1
|
Sims L, Wright C, Crombie AT, Dawson R, Lockwood C, Le Brun NE, Lehtovirta‐Morley L, Murrell JC. Whole-cell studies of substrate and inhibitor specificity of isoprene monooxygenase and related enzymes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:809-819. [PMID: 37935632 PMCID: PMC10667655 DOI: 10.1111/1758-2229.13212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Co-oxidation of a range of alkenes, dienes, and aromatic compounds by whole cells of the isoprene-degrading bacterium Rhodococcus sp. AD45 expressing isoprene monooxygenase was investigated, revealing a relatively broad substrate specificity for this soluble diiron centre monooxygenase. A range of 1-alkynes (C2 -C8 ) were tested as potential inhibitors. Acetylene, a potent inhibitor of the related enzyme soluble methane monooxygenase, had little inhibitory effect, whereas 1-octyne was a potent inhibitor of isoprene monooxygenase, indicating that 1-octyne could potentially be used as a specific inhibitor to differentiate between isoprene consumption by bona fide isoprene degraders and co-oxidation of isoprene by other oxygenase-containing bacteria, such as methanotrophs, in environmental samples. The isoprene oxidation kinetics of a variety of monooxygenase-expressing bacteria were also investigated, revealing that alkene monooxygenase from Xanthobacter and soluble methane monooxygenases from Methylococcus and Methylocella, but not particulate methane monooxygenases from Methylococcus or Methylomicrobium, could co-oxidise isoprene at appreciable rates. Interestingly the ammonia monooxygenase from the nitrifier Nitrosomonas europaea could also co-oxidise isoprene at relatively high rates, suggesting that co-oxidation of isoprene by additional groups of bacteria, under the right conditions, might occur in the environment.
Collapse
Affiliation(s)
- Leanne Sims
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- Present address:
Quadram Institute BiosciencesNorwich Research ParkNorwichUK
| | - Chloe Wright
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Andrew T. Crombie
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Robin Dawson
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Colin Lockwood
- School of Environmental SciencesUniversity of East AngliaNorwichUK
- School of ChemistryUniversity of East AngliaNorwichUK
| | | | | | - J. Colin Murrell
- School of Environmental SciencesUniversity of East AngliaNorwichUK
| |
Collapse
|
2
|
Abdulgader M, Yu QJ, Zinatizadeh AA, Williams P, Rahimi Z. Treatment capacity of a novel flexible fibre biofilm bioreactor treating high-strength milk processing wastewater. ENVIRONMENTAL TECHNOLOGY 2023; 44:1001-1017. [PMID: 34635010 DOI: 10.1080/09593330.2021.1992509] [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: 04/19/2021] [Accepted: 10/03/2021] [Indexed: 06/13/2023]
Abstract
This study was focused on the capacity investigation of a novel multistage flexible fibre biofilm reactor (MS-FFBR) to treat milk processing wastewater (MPW) with high organic loading (OLR). The MS-FFBR performance was evaluated at four intermediate stages separately, and also the final effluent quality of the overall system with an influent chemical oxygen demand (CODin) ranged from 1500 ± 20 to 6000 ± 50 mg/L and hydraulic retention times (HRTs) of 8, 12, and 16 h. By comparting the bioreactors into the four stages effectively enhanced the bioreactor's performance. The maximum TCOD removal efficiency was achieved at the first stage, which was about 89 ± 20, 82 ± 20, and 78 ± 20% at HRTs of 16, 12, 8 h, and low CODin of 1600 ± 20, 1590 ± 20, and 1673 ± 20 mg/L, respectively. However, the first stage had less contribution to TCOD removal at high CODin concentrations, reported to be about 42 ± 4%, 46 ± 4%, and 25 ± 4% at CODin of 5960 ± 40, 5830 ± 40, and 5870 ± 40 mg/L, respectively. Furthermore, the MS-FFBR was effective in removing total suspended solids (TSS) and turbidity. The bioreactor has reduced the effluent turbidity to 9.0 ± 0.2, 20.0 ± 0.6, and 16.1 ± 0.5 NTU at low CODin concentrations of 1600 ± 20, 1590 ± 20, and 1670 ± 20 mg/L and HRTs of 16, 12, and 8 h, respectively. The bioreactor revealed a high COD removal rate increased from 2.3 ± 0.1 to 12.2 ± 0.4 kg TCOD/m3d by increasing the OLR from 2.4 ± 0.1 to 17.6 ± 0.4 kg TCOD/m3d, confirming high reactor capacity for treatment of high-strength wastewater. Kinetic studies confirmed that the biomass yield was low at various HRTs ranging from 0.1 to 0.2 gVSS/gCOD.
