate treatment sludge: A laboratory-scale reactor study. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125497. [PMID: 33652223 DOI: 10.1016/j.jhazmat.2021.125497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/02/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
1,4-Dioxane (DX) is a contaminant of emerging concern in aquatic environments, and is frequently found in landfill leachate. As a biological method applicable to landfill leachate treatment facilities, the feasibility of DX treatment using carriers immobilized with microorganisms indigenous to landfill leachate treatment sludge was explored through laboratory-scale reactor experiments by introducing carriers prepared via microorganism immobilization in the aeration tank of a leachate treatment facility. Three different carrier materials were used to immobilize microorganisms, and a model DX-containing water (10 mg/L) was treated under continuous feeding. Biological DX removal to < 0.5 mg/L was achieved using all carrier types, thereby adhering to the effluent standard for landfill leachate in Japan, which confirms the usefulness of the proposed method. However, weaker aeration and enhanced DX loading drastically impaired the DX removal performance depending on the carrier materials. This suggests the importance of carrier selection and control of the operational variables to ensure stable and effective DX removal. Microbial community analyses revealed that Pseudonocardia with thm genes may largely contribute to the initial oxidation of DX, irrespective of the carrier type, suggesting the importance of this population for the continuous treatment of low DX concentrations with mixed microbial consortia.
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Affiliation(s)
- Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Takumi Yoshikawa
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takuya Okumura
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshinori Yabuki
- Research Institute of Environment, Agriculture and Fisheries, Osaka Prefecture, 442 Syakudo, Habikino, Osaka 583-0862, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Chen R, Miao Y, Liu Y, Zhang L, Zhong M, Adams JM, Dong Y, Mahendra S. Identification of novel 1,4-dioxane degraders and related genes from activated sludge by taxonomic and functional gene sequence analysis. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125157. [PMID: 33540262 DOI: 10.1016/j.jhazmat.2021.125157] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
This study used integrated omics technologies to investigate the potential novel pathways and enzymes for 1,4-dioxane degradation by a consortium enriched from activated sludge of a domestic wastewater treatment plant. An unclassified genus belonging to Xanthobacteraceae increased significantly after magnetic nanoparticle-mediated isolation for 1,4-dioxane degraders. Species with relatively higher abundance (> 0.3%) were identified to present high metabolic activities in the biodegradation process through shotgun sequencing. The functional gene investigations revealed that Xanthobacter sp. 91, Xanthobacter sp. 126, and a Rhizobiales strain carried novel 1,4-dioxane-hydroxylating monooxygenase genes. Xanthobacter sp. 126 contained the genes coding for glycolate oxidase, which was the main enzyme responsible for utilization of 1,4-dioxane intermediates through the TCA cycle, and further proven by the specific glycolate oxidase inhibitor, α-hydroxy-2-pyridinemethanesulfonic acid. An expanded and detailed degradation pathway of 1,4-dioxane was proposed on the basis of the three major intermediates (2-hydroxy-1,4-dioxane, ethylene glycol, and oxalic acid) confirmed by metabolomics. These findings of microbial community and function as well as the novel pathway will be valuable in predicting natural attenuation or reconstruction of a bacterial consortium for enhanced remediation of 1,4-dioxane-contaminated sites as well as wastewater treatment.
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Affiliation(s)
- Ruihuan Chen
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yu Miao
- Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, USA
| | - Yun Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China; National Engineering Laboratory of Site Remediation Technologies, Beijing 100015, China.
| | - Lan Zhang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Ming Zhong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | | | - Yuanhua Dong
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100000, China
| | - Shaily Mahendra
- Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, USA
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Shi M, Zhao Y, Zhang A, Zhao M, Zhai W, Wei Z, Song Y, Tang X, He P. Factoring distinct materials and nitrogen-related microbes into assessments of nitrogen pollution risks during composting. BIORESOURCE TECHNOLOGY 2021; 329:124896. [PMID: 33657502 DOI: 10.1016/j.biortech.2021.124896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 06/12/2023]
Abstract
The aim of this study was to evaluate nitrogen pollution risks from distinct materials composting with the discrepancy of component, including chicken manure, municipal solid and straw waste (CM, MSW, SW). Results showed total nitrogen maximum mean concentrations were observed in CM (39.57 g/kg). Pollution risks in CM were continuous, while MSW and SW mainly concentrated during heating phases. Microbial analysis confirmed that pollution risks from ammonification and nitrification were more prevalent in CM. The risks of pollution caused by nitrate reduction accompanied N2O were the most serious in MSW. The multifunctional nitrogen-related microbes Pseudomonas and Bacillus were affected by microenvironments and contributed to different pollution risks. Furthermore, PICRUSt analysis identified the "inferred" key genes (pmoC-amoC, nrfH, nifD etc.) related to nitrogen pollution risks. This study evaluated nitrogen pollution risks and proposed the future directions, providing theoretical basis and feasible optimization measures for the mitigation of nitrogen pollution during composting.
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Affiliation(s)
- Mingzi Shi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - An Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Maoyuan Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Wenhao Zhai
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
| | - Yangyang Song
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Tang
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
| | - Pingping He
- Heilongjiang Province Environmental Science Research Institute, Harbin 150056, China
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Tusher TR, Shimizu T, Inoue C, Chien MF. Isolation and Characterization of Novel Bacteria Capable of Degrading 1,4-Dioxane in the Presence of Diverse Co-Occurring Compounds. Microorganisms 2021; 9:887. [PMID: 33919159 PMCID: PMC8143092 DOI: 10.3390/microorganisms9050887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Biodegradation is found to be a promising, cost-effective and eco-friendly option for the treatment of industrial wastewater contaminated by 1,4-dioxane (1,4-D), a highly stable synthetic chemical and probable human carcinogen. This study aimed to isolate, identify, and characterize metabolic 1,4-D-degrading bacteria from a stable 1,4-D-degrading microbial consortium. Three bacterial strains (designated as strains TS28, TS32, and TS43) capable of degrading 1,4-D as a sole carbon and energy source were isolated and identified as Gram-positive Pseudonocardia sp. (TS28) and Gram-negative Dokdonella sp. (TS32) and Afipia sp. (TS43). This study, for the first time, confirmed that the genus Dokdonella is involved in the biodegradation of 1,4-D. The results reveal that all of the isolated strains possess inducible 1,4-D-degrading enzymes and also confirm the presence of a gene encoding tetrahydrofuran/dioxane monooxygenase (thmA/dxmA) belonging to group 5 soluble di-iron monooxygenases (SDIMOs) in both genomic and plasmid DNA of each of the strains, which is possibly responsible for the initial oxidation of 1,4-D. Moreover, the isolated strains showed a broad substrate range and are capable of degrading 1,4-D in the presence of additional substrates, including easy-to-degrade compounds, 1,4-D biodegradation intermediates, structural analogs, and co-contaminants of 1,4-D. This indicates the potential of the isolated strains, especially strain TS32, in removing 1,4-D from contaminated industrial wastewater containing additional organic load. Additionally, the results will help to improve our understanding of how multiple 1,4-D-degraders stably co-exist and interact in the consortium, relying on a single carbon source (1,4-D) in order to develop an efficient biological 1,4-D treatment system.
