1
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Haedar JR, Yoshimura A, Wakimoto T. New variochelins from soil-isolated Variovorax sp. H002. Beilstein J Org Chem 2024; 20:692-700. [PMID: 38590537 PMCID: PMC10999976 DOI: 10.3762/bjoc.20.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/08/2024] [Indexed: 04/10/2024] Open
Abstract
The soil bacterial genus Variovorax produce distinct photoreactive siderophores that may play a crucial role in the iron cycle within the rhizosphere. This study focused on exploring the natural products of the soil-isolated Variovorax sp. H002, leading to the isolation of variochelins A-E (1-5), a series of lipohexapeptide siderophores. NMR and MS/MS analyses revealed that these siderophores share a common core structure - a linear hexapeptide with β-hydroxyaspartate and hydroxamate functional groups, serving in iron-binding coordination. Three new variochelins C-E (3-5) were characterized by varied fatty acyl groups at their N-termini; notably, 4 and 5 represent the first variochelins with N-terminal unsaturated fatty acyl groups. Furthermore, the variochelin biosynthetic gene cluster was identified through draft genome sequencing and gene knockout experiments. Compounds 1-5 exhibited antimicrobial activities against Gram-negative bacteria, including several soil-isolated plant pathogens.
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Affiliation(s)
- Jabal Rahmat Haedar
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| | - Aya Yoshimura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
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2
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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.
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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
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3
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Helbich S, Barrantes I, Dos Anjos Borges LG, Pieper DH, Vainshtein Y, Sohn K, Engesser KH. The 2-methylpropene degradation pathway in Mycobacteriaceae family strains. Environ Microbiol 2023; 25:2163-2181. [PMID: 37321960 DOI: 10.1111/1462-2920.16449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023]
Abstract
Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2-methylpropene (isobutene, 2-MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2-methylpropene derived from whole genome sequencing, differential expression analysis and peptide-mass fingerprinting. Key genes identified are coding for a 4-component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2-hydroxyisobutyryl-CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2-methylpropene degraders.
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Affiliation(s)
- Steffen Helbich
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
| | - Israel Barrantes
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Dietmar H Pieper
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yevhen Vainshtein
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Kai Sohn
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Karl-Heinrich Engesser
- Institute for Sanitary Engineering, Water Quality and Solid Waste Management, University of Stuttgart, Stuttgart, Germany
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4
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Guo Y, Gu S, Wu K, Tanentzap AJ, Yu J, Liu X, Li Q, He P, Qiu D, Deng Y, Wang P, Wu Z, Zhou Q. Temperature-mediated microbial carbon utilization in China's lakes. GLOBAL CHANGE BIOLOGY 2023; 29:5044-5061. [PMID: 37427534 DOI: 10.1111/gcb.16840] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/05/2023] [Indexed: 07/11/2023]
Abstract
Microbes play an important role in aquatic carbon cycling but we have a limited understanding of their functional responses to changes in temperature across large geographic areas. Here, we explored how microbial communities utilized different carbon substrates and the underlying ecological mechanisms along a space-for-time substitution temperature gradient of future climate change. The gradient included 47 lakes from five major lake regions in China spanning a difference of nearly 15°C in mean annual temperatures (MAT). Our results indicated that lakes from warmer regions generally had lower values of variables related to carbon concentrations and greater carbon utilization than those from colder regions. The greater utilization of carbon substrates under higher temperatures could be attributed to changes in bacterial community composition, with a greater abundance of Cyanobacteria and Actinobacteriota and less Proteobacteria in warmer lake regions. We also found that the core species in microbial networks changed with increasing temperature, from Hydrogenophaga and Rhodobacteraceae, which inhibited the utilization of amino acids and carbohydrates, to the CL500-29-marine-group, which promoted the utilization of all almost carbon substrates. Overall, our findings suggest that temperature can mediate aquatic carbon utilization by changing the interactions between bacteria and individual carbon substrates, and the discovery of core species that affect carbon utilization provides insight into potential carbon sequestration within inland water bodies under future climate warming.