Collapse
Affiliation(s)
- Mohamed Abdulgader
- School of Engineering and Built Environment, Griffith University, Brisbane, Australia
- Department of Environmental Science, Faculty of Engineering & Technology, Sebha University, Sabha, Libya
| | - Qiming Jimmy Yu
- School of Engineering and Built Environment, Griffith University, Brisbane, Australia
| | - Ali Akbar Zinatizadeh
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Environmental Research Center (ERC), Razi University, Kermanshah, Iran
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, South Africa
| | - Philip Williams
- School of Engineering and Built Environment, Griffith University, Brisbane, Australia
| | - Zahra Rahimi
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| |
Collapse
|
3
|
Dawson RA, Crombie AT, Jansen RS, Smith TJ, Nichol T, Murrell C. Peering down the sink: A review of isoprene metabolism by bacteria. Environ Microbiol 2022; 25:786-799. [PMID: 36567445 DOI: 10.1111/1462-2920.16325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
Isoprene (2-methyl-1,3-butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr-1 ), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NOx ), have implications for global warming and local air quality, respectively. For many years, it has been estimated that soil-dwelling bacteria consume a significant amount of isoprene (~20 Tg C yr-1 ), but the mechanisms underlying the biological sink for isoprene have been poorly understood. Studies have indicated or confirmed the ability of diverse bacterial genera to degrade isoprene, whether by the canonical iso-type isoprene degradation pathway or through other less well-characterized mechanisms. Here, we review current knowledge of isoprene metabolism and highlight key areas for further research. In particular, examples of isoprene-degraders that do not utilize the isoprene monooxygenase have been identified in recent years. This has fascinating implications both for the mechanism of isoprene uptake by bacteria, and also for the ecology of isoprene-degraders in the environments.
Collapse
Affiliation(s)
- Robin A Dawson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert S Jansen
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Thomas J Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Tim Nichol
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
4
|
Singh A, Pandey AK, Dubey SK. Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2. J Biomol Struct Dyn 2022; 41:3821-3834. [PMID: 35380094 DOI: 10.1080/07391102.2022.2057360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The whole genome sequencing of a novel isoprene degrading strain of Sphingobium sp. BHU LFT2, its in silico analysis for identifying and characterizing enzymes, especially isoprene monooxygenases (IsoMO), which initiate the degradation process, and in vitro validation with cell extract of optimal temperature and pH and analysis for utilizing isoprene as the preferential substrate, were conducted. The most efficient monooxygenase was identified through comparative analyses using molecular docking followed by molecular dynamics simulation approach. The in silico results revealed high thermostability for most of the monooxygenases. Most potent monooxygenase with locus ID JQK15_20300 exhibiting high sequence similarity with known monooxygenases of isoprene-degrading Rhodococcus sp. LB1 and SC4 strains was identified. Interaction energy of -17.25 kJ/mol for JQK15_20300 with isoprene, was almost similar as that analysed for above-mentioned similar known counterparts, was exhibited by the molecular docking. Molecular dynamic simulation of 100 ns and free energy analysis of JQK15_20300 in the complex with isoprene gave persistent interaction of isoprene with JQK15_20300 during the simulation with high average binding energy of -47.13 kJ/mol thus proving higher affinity of JQK15_20300 for isoprene. The study revealed that the highly efficient isoprene degrading strain of Sphingobium sp. BHU LFT2 having effective monooxygenase could be utilized for large-scale applications including detoxification of air contaminated with isoprene in closed working systems.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abhishek Singh
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
5
|
Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest. BIOLOGY 2022; 11:biology11040519. [PMID: 35453719 PMCID: PMC9030188 DOI: 10.3390/biology11040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 11/21/2022]
Abstract
Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.