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Affiliation(s)
- Tanmoy Roy Tusher
- Graduate School of Environmental Studies, Tohoku University, Sendai 980–8579, Japan; (T.R.T.); (T.S.); (C.I.)
- Department of Environmental Science and Resource Management, Mawlana Bhashani Science and Technology University, Santosh, Tangail-1902, Bangladesh
| | - Takuya Shimizu
- Graduate School of Environmental Studies, Tohoku University, Sendai 980–8579, Japan; (T.R.T.); (T.S.); (C.I.)
| | - Chihiro Inoue
- Graduate School of Environmental Studies, Tohoku University, Sendai 980–8579, Japan; (T.R.T.); (T.S.); (C.I.)
| | - Mei-Fang Chien
- Graduate School of Environmental Studies, Tohoku University, Sendai 980–8579, Japan; (T.R.T.); (T.S.); (C.I.)
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18
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Ma F, Wang Y, Yang J, Guo H, Su D, Yu L. Degradation of 1,4-Dioxane by Xanthobacter sp. YN2. Curr Microbiol 2021; 78:992-1005. [PMID: 33547937 DOI: 10.1007/s00284-021-02347-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/10/2021] [Indexed: 12/28/2022]
Abstract
1,4-Dioxane is a highly toxic and carcinogenic pollutant found worldwide in groundwater and soil environments. Several microorganisms have been isolated by their ability to grow on 1,4-dioxane; however, low 1,4-dioxane tolerance and slow degradation kinetics remain obstacles for their use in 1,4-dioxane bioremediation. We report here the isolation and characterization of a new strain, Xanthobacter sp. YN2, capable of highly efficient 1,4-dioxane degradation. High degradation efficiency and high tolerance to 1,4-dioxane make this new strain an ideal candidate for the biodegradation of 1,4-dioxane in various treatment facilities. The maximum degradation rate of 1,4-dioxane was found to be 1.10 mg-1,4-dioxane/h mg-protein. Furthermore, Xanthobacter sp. YN2 was shown to grow in the presence of higher than 3000 mg/L 1,4-dioxane with little to no degradation inhibition. In addition, Xanthobacter sp. YN2 could grow on and degrade 1,4-dioxane at pH ranges 5 to 8 and temperatures between 20 and 40 °C. Xanthobacter sp. YN2 was also found to be able to grow on a variety of other substrates including several analogs of 1,4-dioxane. Genome sequence analyses revealed the presence of two soluble di-iron monooxygenase (SDIMO) gene clusters, and regulation studies determined that all of the genes in these two clusters were upregulated in the presence of 1,4-dioxane. This study provides insights into the bacterial stress response and the highly efficient biodegradation of 1,4-dioxane as well as the identification of a novel Group-2 SDIMO.
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Affiliation(s)
- Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China.
| | - Yingning Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Haijuan Guo
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, China
| | - Delin Su
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
| | - Lan Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin, China
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Detection of an alkene monooxygenase in vinyl chloride-oxidizing bacteria with GeneFISH. J Microbiol Methods 2021; 181:106147. [PMID: 33493490 DOI: 10.1016/j.mimet.2021.106147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 11/23/2022]
Abstract
Fluorescence in situ hybridization (FISH) can provide information on the morphology, spatial arrangement, and local environment of individual cells enabling the investigation of intact microbial communities. GeneFISH uses polynucleotide probes and enzymatic signal amplification to detect genes that are present in low copy numbers. Previously, this technique has only been applied in a small number of closely related organisms. However, many important functional genes, such as those involved in xenobiotic degradation or pathogenesis, are present in diverse microbial strains. Here, we present a geneFISH method for the detection of the functional gene etnC, which encodes the alpha subunit of an alkene monooxygenase used by aerobic ethene and vinyl chloride oxidizing bacteria (etheneotrophs). The probe concentration was optimized and found to be 100 pg/μl, similar to previous geneFISH reports. Permeabilization was necessary for successful geneFISH labeling of Mycobacteria; sequential treatment with lysozyme and achromopeptidase was the most effective treatment. This method was able to detect etnC in several organisms including Mycobacteria and Nocardioides, demonstrating for the first time that a single geneFISH probe can detect a variety of alleles (>80% sequence similarity) across multiple species. Detection of etnC with geneFISH has practical applications for bioremediation. This method can be readily adapted for other functional genes and has broad applications for investigating microbial communities in natural and engineered systems.