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Affiliation(s)
- Yao Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
- University of Chinese Academy of Sciences, Beijing, the People's Republic of China
| | - Songsong Gu
- University of Chinese Academy of Sciences, Beijing, the People's Republic of China
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, the People's Republic of China
| | - Kaixuan Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
- University of Chinese Academy of Sciences, Beijing, the People's Republic of China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario, Canada
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Junqi Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
| | - Xiangfen Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
- University of Chinese Academy of Sciences, Beijing, the People's Republic of China
| | - Qianzheng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
- University of Chinese Academy of Sciences, Beijing, the People's Republic of China
| | - Peng He
- School of Environmental Studies, China University of Geosciences, Wuhan, the People's Republic of China
| | - Dongru Qiu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
| | - Ye Deng
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, the People's Republic of China
| | - Pei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
- School of Environmental Studies, China University of Geosciences, Wuhan, the People's Republic of China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, the People's Republic of China
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5
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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6
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Analysis of Essential Isoprene Metabolic Pathway Proteins in Variovorax sp. Strain WS11. Appl Environ Microbiol 2023; 89:e0212222. [PMID: 36840579 PMCID: PMC10057887 DOI: 10.1128/aem.02122-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Isoprene monooxygenase (IsoMO, encoded by isoABCDEF) initiates the oxidation of the climate-active gas isoprene, with the genes isoGHIJ and aldH nearly always found adjacent to isoABCDEF in extant and metagenome-derived isoprene degraders. The roles of isoGHIJ and aldH are uncertain, although each is essential to isoprene degradation. We report here the characterization of these proteins from two model isoprene degraders, Rhodococcus sp. strain AD45 and Variovorax sp. strain WS11. The genes isoHIJ and aldH from Variovorax and aldH from Rhodococcus were expressed individually in Escherichia coli as maltose binding protein fusions to overcome issues of insolubility. The activity of two glutathione S-transferases from Variovorax, IsoI and IsoJ was assessed with model substrates, and the conversion of epoxyisoprene to the intermediate 1-hydroxy-2-glutathionyl-2-methyl-3-butene (HGMB) was demonstrated. The next step of the isoprene metabolic pathway of Variovorax is catalyzed by the dehydrogenase IsoH, resulting in the conversion of HGMB to 2-glutathionyl-2-methyl-3-butenoic acid (GMBA). The aldehyde dehydrogenases (AldH) from Variovorax and Rhodococcus were examined with a variety of aldehydes, with both exhibiting maximum activity with butanal. AldH significantly increased the rate of production of NADH when added to the IsoH-catalyzed conversion of HGMB to GMBA (via GMB), suggesting a synergistic role for AldH in the isoprene metabolic pathway. An in silico analysis of IsoG revealed that this protein, which is essential for isoprene metabolism in Variovorax, is an enzyme of the formyl CoA-transferase family and is predicted to catalyze the formation of a GMBA-CoA thioester as an intermediate in the isoprene oxidation pathway. IMPORTANCE Isoprene is a climate-active gas, largely produced by trees, which is released from the biosphere in amounts equivalent to those of methane and all other volatile organic compounds combined. Bacteria found in many environments, including soils and on the surface of leaves of isoprene-producing trees, can grow on isoprene and thus may represent a significant biological sink for this globally significant volatile compound and remove isoprene before it escapes to the atmosphere, thus reducing its potency as a climate-active gas. The initial oxidation of isoprene by bacteria is mediated by isoprene monooxygenase encoded by the genes isoABCDEF. In isoprene-degrading bacteria, a second gene cluster, isoGHIJ, is also present, although the exact role in isoprene degradation by the proteins encoded by these genes is uncertain. This investigation sheds new light on the roles of these proteins in the isoprene oxidation pathway in two model isoprene-degrading bacteria of the genera Rhodococcus and Variovorax.
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7
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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.
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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
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8
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Dawson RA, Rix GD, Crombie AT, Murrell JC. 'Omics-guided prediction of the pathway for metabolism of isoprene by Variovorax sp. WS11. Environ Microbiol 2022; 24:5151-5164. [PMID: 35920040 PMCID: PMC9804861 DOI: 10.1111/1462-2920.16149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023]
Abstract
Bacteria that inhabit soils and the leaves of trees partially mitigate the release of the abundant volatile organic compound, isoprene (2-methyl-1,3-butadiene). While the initial steps of isoprene metabolism were identified in Rhodococcus sp. AD45 two decades ago, the isoprene metabolic pathway still remains largely undefined. Limited understanding of the functions of isoG, isoJ and aldH and uncertainty in the route of isoprene-derived carbon into central metabolism have hindered our understanding of isoprene metabolism. These previously uncharacterised iso genes are essential in Variovorax sp. WS11, determined by targeted mutagenesis. Using combined 'omics-based approaches, we propose the complete isoprene metabolic pathway. Isoprene is converted to propionyl-CoA, which is assimilated by the chromosomally encoded methylmalonyl-CoA pathway, requiring biotin and vitamin B12, with the plasmid-encoded methylcitrate pathway potentially providing robustness against limitations in these vitamins. Key components of this pathway were induced by both isoprene and its initial oxidation product, epoxyisoprene, the principal inducer of isoprene metabolism in both Variovorax sp. WS11 and Rhodococcus sp. AD45. Analysis of the genomes of distinct isoprene-degrading bacteria indicated that all of the genetic components of the methylcitrate and methylmalonyl-CoA pathways are not always present in isoprene degraders, although incorporation of isoprene-derived carbon via propionyl-CoA and acetyl-CoA is universally indicated.