Collapse
|
6
|
Singh A, Kumar Pandey A, Kumar Dubey S. Biodegradation of isoprene by Arthrobacter sp. strain BHU FT2: Genomics-proteomics enabled novel insights. BIORESOURCE TECHNOLOGY 2021; 340:125634. [PMID: 34325393 DOI: 10.1016/j.biortech.2021.125634] [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: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The bacterial degradation of isoprene is important for maintaining its atmospheric concentration in unpolluted environment. It may be possible to use natural isoprene degrading bacteria in engineered systems to eliminate or limit isoprene emissions from various sources. Biodegradation of isoprene by Arthrobacter sp. strain BHU FT2 was investigated. The genome was found to contain 4151545 bp long chromosome having 3747 coding genes, and coded potential isoprene degrading enzymes. The molecular docking of monooxygenases with isoprene displayed a higher binding energy (-4.59 kcal/mol) for WP_015938387.1 monooxygenase. Analysis of the identified monooxygenases with the known isoprene monooxygenases revealed 67% sequence identity of WP_015938387.1 (Locus tag JHV56_10705) monooxygenase of the considered strain with the OPX16961.1 monooxygenase of Gordonia sp. i37 isoprene degrading starin. These results provided a strong evidence for the high isoprene degrading potential of the Arthrobacter sp. BHU FT2 which could be efficiently exploited for isoprene degradation in large scale bio-filtration units.
Collapse
Affiliation(s)
- Abhishek Singh
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Anand Kumar Pandey
- Department of Biotechnology Engineering, Institute of Engineering and Technology, Bundelkhand University, Jhansi 284128, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
7
|
Gibson L, Crombie AT, McNamara NP, Murrell JC. Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere. ENVIRONMENTAL MICROBIOME 2021; 16:17. [PMID: 34446108 PMCID: PMC8394569 DOI: 10.1186/s40793-021-00386-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/12/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Isoprene accounts for about half of total biogenic volatile organic compound emissions globally, and as a climate active gas it plays a significant and varied role in atmospheric chemistry. Terrestrial plants are the largest source of isoprene, with willow (Salix) making up one of the most active groups of isoprene producing trees. Bacteria act as a biological sink for isoprene and those bacteria associated with high isoprene-emitting trees may provide further insight into its biodegradation. RESULTS A DNA-SIP experiment incubating willow (Salix fragilis) leaves with 13C-labelled isoprene revealed an abundance of Comamonadaceae, Methylobacterium, Mycobacterium and Polaromonas in the isoprene degrading community when analysed by 16S rRNA gene amplicon sequencing. Metagenomic analysis of 13C-enriched samples confirmed the abundance of Comamonadaceae, Acidovorax, Polaromonas, Variovorax and Ramlibacter. Mycobacterium and Methylobacterium were also identified after metagenomic analysis and a Mycobacterium metagenome-assembled genome (MAG) was recovered. This contained two complete isoprene degradation metabolic gene clusters, along with a propane monooxygenase gene cluster. Analysis of the abundance of the alpha subunit of the isoprene monooxygenase, isoA, in unenriched DNA samples revealed that isoprene degraders associated with willow leaves are abundant, making up nearly 0.2% of the natural bacterial community. CONCLUSIONS Analysis of the isoprene degrading community associated with willow leaves using DNA-SIP and focused metagenomics techniques enabled recovery of the genome of an active isoprene-degrading Mycobacterium species and provided valuable insight into bacteria involved in degradation of isoprene on the leaves of a key species of isoprene-emitting tree in the northern hemisphere.