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20
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Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves. Microorganisms 2020; 8:microorganisms8101557. [PMID: 33050387 PMCID: PMC7600658 DOI: 10.3390/microorganisms8101557] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/30/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022] Open
Abstract
The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Lu L, Wang G, Yeung M, Xi J, Hu HY. Shift of microbial community in gas-phase biofilters with different inocula, inlet loads and nitrogen sources. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Li F, Deng D, Li M. Distinct Catalytic Behaviors between Two 1,4-Dioxane-Degrading Monooxygenases: Kinetics, Inhibition, and Substrate Range. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:1898-1908. [PMID: 31877031 DOI: 10.1021/acs.est.9b05671] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Monitored natural attenuation (MNA) and engineered bioremediation have been recognized as effective and cost-efficient in situ treatments to mitigate 1,4-dioxane (dioxane) contamination. Dioxane metabolism can be initiated by two catabolic enzymes, propane monooxygenase (PRM) and tetrahydrofuran monooxygenase (THM), belonging to the group-6 and 5 of soluble di-iron monooxygenase family, respectively. In this study, we comprehensively compared catalytic behaviors of PRM and THM when individually expressed in the heterologous host, Mycobacterium smegmatis mc2-155. Kinetic results revealed a half-saturation coefficient (Km) of 53.0 ± 13.1 mg/L for PRM, nearly 4 times lower than that of THM (235.8 ± 61.6 mg/L), suggesting that PRM has a higher affinity to dioxane. Exposure with three common co-contaminants (1,1-dichloroethene, trichloroethene, and 1,1,1-trichloroethane) demonstrated that PRM was also more resistant to their inhibition than THM. Thus, dioxane degraders expressing PRM may be more physiologically and ecologically advantageous than those with THM at impacted sites, where dioxane concentration is relatively low (e.g., 250 to 1000 μg/L) with co-occurrence of chlorinated solvents (e.g., 0.5 to 8 mg/L), underscoring the need of surveying both PRM and THM-encoding genes for MNA potential assessment. PRM is also highly versatile, which breaks down cyclic molecules (dioxane, tetrahydrofuran, and cyclohexane), as well as chlorinated and aromatic pollutants, including vinyl chloride, 1,2-dichloroethane, benzene, and toluene. This is the first report regarding the ability of PRM to degrade a variety of short-chain alkanes and ethene in addition to dioxane, unraveling its pivotal role in aerobic biostimulation that utilizes propane, isobutane, or other gaseous alkanes/alkenes (e.g., ethane, butane, and ethene) to select and fuel indigenous microorganisms to tackle the commingled contamination of dioxane and chlorinated compounds.
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Affiliation(s)
- Fei Li
- Department of Chemistry and Environmental Science , New Jersey Institute of Technology , Newark , New Jersey 07102 , United States
| | - Daiyong Deng
- Department of Chemistry and Environmental Science , New Jersey Institute of Technology , Newark , New Jersey 07102 , United States
| | - Mengyan Li
- Department of Chemistry and Environmental Science , New Jersey Institute of Technology , Newark , New Jersey 07102 , United States
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Enrichment of novel Actinomycetales and the detection of monooxygenases during aerobic 1,4-dioxane biodegradation with uncontaminated and contaminated inocula. Appl Microbiol Biotechnol 2020; 104:2255-2269. [DOI: 10.1007/s00253-020-10376-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/22/2019] [Accepted: 01/14/2020] [Indexed: 02/06/2023]
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Tusher TR, Shimizu T, Inoue C, Chien MF. Enrichment and Analysis of Stable 1,4-dioxane-Degrading Microbial Consortia Consisting of Novel Dioxane-Degraders. Microorganisms 2019; 8:microorganisms8010050. [PMID: 31881778 PMCID: PMC7022751 DOI: 10.3390/microorganisms8010050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022] Open
Abstract
Biodegradation of 1,4-dioxane, a water contaminant of emerging concern, has drawn substantial attention over the last two decades. A number of dioxane-degraders have been identified, though many of them are unable to metabolically utilize 1,4-dioxane. Moreover, it is considered more preferable to use microbial consortia rather than the pure strains, especially in conventional bioreactors for industrial wastewater treatment. In the present study, a stable 1,4-dioxane-degrading microbial consortium was enriched, namely 112, from industrial wastewater by nitrate mineral salt medium (NMSM). The consortium 112 is capable of utilizing 1,4-dioxane as a sole carbon and energy source, and can completely degrade 1,4-dioxane up to 100 mg/L. From the consortium 112, two 1,4-dioxane-degrading bacterial strains were isolated and identified, in which the Variovorax sp. TS13 was found to be a novel 1,4-dioxane-degrader that can utilize 100 mg/L of 1,4-dioxane. The efficacy of the consortium 112 was increased significantly when we cultured the consortium with mineral salt medium (MSM). The new consortium, N112, could utilize 1,4-dioxane at a rate of 1.67 mg/L·h. The results of the ribosomal RNA intergenic spacer analysis (RISA) depicted that changes in the microbial community structure of consortium 112 was the reason behind the improved degradation efficiency of consortium N112, which was exhibited as a stable and effective microbial consortium with a high potential for bioremediation of the dioxane-impacted sites and contaminated industrial wastewater.
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Farhan Ul Haque M, Crombie AT, Murrell JC. Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps. MICROBIOME 2019; 7:134. [PMID: 31585550 PMCID: PMC6778391 DOI: 10.1186/s40168-019-0741-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, play a significant role in reducing the emissions of methane from many environments. Methylocella-like facultative methanotrophs are a unique group of bacteria that grow on other components of natural gas (i.e. ethane and propane) in addition to methane but a little is known about the distribution and activity of Methylocella in the environment. The purposes of this study were to identify bacteria involved in cycling methane emitted from natural gas seeps and, most importantly, to investigate if Methylocella-like facultative methanotrophs were active utilisers of natural gas at seep sites. RESULTS The community structure of active methane-consuming bacteria in samples from natural gas seeps from Andreiasu Everlasting Fire (Romania) and Pipe Creek (NY, USA) was investigated by DNA stable isotope probing (DNA-SIP) using 13C-labelled methane. The 16S rRNA gene sequences retrieved from DNA-SIP experiments revealed that of various active methanotrophs, Methylocella was the only active methanotrophic genus common to both natural gas seep environments. We also isolated novel facultative methanotrophs, Methylocella sp. PC1 and PC4 from Pipe Creek, able to utilise methane, ethane, propane and various non-gaseous multicarbon compounds. Functional and comparative genomics of these new isolates revealed genomic and physiological divergence from already known methanotrophs, in particular, the absence of mxa genes encoding calcium-containing methanol dehydrogenase. Methylocella sp. PC1 and PC4 had only the soluble methane monooxygenase (sMMO) and lanthanide-dependent methanol dehydrogenase (XoxF). These are the first Alphaproteobacteria methanotrophs discovered with this reduced functional redundancy for C-1 metabolism (i.e. sMMO only and XoxF only). CONCLUSIONS Here, we provide evidence, using culture-dependent and culture-independent methods, that Methylocella are abundant and active at terrestrial natural gas seeps, suggesting that they play a significant role in the biogeochemical cycling of these gaseous alkanes. This might also be significant for the design of biotechnological strategies for controlling natural gas emissions, which are increasing globally due to unconventional exploitation of oil and gas.