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Affiliation(s)
- Robin A. Dawson
- School of Environmental ScienceUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Gregory D. Rix
- School of Environmental ScienceUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - Andrew T. Crombie
- School of Environmental ScienceUniversity of East Anglia, Norwich Research ParkNorwichUK
| | - J. Colin Murrell
- School of Environmental ScienceUniversity of East Anglia, Norwich Research ParkNorwichUK
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9
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Iquebal MA, Jagannadham J, Jaiswal S, Prabha R, Rai A, Kumar D. Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. Front Microbiol 2022; 13:708335. [PMID: 35655999 PMCID: PMC9152772 DOI: 10.3389/fmicb.2022.708335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.
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Affiliation(s)
- Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
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10
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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.
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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
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11
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Purification and Characterization of the Isoprene Monooxygenase from Rhodococcus sp. Strain AD45. Appl Environ Microbiol 2022; 88:e0002922. [PMID: 35285709 PMCID: PMC9004368 DOI: 10.1128/aem.00029-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Isoprene (2-methyl-1,3-butadiene) is a climate-active gas released to the atmosphere in large quantities, comparable to methane in magnitude. Several bacteria have been isolated which can grow on isoprene as a sole carbon and energy source, but very little information is available about the degradation of isoprene by these bacteria at the biochemical level. Isoprene utilization is dependent on a multistep pathway, with the first step being the oxidation of isoprene to epoxy-isoprene. This is catalyzed by a four-component soluble diiron monooxygenase, isoprene monooxygenase (IsoMO). IsoMO is a six-protein complex comprising an oxygenase (IsoABE), containing the di-iron active site, a Rieske-type ferredoxin (IsoC), a NADH reductase (IsoF), and a coupling/effector protein (IsoD), homologous to the soluble methane monooxygenase and alkene/aromatic monooxygenases. Here, we describe the purification of the IsoMO components from Rhodococcus sp. AD45 and reconstitution of isoprene-oxidation activity in vitro. Some IsoMO components were expressed and purified from the homologous host Rhodococcus sp. AD45-ID, a Rhodococcus sp. AD45 strain lacking the megaplasmid which contains the isoprene metabolic gene cluster. Others were expressed in Escherichia coli and purified as fusion proteins. We describe the characterization of these purified components and demonstrate their activity when combined with Rhodococcus sp. AD45 cell lysate. Demonstration of IsoMO activity in vitro provides a platform for further biochemical and biophysical characterization of this novel soluble diiron center monooxygenase, facilitating new insights into the enzymatic basis for the bacterial degradation of isoprene. IMPORTANCE Isoprene is a highly abundant climate-active gas and a carbon source for some bacteria. Analyses of the genes encoding isoprene monooxygenase (IsoMO) indicate this enzyme is a soluble diiron center monooxygenase in the same family of oxygenases as soluble methane monooxygenase, alkene monooxygenase, and toluene monooxygenase. We report the initial biochemical characterization of IsoMO from Rhodococcus, the first from any bacterium, describing the challenging purification and reconstitution of in vitro activity of its four components. This study lays the foundation for future detailed mechanistic studies of IsoMO, a key enzyme in the global isoprene cycle.
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12
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Meredith LK, Tfaily MM. Capturing the microbial volatilome: an oft overlooked 'ome'. Trends Microbiol 2022; 30:622-631. [PMID: 35039213 DOI: 10.1016/j.tim.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022]
Abstract
Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. Advances in VOC detection now allow simultaneous observation of the numerous VOCs constituting the 'volatilome' of microbial systems. We present a roadmap for integrating and advancing VOC and other 'omics approaches and highlight the potential for realtime VOC measurements to help overcome limitations in discrete 'omics sampling. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.