Collapse
Affiliation(s)
- Lisa Gibson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Niall P McNamara
- Centre of Ecology and Hydrology, Lancaster University, Bailrigg, Lancaster, LA1 4AP, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
8
|
Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees. Microorganisms 2021; 9:microorganisms9051024. [PMID: 34068745 PMCID: PMC8150984 DOI: 10.3390/microorganisms9051024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 11/17/2022] Open
Abstract
Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4-31% and 15-52% in soils subjected to a lower (7.2 × 105 ppbv) and a higher (7.2 × 106 ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene.
Collapse
|
9
|
Bismuth-Graphene Nanohybrids: Synthesis, Reaction Mechanisms, and Photocatalytic Applications—A Review. ENERGIES 2021. [DOI: 10.3390/en14082281] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Photocatalysis is a classical solution to energy conversion and environmental pollution control problems. In photocatalysis, the development and exploration of new visible light catalysts and their synthesis and modification strategies are crucial. It is also essential to understand the mechanism of these reactions in the various reaction media. Recently, bismuth and graphene’s unique geometrical and electronic properties have attracted considerable attention in photocatalysis. This review summarizes bismuth-graphene nanohybrids’ synthetic processes with various design considerations, fundamental mechanisms of action, heterogeneous photocatalysis, benefits, and challenges. Some key applications in energy conversion and environmental pollution control are discussed, such as CO2 reduction, water splitting, pollutant degradation, disinfection, and organic transformations. The detailed perspective of bismuth-graphene nanohybrids’ applications in various research fields presented herein should be of equal interest to academic and industrial scientists.
Collapse
|
10
|
Andler R, Valdés C, Díaz-Barrera A, Steinbüchel A. Biotransformation of poly(cis-1,4-isoprene) in a multiphase enzymatic reactor for continuous extraction of oligo-isoprenoid molecules. N Biotechnol 2020; 58:10-16. [DOI: 10.1016/j.nbt.2020.05.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 11/28/2022]
|
11
|
Carrión O, McGenity TJ, Murrell JC. Molecular Ecology of Isoprene-Degrading Bacteria. Microorganisms 2020; 8:E967. [PMID: 32605141 PMCID: PMC7409078 DOI: 10.3390/microorganisms8070967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/16/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth's climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle.
Collapse
Affiliation(s)
- Ornella Carrión
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK;
| | - J. Colin Murrell
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| |
Collapse
|
12
|
Murrell JC, McGenity TJ, Crombie AT. Microbial metabolism of isoprene: a much-neglected climate-active gas. MICROBIOLOGY-SGM 2020; 166:600-613. [PMID: 32441612 PMCID: PMC7657509 DOI: 10.1099/mic.0.000931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.
Collapse
Affiliation(s)
- J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Terry J McGenity
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| |
Collapse
|
13
|
Larke-Mejía NL, Crombie AT, Pratscher J, McGenity TJ, Murrell JC. Novel Isoprene-Degrading Proteobacteria From Soil and Leaves Identified by Cultivation and Metagenomics Analysis of Stable Isotope Probing Experiments. Front Microbiol 2019; 10:2700. [PMID: 31866954 PMCID: PMC6908491 DOI: 10.3389/fmicb.2019.02700] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/07/2019] [Indexed: 02/01/2023] Open
Abstract
Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with 13C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the 13C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of 13C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the α-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.