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Affiliation(s)
- Muhammad Farhan Ul Haque
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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Carbon sources that enable enrichment of 1,4-dioxane-degrading bacteria in landfill leachate. Biodegradation 2019; 31:23-34. [PMID: 31520343 DOI: 10.1007/s10532-019-09891-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
1,4-Dioxane (DX) is a recalcitrant cyclic ether that has gained attention as an emerging pollutant in the aquatic environment. Enrichment of indigenous DX-degrading bacteria, which are considered to be minor populations even in DX-impacted environments, is the key for efficient biological DX removal. Therefore, this study aimed to explore carbon sources applicable for the enrichment of DX-degrading bacteria present in landfill leachate, which is a potential source of DX pollution. Microorganisms collected from landfill leachate were cultivated on six different carbon sources (DX, tetrahydrofuran (THF), 1,3,5-trioxane (TX), ethylene glycol (EG), diethylene glycol (DEG), and 1,4-butanediol (BD)) in a sequential batch mode. Consequently, enrichment cultures cultivated on THF in addition to DX improved the DX degradation ability compared to that of the original leachate sample, while those on the other test carbon sources did not. The results indicated that THF can be an alternative carbon source to enrich DX-degrading bacteria, and that TX, EG, DEG and BD are not applicable to concentrate DX-degrading bacteria in complex microbial consortia. In addition, sequencing analyses of 16S rRNA and soluble di-iron monooxygenase (SDIMO) genes revealed notable dominance of thm/dxm genes involved in group 5 SDIMO both in DX- and THF-enrichment cultures. The analysis also showed a predominance of Pseudonocardia in THF-enrichment culture, suggesting that Pseudonocardia harboring thm/dxm genes contributes to enhanced DX degradation in THF-enrichment culture.
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Abstract
The aromatic N-oxides have received increased attention over the last few years due to their potential application in medicine, agriculture and organic chemistry. As a green alternative in their synthesis, the biocatalytic method employing whole cells of Escherichia coli bearing phenol monooxygenase like protein PmlABCDEF (from here on – PML monooxygenase) has been introduced. In this work, site-directed mutagenesis was used to study the contributions of active site neighboring residues I106, A113, G109, F181, F200, F209 to the regiospecificity of N-oxidation. Based on chromogenic indole oxidation screening, a collection of PML mutants with altered catalytic properties was created. Among the tested mutants, the A113G variant acquired the most distinguishable N-oxidations capacity. This new variant of PML was able to produce dioxides (quinoxaline-1,4-dioxide, 2,5-dimethylpyrazine-1,4-dioxide) and specific mono-N-oxides (2,3,5-trimethylpyrazine-1-oxide) that were unachievable using the wild type PML. This mutant also featured reshaped regioselectivity as N-oxidation shifted towards quinazoline-1-oxide compared to quinazoline-3-oxide that is produced by the wild type PML.
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Ji N, Wang X, Yin C, Peng W, Liang R. CrgA Protein Represses AlkB2 Monooxygenase and Regulates the Degradation of Medium-to-Long-Chain n-Alkanes in Pseudomonas aeruginosa SJTD-1. Front Microbiol 2019; 10:400. [PMID: 30915046 PMCID: PMC6422896 DOI: 10.3389/fmicb.2019.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
AlkB monooxygenases in bacteria are responsible for the hydroxylation of medium- and long-chain n-alkanes. In this study, one CrgA protein of Pseudomonas aeruginosa SJTD-1, a member of LysR family, was proved to regulate AlkB2 monooxygenase and the degradation of medium-to-long-chain n-alkanes (C14-C20) by directly binding to the upstream of alkB2 gene. Two specific sites for CrgA binding were found in the promoter region of alkB2 gene, and the imperfect mirror repeat (IIR) structure was proved critical for CrgA recognition and binding. Hexadecyl CoA and octadecyl CoA could effectively release the CrgA binding and start the transcription of alkB2 gene, implying a positive regulation of metabolic intermediate. In the presence of medium-to-long-chain n-alkanes (C14-C20), deletion of crgA gene could enhance the transcription and expression of AlkB2 monooxygenase significantly; and in n-octadecane culture, strain S1ΔalkB1&crgA grew more vigorously than strain S1 ΔalkB1 &crgA . Almost no regulation of CrgA protein was observed to alkB1 gene in vitro and in vivo. Therefore, CrgA acted as a negative regulator for the medium-to-long-chain n-alkane utilization in P. aeruginosa SJTD-1. The work will promote the regulation mechanism study of n-alkane degradation in bacteria and help the bioremediation method development for petroleum pollution.
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Affiliation(s)
- Nannan Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Carrión O, Larke-Mejía NL, Gibson L, Farhan Ul Haque M, Ramiro-García J, McGenity TJ, Murrell JC. Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment. MICROBIOME 2018; 6:219. [PMID: 30526688 PMCID: PMC6286570 DOI: 10.1186/s40168-018-0607-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/25/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting isoA encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel isoA PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments. RESULTS The new isoA probes specifically amplified isoA genes from taxonomically diverse isoprene-degrading bacteria including members of the genera Rhodococcus, Variovorax, and Sphingopyxis. There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of isoA amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of isoA sequences, with poplar leaf enrichments containing more phylogenetically diverse isoA genes. Quantification by qPCR using these isoA probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria. CONCLUSION This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.