Collapse
Affiliation(s)
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - Terry J McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| |
Collapse
|
14
|
Sonwani RK, Swain G, Giri BS, Singh RS, Rai BN. A novel comparative study of modified carriers in moving bed biofilm reactor for the treatment of wastewater: Process optimization and kinetic study. BIORESOURCE TECHNOLOGY 2019; 281:335-342. [PMID: 30831512 DOI: 10.1016/j.biortech.2019.02.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 06/09/2023]
Abstract
In this work, modified plastic carriers; polypropylene (PP), low-density polyethylene- polypropylene (LDPE-PP), and polyurethane foam-polypropylene (PUF-PP) were developed and used in moving bed bioreactor (MBBR) for the wastewater treatment containing naphthalene. To optimized the process parameters using response surface methodology (RSM), two numerical variables; pH (5.0-9.0) and hydraulic retention time (HRT) (1.0-5.0 day) along with the type of carriers (PP, LDPE-PP, and PUF-PP) were selected as a categorical factor. At 7.0 pH and 5 days HRT, maximum removal efficiencies were observed to be 72.4, 84.4, and 90.2% for MBBR packed with PP, LDPE-PP, and PUF-PP carriers, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis reveals catechol and 2-naphthol were observed as intermediate metabolites for naphthalene degradation. Modified Stover-Kincannon model was applied for biodegradation kinetic and constants were observed as Umax: 0.476, 0.666, and 0.769 g/L.day and KB: 0.565, 0.755, and 0.874 g/L.day for PP, LDPE-PP, PUF-PP, respectively.
Collapse
Affiliation(s)
- Ravi Kumar Sonwani
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Ganesh Swain
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Balendu Shekhar Giri
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Ram Sharan Singh
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India
| | - Birendra Nath Rai
- Department of Chemical Engineering & Technology Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| |
Collapse
|
15
|
Singh A, Srivastava N, Dubey SK. Molecular characterization and kinetics of isoprene degrading bacteria. BIORESOURCE TECHNOLOGY 2019; 278:51-56. [PMID: 30677698 DOI: 10.1016/j.biortech.2019.01.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 06/09/2023]
Abstract
Isoprene, the highly reactive volatile organic compound, is used as monomer for the synthesis of several useful polymers. Its extensive production and usage leads to contamination of air. Once released, it alters the atmospheric chemistry by reacting with hydroxyl radicals (OH) and nitrogen oxides (NOx) to generate tropospheric ozone. Its prolonged exposure causes deleterious effects in human and plants. Therefore, its removal from the contaminated environment through biodegradation, provides a promising remedial solution. In the present study, isoprene utilizing bacteria namely, Pseudomonas sp., Arthrobacter sp., Bacillus sp. Sphingobacterium sp., Sphingobium sp., and Pantoea sp. were isolated and characterized from leaf surface of Madhuca latifolia and Tectona grandis, and also from soils under these plants. Their isoprene degrading capability and kinetics were assessed in batch mode. The isoprene degradation study indicated Pseudomonas sp. to be the most efficient isoprene degrader.
Collapse
Affiliation(s)
- Abhishek Singh
- Molecular Ecology Laboratory, Department of Botany, Banaras Hindu University, Varanasi 221005, India
| | - Navnita Srivastava
- Molecular Ecology Laboratory, Department of Botany, Banaras Hindu University, Varanasi 221005, India
| | - Suresh Kumar Dubey
- Molecular Ecology Laboratory, Department of Botany, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Palomo-Briones R, Esquivel-González S, Aizpuru A, Gómez-Hernández N, Casas-Flores S, Barba de la Rosa AP, Arriaga S. Microbial contamination in methanol biofilters inoculated with a pure strain of Pichia pastoris: A potential limitation for waste revalorization. Biotechnol Prog 2018; 35:e2715. [PMID: 30294912 DOI: 10.1002/btpr.2715] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/27/2018] [Indexed: 11/05/2022]
Abstract
Novel biotechnologies to valorize waste emissions are based on the use of specialized microbial groups that produce different compounds of industrial interest. On this scenario, the retention of such specific microorganisms in the system is of critical interest; however, the potential limitations of working with simplified cultures in a competitive open environment are neither fully explored nor well understood. In this work, a series of biofilters treating methanol vapors coupled with heterologous endochitinase production were used to evaluate the performance of a specialized microbial population during a typical open-to-environment operation. The biofilters were inoculated with a transformed strain of Pichia pastoris and were operated identically for about 90 days. The results showed that the biofiltration performance became diverse with time in terms of the elimination capacity (EC) shifting from a variation coefficient of 1.5% (EC = 274 ± 24, 279 ± 5, and 281.9 ± 25 g/[m3 h]) at the beginning of the operation to 33% (EC = 297 ± 9, 338 ± 7, and 341 ± 2 g/[m3 h]) at the end of operation. Epifluorescence analysis and cloning-sequencing suggested that P. pastoris remained as the dominant microorganism of methanol degradation, whereas diverse airborne bacteria, including Ochrobactrum spp. and Klebsiella oxytoca, played a secondary role possibly associated with the consumption of intermediates. Overall, this study found that low diversity systems operated under non-sterile conditions could be susceptible to contamination with external microorganisms causing a diversifying behavior at the performance and microbial community levels. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2715, 2019.
Collapse
Affiliation(s)
- Rodolfo Palomo-Briones
- Div. de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Saúl Esquivel-González
- Div. de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Aitor Aizpuru
- Universidad del Mar, Campus Purto Ángel, San Pedro Pochutla, México
| | - Nicolás Gómez-Hernández
- Div. de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Sergio Casas-Flores
- Div. de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Ana Paulina Barba de la Rosa
- Div. de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Sonia Arriaga
- Div. de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| |
Collapse
|
18
|
Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on Earth. ISME JOURNAL 2018; 12:931-941. [PMID: 29463892 PMCID: PMC5864225 DOI: 10.1038/s41396-018-0072-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/26/2017] [Accepted: 12/12/2017] [Indexed: 01/28/2023]
Abstract
Isoprene (2-methyl-1,3-butadiene), the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, is highly reactive and can have diverse and often detrimental atmospheric effects, which impact on climate and health. Most isoprene is produced by terrestrial plants, but (micro)algal production is important in aquatic environments, and the relative bacterial contribution remains unknown. Soils are a sink for isoprene, and bacteria that can use isoprene as a carbon and energy source have been cultivated and also identified using cultivation-independent methods from soils, leaves and coastal/marine environments. Bacteria belonging to the Actinobacteria are most frequently isolated and identified, and Proteobacteria have also been shown to degrade isoprene. In the freshwater-sediment isolate, Rhodococcus strain AD45, initial oxidation of isoprene to 1,2-epoxy-isoprene is catalyzed by a multicomponent isoprene monooxygenase encoded by the genes isoABCDEF. The resultant epoxide is converted to a glutathione conjugate by a glutathione S-transferase encoded by isoI, and further degraded by enzymes encoded by isoGHJ. Genome sequence analysis of actinobacterial isolates belonging to the genera Rhodococcus, Mycobacterium and Gordonia has revealed that isoABCDEF and isoGHIJ are linked in an operon, either on a plasmid or the chromosome. In Rhodococcus strain AD45 both isoprene and epoxy-isoprene induce a high level of transcription of 22 contiguous genes, including isoABCDEF and isoGHIJ. Sequence analysis of the isoA gene, encoding the large subunit of the oxygenase component of isoprene monooxygenase, from isolates has facilitated the development of PCR primers that are proving valuable in investigating the ecology of uncultivated isoprene-degrading bacteria.