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Affiliation(s)
- Ornella Carrión
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Nasmille L Larke-Mejía
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lisa Gibson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Muhammad Farhan Ul Haque
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Javier Ramiro-García
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Terry J McGenity
- School of Biological Sciences, University of Essex, Colchester, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Kwon M, Ho A, Yoon S. Novel approaches and reasons to isolate methanotrophic bacteria with biotechnological potentials: recent achievements and perspectives. Appl Microbiol Biotechnol 2018; 103:1-8. [PMID: 30315351 DOI: 10.1007/s00253-018-9435-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 10/28/2022]
Abstract
The recent drop in the price of natural gas has rekindled the interests in methanotrophs, the organisms capable of utilizing methane as the sole electron donor and carbon source, as biocatalysts for various industrial applications. As heterologous expression of the methane monooxygenases in more amenable hosts has been proven to be nearly impossible, future success in methanotroph biotechnology largely depends on securing phylogenetically and phenotypically diverse methanotrophs with relatively high growth rates. For long, isolation of methanotrophs have relied on repeated single colony picking after initial batch enrichment with methane, which is a very rigorous and time-consuming process. In this review, three unconventional isolation methods devised for facilitation of the isolation process, diversification of targeted methanotrophs, and/or screening of rapid growers are summarized. The soil substrate membrane method allowed for isolation of previously elusive methanotrophs and application of high-throughput extinction plating technique facilitated the isolation procedure. Use of a chemostat with gradually increased dilution rates proved effective in screening for the fastest-growing methanotrophs from environmental samples. Development of new isolation technologies incorporating microfluidics and single-cell techniques may lead to discovery of previously unculturable methanotrophs with unexpected metabolic potentials and thus, certainly warrant future investigation.
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Affiliation(s)
- Miye Kwon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
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Lu L, Wang G, Yeung M, Xi J, Hu HY. Response of microbial community structure and metabolic profile to shifts of inlet VOCs in a gas-phase biofilter. AMB Express 2018; 8:160. [PMID: 30284060 PMCID: PMC6170518 DOI: 10.1186/s13568-018-0687-z] [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: 09/15/2018] [Accepted: 09/25/2018] [Indexed: 12/31/2022] Open
Abstract
The effects of inlet VOCs (Volatile Organic Compounds) shifts on microbial community structure in a biofiltration system were investigated. A lab-scale biofilter was set up to treat eight VOCs sequentially. Short declines in removal efficiency appeared after VOCs shifts and then later recovered. The number of OTUs in the biofilter declined from 690 to 312 over time. At the phylum level, Actinobacteria and Proteobacteria remained dominant throughout the operation for all VOCs, with their combined abundance ranging from 60 to 90%. The abundances of Planctomycetes and Thermi increased significantly to 20% and 5%, respectively, with the intake of non-aromatic hydrocarbons. At the genus level, Rhodococcus was present in the highest abundance (≥ 10%) throughout the experiment, indicating its wide degradability. Some potential degraders were also found; namely, Thauera and Pseudomonas, which increased in abundance to 19% and 12% during treatment with ethyl acetate and toluene, respectively. Moreover, the microbial metabolic activity declined gradually with time, and the metabolic profile of the toluene-treating community differed significantly from those of other communities.
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McCarl V, Somerville MV, Ly MA, Henry R, Liew EF, Wilson NL, Holmes AJ, Coleman NV. Heterologous Expression of Mycobacterium Alkene Monooxygenases in Gram-Positive and Gram-Negative Bacterial Hosts. Appl Environ Microbiol 2018; 84:e00397-18. [PMID: 29802186 PMCID: PMC6052275 DOI: 10.1128/aem.00397-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/15/2018] [Indexed: 01/01/2023] Open
Abstract
Alkene monooxygenases (MOs) are soluble di-iron-containing enzymes found in bacteria that grow on alkenes. Here, we report improved heterologous expression systems for the propene MO (PmoABCD) and ethene MO (EtnABCD) from Mycobacterium chubuense strain NBB4. Strong functional expression of PmoABCD and EtnABCD was achieved in Mycobacterium smegmatis mc2155, yielding epoxidation activities (62 and 27 nmol/min/mg protein, respectively) higher than any reported to date for heterologous expression of a di-iron MO system. Both PmoABCD and EtnABCD were specialized for the oxidation of gaseous alkenes (C2 to C4), and their activity was much lower on liquid alkenes (C5 to C8). Despite intensive efforts to express the complete EtnABCD enzyme in Escherichia coli, this was not achieved, although recombinant EtnB and EtnD proteins could be purified individually in soluble form. The biochemical function of EtnD as an oxidoreductase was confirmed (1.36 μmol cytochrome c reduced/min/mg protein). Cloning the EtnABCD gene cluster into Pseudomonas putida KT2440 yielded detectable epoxidation of ethene (0.5 nmol/min/mg protein), and this could be stimulated (up to 1.1 nmol/min/mg protein) by the coexpression of cpn60 chaperonins from either Mycobacterium spp. or E. coli Successful expression of the ethene MO in a Gram-negative host was validated by both whole-cell activity assays and peptide mass spectrometry of induced proteins seen on SDS-PAGE gels.IMPORTANCE Alkene MOs are of interest for their potential roles in industrial biocatalysis, most notably for the stereoselective synthesis of epoxides. Wild-type bacteria that grow on alkenes have high activities for alkene oxidation but are problematic for biocatalysis, since they tend to consume the epoxide products. Using recombinant biocatalysts is the obvious alternative, but a major bottleneck is the low activities of recombinant alkene MOs. Here, we provide new high-activity recombinant biocatalysts for alkene oxidation, and we provide insights into how to further improve these systems.
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Affiliation(s)
- Victoria McCarl
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mark V Somerville
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Mai-Anh Ly
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Rebecca Henry
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Elissa F Liew
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Neil L Wilson
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Andrew J Holmes
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
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Deng Y, Deng C, Yang J, Li B, Wang E, Yuan H. Novel Butane-Oxidizing Bacteria and Diversity of bmoX Genes in Puguang Gas Field. Front Microbiol 2018; 9:1576. [PMID: 30065710 PMCID: PMC6056644 DOI: 10.3389/fmicb.2018.01576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
To investigate the diversity of butane-oxidizing bacteria in soils contaminated by long-term light hydrocarbon microseepage and the influence of butane on the soil microbial community, a quantitative study and identification of butane-oxidizing bacteria (BOB) in soils at the Puguang gas field were performed by DNA-based stable isotope probing (DNA-SIP). For the first time, two phylotypes corresponding to the genera Giesbergeria and Ramlibacter were identified as being directly involved in butane oxidation, in addition to the well-known light hydrocarbon degrader Pseudomonas. Furthermore, bmoX genes were strongly labeled by 13C-butane, and their abundances in gas field soils increased by 43.14-, 17.39-, 21.74-, and 30.14-fold when incubated with butane for 6, 9, 12, and 14 days, respectively, indicating that these bmoX-harboring bacteria could use butane as the sole carbon and energy source and they play an important role in butane degradation. We also found that the addition of butane rapidly shaped the bacterial community and reduced the diversity of bmoX genes in the gas field soils. These findings improve our understanding of BOB in the gas field environment and reveal the potential for their applications in petroleum exploration and bioremediation.
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Affiliation(s)
- Yue Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chunping Deng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Baozhen Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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Liu X, Wu Y, Wilson FP, Yu K, Lintner C, Cupples AM, Mattes TE. Integrated methodological approach reveals microbial diversity and functions in aerobic groundwater microcosms adapted to vinyl chloride. FEMS Microbiol Ecol 2018; 94:5045312. [DOI: 10.1093/femsec/fiy124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/25/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Xikun Liu
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Yang Wu
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Fernanda P Wilson
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Ke Yu
- School of Environment and Energy, Peking University Shenzhen Graduate School, University Town, Nanshan District, Shenzhen 518055, China
| | - Carly Lintner
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Alison M Cupples
- Department of Civil and Environmental Engineering, Engineering Building, 428 S. Shaw Lane, Room 3546, East Lansing, MI 48824, USA
| | - Timothy E Mattes
- Department of Civil and Environmental Engineering, 4105 Seamans Center, University of Iowa, Iowa City, IA, 52242, USA
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He Y, Mathieu J, da Silva MLB, Li M, Alvarez PJJ. 1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes. Microb Biotechnol 2017; 11:189-198. [PMID: 28984418 PMCID: PMC5743803 DOI: 10.1111/1751-7915.12850] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/07/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4‐dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g‐dioxane per g‐protein per day) were comparable to those of two dioxane‐metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH‐06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di‐iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane‐degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
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Affiliation(s)
- Ya He
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Marcio L B da Silva
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
| | - Mengyan Li
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, 77005, USA
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Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils. Appl Environ Microbiol 2017; 83:AEM.00287-17. [PMID: 28576763 DOI: 10.1128/aem.00287-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.
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Lock M, Nichol T, Murrell JC, Smith TJ. Mutagenesis and expression of methane monooxygenase to alter regioselectivity with aromatic substrates. FEMS Microbiol Lett 2017; 364:3906680. [PMID: 28854685 PMCID: PMC5812538 DOI: 10.1093/femsle/fnx137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/27/2017] [Indexed: 11/13/2022] Open
Abstract
Soluble methane monooxygenase (sMMO) from methane-oxidising bacteria can oxygenate more than 100 hydrocarbons and is one of the most catalytically versatile biological oxidation catalysts. Expression of recombinant sMMO has to date not been achieved in Escherichia coli and so an alternative expression system must be used to manipulate it genetically. Here we report substantial improvements to the previously described system for mutagenesis of sMMO and expression of recombinant enzymes in a methanotroph (Methylosinus trichosporium OB3b) expression system. This system has been utilised to make a number of new mutants and to engineer sMMO to increase its catalytic precision with a specific substrate whilst increasing activity by up to 6-fold. These results are the first 'proof-of-principle' experiments illustrating the feasibility of developing sMMO-derived catalysts for diverse applications.
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Affiliation(s)
- Malcolm Lock
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - Tim Nichol
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Thomas J. Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK
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Dolinová I, Štrojsová M, Černík M, Němeček J, Macháčková J, Ševců A. Microbial degradation of chloroethenes: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:13262-13283. [PMID: 28378313 DOI: 10.1007/s11356-017-8867-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/17/2017] [Indexed: 05/28/2023]
Abstract
Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.
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Affiliation(s)
- Iva Dolinová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Martina Štrojsová
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Miroslav Černík
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jan Němeček
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Jiřina Macháčková
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
- Faculty of Mechatronics, Informatics and Interdisciplinary Studies, Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
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Inoue D, Tsunoda T, Sawada K, Yamamoto N, Saito Y, Sei K, Ike M. 1,4-Dioxane degradation potential of members of the genera Pseudonocardia and Rhodococcus. Biodegradation 2016; 27:277-286. [PMID: 27623820 DOI: 10.1007/s10532-016-9772-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/07/2016] [Indexed: 11/30/2022]
Abstract
In recent years, several strains capable of degrading 1,4-dioxane have been isolated from the genera Pseudonocardia and Rhodococcus. This study was conducted to evaluate the 1,4-dioxane degradation potential of phylogenetically diverse strains in these genera. The abilities to degrade 1,4-dioxane as a sole carbon and energy source and co-metabolically with tetrahydrofuran (THF) were evaluated for 13 Pseudonocardia and 12 Rhodococcus species. Pseudonocardia dioxanivorans JCM 13855T, which is a 1,4-dioxane degrading bacterium also known as P. dioxanivorans CB1190, and Rhodococcus aetherivorans JCM 14343T could degrade 1,4-dioxane as the sole carbon and energy source. In addition to these two strains, ten Pseudonocardia strains could degrade THF, but no Rhodococcus strains could degrade THF. Of the ten Pseudonocardia strains, Pseudonocardia acacia JCM 16707T and Pseudonocardia asaccharolytica JCM 10410T degraded 1,4-dioxane co-metabolically with THF. These results indicated that 1,4-dioxane degradation potential, including degradation for growth and by co-metabolism with THF, is possessed by selected strains of Pseudonocardia and Rhodococcus, although THF degradation potential appeared to be widely distributed in Pseudonocardia. Analysis of soluble di-iron monooxygenase (SDIMO) α-subunit genes in THF and/or 1,4-dioxane degrading strains revealed that not only THF and 1,4-dioxane monooxygenases but also propane monooxygenase-like SDIMOs can be involved in 1,4-dioxane degradation.