Collapse
|
19
|
Srivastva N, Singh A, Bhardwaj Y, Dubey SK. Biotechnological potential for degradation of isoprene: a review. Crit Rev Biotechnol 2017; 38:587-599. [DOI: 10.1080/07388551.2017.1379467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Navnita Srivastva
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Abhishek Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Yashpal Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Suresh Kumar Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| |
Collapse
|
20
|
Srivastva N, Vishwakarma P, Bhardwaj Y, Singh A, Manjunath K, Dubey SK. Kinetic and molecular analyses reveal isoprene degradation potential of Methylobacterium sp. BIORESOURCE TECHNOLOGY 2017; 242:87-91. [PMID: 28256295 DOI: 10.1016/j.biortech.2017.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 01/28/2017] [Accepted: 02/01/2017] [Indexed: 06/06/2023]
Abstract
Efforts were made to isolate and characterize bacteria capable of growing on methane and organic compounds, and to achieve the simultaneous degradation of more than one pollutant. Among the methanotrophs, species of Methylobacterium was able to catabolize a variety of hydrocarbons, including the branched-chain alkenes. Therefore, laboratory incubations experiments were carried out in batch mode to assess the potential of Methylobacterium sp. PV1 for degrading isoprene, the low-molecular-weight alkene, the most abundant non-methane volatile hydrocarbon present in the environment. Methylobacterium sp. PV1, isolated from paddy field soil, was characterized by pmoA and 16S rRNA gene sequencing and FAME analysis, and used for isoprene degradation. The kinetics of biodegradation is studied using the Michaelis-Menten model. The optimum degradation (80%) with maximum average relative degradation rate was observed at 150ppm isoprene. The degradation products were also analyzed using FTIR.
Collapse
Affiliation(s)
- Navnita Srivastva
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - P Vishwakarma
- Department of Microbiology and Biotechnology, Bangalore University, Bangalore 560056, India
| | - Y Bhardwaj
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - A Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - K Manjunath
- Department of Microbiology and Biotechnology, Bangalore University, Bangalore 560056, India
| | - Suresh K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|
21
|
Srivastva N, Singh RS, Dubey SK. Efficacy of wood charcoal and its modified form as packing media for biofiltration of isoprene. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 196:252-260. [PMID: 28288359 DOI: 10.1016/j.jenvman.2017.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 02/08/2017] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
The efficacy of wood charcoal (WC) and nutrient-enriched wood charcoal (NWC) as biofilter packing media were assessed for isoprene biodegradation in a bioreactor comprising bioscrubber and a biofilter connected in series and inoculated with Pseudomonas sp. The bioreactors using WC and NWC exhibited >90% removal efficiency and around 369 g m-3 h-1 elimination capacity at around 404 g m-3 h-1 inlet loading rate. In both the bioreactors, the biofilter component showed better degradation capacity compared to the bioscrubber unit. The kinetic parameters, maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks for Michaelis-Menten model were evaluated. The lower Ks for the WC packed bioreactor indicated that ECmax achieved, was faster compared to others, while higher ECmax and ECmax/Ks for the NWC packed bioreactor suggests its superiority in isoprene abatement in the continuous mode. A comparison of the available published information on biofiltration of isoprene reflected polyurethane foam as the superior packing media.
Collapse
Affiliation(s)
- Navnita Srivastva
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ram S Singh
- Department of Chemical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
| |
Collapse
|
22
|
Yuan Y, Liu Y, Li B, Wang B, Wang S, Peng Y. Short-chain fatty acids production and microbial community in sludge alkaline fermentation: Long-term effect of temperature. BIORESOURCE TECHNOLOGY 2016; 211:685-690. [PMID: 27060243 DOI: 10.1016/j.biortech.2016.03.138] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/22/2016] [Accepted: 03/25/2016] [Indexed: 06/05/2023]
Abstract
Sludge alkaline fermentation has been reported to achieve efficient short-chain fatty acids (SCFAs) production. Temperature played important role in further improved SCFAs production. Long-term SCFAs production from sludge alkaline fermentation was compared between mesotherm (30±2°C) and microtherm (15±2°C). The study of 90days showed that mesotherm led to 2.2-folds production of SCFAs as microtherm and enhanced the production of acetic acid as major component of SCFAs. Soluble protein and carbohydrate at mesotherm was 2.63-folds as that at microtherm due to higher activities of protease and α-glucosidase, guaranteeing efficient substrates to produce SCFAs. Illumina MiSeq sequencing revealed that microtherm increased the abundance of Corynebacterium, Alkaliflexus, Pseudomonas and Guggenheimella, capable of enhancing hydrolysis. Hydrolytic bacteria, i.e. Alcaligenes, Anaerolinea and Ottowia, were enriched at mesotherm. Meanwhile, acidogenic bacteria showed higher abundance at mesotherm than microtherm. Therefore, enrichment of functional bacteria and higher microbial activities resulted in the improved SCFAs at mesotherm.