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Affiliation(s)
- Daisuke Inoue
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan. .,Environment and Medical Sciences Course, Graduate School of Medical Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan.
| | - Tsubasa Tsunoda
- Environment and Medical Sciences Course, Graduate School of Medical Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Kazuko Sawada
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Norifumi Yamamoto
- Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama, Kanagawa, 245-0051, Japan.,Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuji Saito
- Technology Center, Taisei Corporation, 344-1 Nase-cho, Totsuka-ku, Yokohama, Kanagawa, 245-0051, Japan
| | - Kazunari Sei
- Department of Health Science, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan.,Environment and Medical Sciences Course, Graduate School of Medical Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Furuya T, Nakao T, Kino K. Catalytic function of the mycobacterial binuclear iron monooxygenase in acetone metabolism. FEMS Microbiol Lett 2015; 362:fnv136. [PMID: 26293913 DOI: 10.1093/femsle/fnv136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria such as Mycobacterium smegmatis strain mc(2)155 and Mycobacterium goodii strain 12523 are able to grow on acetone and use it as a source of carbon and energy. We previously demonstrated by gene deletion analysis that the mimABCD gene cluster, which encodes a binuclear iron monooxygenase, plays an essential role in acetone metabolism in these mycobacteria. In the present study, we determined the catalytic function of MimABCD in acetone metabolism. Whole-cell assays were performed using Escherichia coli cells expressing the MimABCD complex. When the recombinant E. coli cells were incubated with acetone, a product was detected by gas chromatography (GC) analysis. Based on the retention time and the gas chromatography-mass spectrometry (GC-MS) spectrum, the reaction product was identified as acetol (hydroxyacetone). The recombinant E. coli cells produced 1.02 mM of acetol from acetone within 24 h. Furthermore, we demonstrated that MimABCD also was able to convert methylethylketone (2-butanone) to 1-hydroxy-2-butanone. Although it has long been known that microorganisms such as mycobacteria metabolize acetone via acetol, this study provides the first biochemical evidence for the existence of a microbial enzyme that catalyses the conversion of acetone to acetol.
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Affiliation(s)
- Toshiki Furuya
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tomomi Nakao
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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Das S, Pettersson BMF, Behra PRK, Ramesh M, Dasgupta S, Bhattacharya A, Kirsebom LA. Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics. Genome Biol Evol 2015; 7:1871-86. [PMID: 26079817 PMCID: PMC4524478 DOI: 10.1093/gbe/evv111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum, M. chubuense, and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.
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Affiliation(s)
- Sarbashis Das
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | | | | | - Malavika Ramesh
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Sweden
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He Z, Zhang K, Wang H, Lv Z. Trehalose promotes Rhodococcus sp. strain YYL colonization in activated sludge under tetrahydrofuran (THF) stress. Front Microbiol 2015; 6:438. [PMID: 26029182 PMCID: PMC4429620 DOI: 10.3389/fmicb.2015.00438] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/23/2015] [Indexed: 12/20/2022] Open
Abstract
Few studies have focused on the role of compatible solutes in changing the microbial community structure in bioaugmentation systems. In this study, we investigated the influence of trehalose as a biostimulant on the microbial community in tetrahydrofuran (THF)-treated wastewater bioaugmentation systems with Rhodococcus sp. YYL. Functional gene profile changes were used to study the variation in the microbial community. Soluble di-iron monooxygenases (SDIMO), particularly group-5 SDIMOs (i.e., tetrahydrofuran and propane monooxygenases), play a significant role in the initiation of the ring cleavage of tetrahydrofuran. Group-5 SDIMOs genes are enriched upon trehalose addition, and exogenous tetrahydrofuran monooxygenase (thmA) genes can successfully colonize bioaugmentation systems. Cytochrome P450 monooxygenases (P450s) have a significant role in catalyzing the region- and stereospecific oxidation of non-activated hydrocarbons, and THF was reported to inhibit P450s in the environment. The CYP153 family was chosen as a representative P450 to study the inhibitory effects of THF. The results demonstrated that CYP153 family genes exhibited significant changes upon THF treatment and that trehalose helped maintain a rich diversity and high abundance of CYP153 family genes. Biostimulation with trehalose could alleviate the negative effects of THF stress on microbial diversity in bioaugmentation systems. Our results indicated that trehalose as a compatible solute plays a significant role for environmental strains under extreme conditions.
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Affiliation(s)
- Zhixing He
- College of Life Sciences, Zhejiang University Hangzhou, China
| | - Kai Zhang
- College of Life Sciences, Zhejiang University Hangzhou, China
| | - Haixia Wang
- College of Life Sciences, Zhejiang University Hangzhou, China
| | - Zhenmei Lv
- College of Life Sciences, Zhejiang University Hangzhou, China
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Cappelletti M, Presentato A, Milazzo G, Turner RJ, Fedi S, Frascari D, Zannoni D. Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes. Front Microbiol 2015; 6:393. [PMID: 26029173 PMCID: PMC4428276 DOI: 10.3389/fmicb.2015.00393] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/16/2015] [Indexed: 11/16/2022] Open
Abstract
Rhodococcus sp. strain BCP1 was initially isolated for its ability to grow on gaseous n-alkanes, which act as inducers for the co-metabolic degradation of low-chlorinated compounds. Here, both molecular and metabolic features of BCP1 cells grown on gaseous and short-chain n-alkanes (up to n-heptane) were examined in detail. We show that propane metabolism generated terminal and sub-terminal oxidation products such as 1- and 2-propanol, whereas 1-butanol was the only terminal oxidation product detected from n-butane metabolism. Two gene clusters, prmABCD and smoABCD—coding for Soluble Di-Iron Monooxgenases (SDIMOs) involved in gaseous n-alkanes oxidation—were detected in the BCP1 genome. By means of Reverse Transcriptase-quantitative PCR (RT-qPCR) analysis, a set of substrates inducing the expression of the sdimo genes in BCP1 were assessed as well as their transcriptional repression in the presence of sugars, organic acids, or during the cell growth on rich medium (Luria–Bertani broth). The transcriptional start sites of both the sdimo gene clusters were identified by means of primer extension experiments. Finally, proteomic studies revealed changes in the protein pattern induced by growth on gaseous- (n-butane) and/or liquid (n-hexane) short-chain n-alkanes as compared to growth on succinate. Among the differently expressed protein spots, two chaperonins and an isocytrate lyase were identified along with oxidoreductases involved in oxidation reactions downstream of the initial monooxygenase reaction step.
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Affiliation(s)
- Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | | | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary Calgary, Alberta, Canada
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Dario Frascari
- Department of Civil, Chemical, Environmental and Materials Engineering, University of Bologna Bologna, Italy
| | - Davide Zannoni
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
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Sigdel S, Hui G, Smith TJ, Murrell JC, Lee JK. Molecular dynamics simulation to rationalize regioselective hydroxylation of aromatic substrates by soluble methane monooxygenase. Bioorg Med Chem Lett 2015; 25:1611-5. [DOI: 10.1016/j.bmcl.2015.01.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
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Sheu YT, Chen SC, Chien CC, Chen CC, Kao CM. Application of a long-lasting colloidal substrate with pH and hydrogen sulfide control capabilities to remediate TCE-contaminated groundwater. JOURNAL OF HAZARDOUS MATERIALS 2015; 284:222-232. [PMID: 25463237 DOI: 10.1016/j.jhazmat.2014.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/15/2014] [Accepted: 11/19/2014] [Indexed: 06/04/2023]
Abstract
A long-lasting emulsified colloidal substrate (LECS) was developed for continuous carbon and nanoscale zero-valent iron (nZVI) release to remediate trichloroethylene (TCE)-contaminated groundwater under reductive dechlorinating conditions. The developed LECS contained nZVI, vegetable oil, surfactants (Simple Green™ and lecithin), molasses, lactate, and minerals. An emulsification study was performed to evaluate the globule droplet size and stability of LECS. The results show that a stable oil-in-water emulsion with uniformly small droplets (0.7 μm) was produced, which could continuously release the primary substrates. The emulsified solution could serve as the dispensing agent, and nZVI particles (with diameter 100-200 nm) were distributed in the emulsion evenly without aggregation. Microcosm results showed that the LECS caused a rapid increase in the total organic carbon concentration (up to 488 mg/L), and reductive dechlorination of TCE was significantly enhanced. Up to 99% of TCE (with initial concentration of 7.4 mg/L) was removed after 130 days of operation. Acidification was prevented by the production of hydroxide ion by the oxidation of nZVI. The formation of iron sulfide reduced the odor from produced hydrogen sulfide. Microbial analyses reveal that dechlorinating bacteria existed in soils, which might contribute to TCE dechlorination.
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Affiliation(s)
- Y T Sheu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - S C Chen
- Department of Life Sciences, National Central University, Chung-Li, Taiwan
| | - C C Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, Chung-Li, Taiwan
| | - C C Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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48
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Coleman NV. Primers: Functional Genes for Aerobic Chlorinated Hydrocarbon-Degrading Microbes. SPRINGER PROTOCOLS HANDBOOKS 2015. [DOI: 10.1007/8623_2015_91] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Yang HY, Jia RB, Chen B, Li L. Degradation of recalcitrant aliphatic and aromatic hydrocarbons by a dioxin-degrader Rhodococcus sp. strain p52. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:11086-11093. [PMID: 24859700 DOI: 10.1007/s11356-014-3027-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
This study investigates the ability of Rhodococcus sp. strain p52, a dioxin degrader, to biodegrade petroleum hydrocarbons. Strain p52 can use linear alkanes (tetradecane, tetracosane, and dotriacontane), branched alkane (pristane), and aromatic hydrocarbons (naphthalene and phenanthrene) as sole carbon and energy sources. Specifically, the strain removes 85.7 % of tetradecane within 48 h at a degradation rate of 3.8 mg h(-1) g(-1) dry cells, and 79.4 % of tetracosane, 66.4 % of dotriacontane, and 63.9 % of pristane within 9-11 days at degradation rates of 20.5, 14.7, and 20.3 mg day(-1) g(-1) dry cells, respectively. Moreover, strain p52 consumes 100 % naphthalene and 55.3 % phenanthrene within 9-11 days at respective degradation rates of 16 and 12.9 mg day(-1) g(-1) dry cells. Metabolites of the petroleum hydrocarbons by strain p52 were analyzed. Genes encoding alkane-hydroxylating enzymes, including cytochrome P450 (CYP450) enzyme (CYP185) and two alkane-1-monooxygenases, were amplified by polymerase chain reaction. The transcriptional activities of these genes in the presence of petroleum hydrocarbons were detected by reverse transcription-polymerase chain reaction. The results revealed potential of strain p52 to degrade petroleum hydrocarbons.
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Affiliation(s)
- Hai-Yan Yang
- Shandong Provincial Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, 27 ShandaNanlu, Jinan, 250100, China
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SmoXYB1C1Z of Mycobacterium sp. strain NBB4: a soluble methane monooxygenase (sMMO)-like enzyme, active on C2 to C4 alkanes and alkenes. Appl Environ Microbiol 2014; 80:5801-6. [PMID: 25015887 DOI: 10.1128/aem.01338-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monooxygenase (MO) enzymes initiate the aerobic oxidation of alkanes and alkenes in bacteria. A cluster of MO genes (smoXYB1C1Z) of thus-far-unknown function was found previously in the genomes of two Mycobacterium strains (NBB3 and NBB4) which grow on hydrocarbons. The predicted Smo enzymes have only moderate amino acid identity (30 to 60%) to their closest homologs, the soluble methane and butane MOs (sMMO and sBMO), and the smo gene cluster has a different organization from those of sMMO and sBMO. The smoXYB1C1Z genes of NBB4 were cloned into pMycoFos to make pSmo, which was transformed into Mycobacterium smegmatis mc(2)-155. Cells of mc(2)-155(pSmo) metabolized C2 to C4 alkanes, alkenes, and chlorinated hydrocarbons. The activities of mc(2)-155(pSmo) cells were 0.94, 0.57, 0.12, and 0.04 nmol/min/mg of protein with ethene, ethane, propane, and butane as substrates, respectively. The mc(2)-155(pSmo) cells made epoxides from ethene, propene, and 1-butene, confirming that Smo was an oxygenase. Epoxides were not produced from larger alkenes (1-octene and styrene). Vinyl chloride and 1,2-dichloroethane were biodegraded by cells expressing Smo, with production of inorganic chloride. This study shows that Smo is a functional oxygenase which is active against small hydrocarbons. M. smegmatis mc(2)-155(pSmo) provides a new model for studying sMMO-like monooxygenases.
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