Collapse
Affiliation(s)
- Yue Yuan
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Ye Liu
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Baikun Li
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China; Department of Civil and Environmental Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Bo Wang
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Shuying Wang
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China
| | - Yongzhen Peng
- Engineering Research Center of Beijing, Key Laboratory of Beijing for Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, Beijing 100124, PR China.
| |
Collapse
|
23
|
El Khawand M, Crombie AT, Johnston A, Vavlline DV, McAuliffe JC, Latone JA, Primak YA, Lee SK, Whited GM, McGenity TJ, Murrell JC. Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing. Environ Microbiol 2016; 18:2743-53. [PMID: 27102583 DOI: 10.1111/1462-2920.13345] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Emissions of biogenic volatile organic compounds (bVOCs), are an important element in the global carbon cycle, accounting for a significant proportion of fixed carbon. They contribute directly and indirectly to global warming and climate change and have a major effect on atmospheric chemistry. Plants emit isoprene to the atmosphere in similar quantities to emissions of methane from all sources and each accounts for approximately one third of total VOCs. Although methanotrophs, capable of growth on methane, have been intensively studied, we know little of isoprene biodegradation. Here, we report the isolation of two isoprene-degrading strains from the terrestrial environment and describe the design and testing of polymerase chain reaction (PCR) primers targeting isoA, the gene encoding the active-site component of the conserved isoprene monooxygenase, which are capable of retrieving isoA sequences from isoprene-enriched environmental samples. Stable isotope probing experiments, using biosynthesized (13) C-labelled isoprene, identified the active isoprene-degrading bacteria in soil. This study identifies novel isoprene-degrading strains using both culture-dependent and, for the first time, culture-independent methods and provides the tools and foundations for continued investigation of the biogeography and molecular ecology of isoprene-degrading bacteria.
Collapse
Affiliation(s)
| | | | | | - Dmitrii V Vavlline
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Joseph C McAuliffe
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Jacob A Latone
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Yuliya A Primak
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Sang-Kyu Lee
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Gregg M Whited
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | | | - J Colin Murrell
- University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
24
|
Srivastva N, Singh RS, Upadhyay SN, Dubey SK. Degradation kinetics and metabolites in continuous biodegradation of isoprene. BIORESOURCE TECHNOLOGY 2016; 206:275-278. [PMID: 26883059 DOI: 10.1016/j.biortech.2016.01.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/14/2016] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
The kinetic parameters of isoprene biodegradation were studied in a bioreactor, comprising of bioscrubber and polyurethane foam packed biofilter in series and inoculated with Pseudomonas sp., using a Michaelis-Menten type model. The maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks values for bioscrubber were found to be 666.7 g m(-3) h(-1), 9.86 g m(-3) and 67.56 h(-1), respectively while those for biofilter were 3333 g m(-3) h(-1), 13.96 g m(-3) and 238.7 h(-1), respectively. The biofilter section exhibited better degradation efficiency compared to the bioscrubber unit. Around 62-75% of the feed isoprene got converted to carbon dioxide, indicating the efficient capability of bacteria to mineralize isoprene. The FTIR and GC-MS analyses of degradation products indicated oxidative cleavage of unsaturated bond of isoprene. These results were used for proposing a plausible degradation pathway for isoprene.
Collapse
Affiliation(s)
- Navnita Srivastva
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ram S Singh
- Department of Chemical Engineering and Technology, Institute of Technology, Banaras Hindu University, Varanasi 221005, India
| | - Siddh N Upadhyay
- Department of Chemical Engineering and Technology, Institute of Technology, Banaras Hindu University, Varanasi 221005, India
| | - Suresh K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| |
Collapse
|