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Affiliation(s)
- Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
| | - Malak M Tfaily
- BIO5 Institute, University of Arizona, Tucson, AZ, USA; Department of Environmental Science, University of Arizona, Tucson, AZ, USA.
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13
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Chalkos D, Karamanoli K, Vokou D. Monoterpene Enrichments Have Positive Impacts on Soil Bacterial Communities and the Potential of Application in Bioremediation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112536. [PMID: 34834898 PMCID: PMC8623845 DOI: 10.3390/plants10112536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We study here how soil bacterial communities of different ecosystems respond to disturbances caused by enrichments with monoterpenes that are common essential oil constituents. We used fenchone, 1,8-cineol and α-pinene, and soils from phrygana, a typical Mediterranean-type ecosystem where aromatic plants abound, and from another five ecosystem types, focusing on culturable bacteria. Patterns of response were common to all ecosystems, but responses themselves were not always as pronounced in phrygana as in the other ecosystems, suggesting that these enrichments are less of a disturbance there. More specifically, soil respiration and abundance of the bacterial communities increased, becoming from below two up to 16 times as high as in control soils (for both attributes) and remained at high levels as long as these compounds were present. Bacteria that can utilize these three compounds as substrates of growth became dominant members of the bacterial communities in the enriched soils. All changes were readily reversible once monoterpene addition stopped. Bacteria with the ability to utilize these monoterpenes as carbon sources were found in soils from all ecosystems, 15 strains in total, suggesting a rather universal presence; of these, six could also utilize the organic pollutants toluene or p-xylene. These results suggest also potential novel applications of monoterpenes in combating soil pollution.
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Affiliation(s)
- Dimitris Chalkos
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Katerina Karamanoli
- Laboratory of Agricultural Chemistry, School of Agriculture, Faculty of Agriculture Forestry and Natural Environment, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
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Lienkamp AC, Burnik J, Heine T, Hofmann E, Tischler D. Characterization of the Glutathione S-Transferases Involved in Styrene Degradation in Gordonia rubripertincta CWB2. Microbiol Spectr 2021; 9:e0047421. [PMID: 34319142 PMCID: PMC8552685 DOI: 10.1128/spectrum.00474-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 11/29/2022] Open
Abstract
The glutathione S-transferases carried on the plasmid for the styrene-specific degradation pathway in the Actinobacterium Gordonia rubripertincta CWB2 were heterologously expressed in Escherichia coli. Both enzymes were purified via affinity chromatography and subjected to activity investigations. StyI and StyJ displayed activity toward the commonly used glutathione S-transferase model substrate 1-chloro-2,4-dinitrobenzene (CDNB) with Km values of 0.0682 ± 0.0074 and 2.0281 ± 0.1301 mM and Vmax values of 0.0158 ± 0.0002 and 0.348 ± 0.008 U mg-1 for StyI and StyJ, respectively. The conversion of the natural substrate styrene oxide to the intermediate (1-phenyl-2-hydroxyethyl)glutathione was detected for StyI with 48.3 ± 2.9 U mg-1. This elucidates one more step in the not yet fully resolved styrene-specific degradation pathway of Gordonia rubripertincta CWB2. A characterization of both purified enzymes adds more insight into the scarce research field of actinobacterial glutathione S-transferases. Moreover, a sequence and phylogenetic analysis puts both enzymes into a physiological and evolutionary context. IMPORTANCE Styrene is a toxic compound that is used at a large scale by industry for plastic production. Bacterial degradation of styrene is a possibility for bioremediation and pollution prevention. Intermediates of styrene derivatives degraded in the styrene-specific pathways are precursors for valuable chemical compounds. The pathway in Gordonia rubripertincta CWB2 has proven to accept a broader substrate range than other bacterial styrene degraders. The enzymes characterized in this study, distinguish CWB2s pathway from other known styrene degradation routes and thus might be the main key for its ability to produce ibuprofen from the respective styrene derivative. A biotechnological utilization of this cascade could lead to efficient and sustainable production of drugs, flavors, and fragrances. Moreover, research on glutathione metabolism in Actinobacteria is rare. Here, a characterization of two glutathione S-transferases of actinobacterial origin is presented, and the utilization of glutathione in the metabolism of an Actinobacterium is proven.
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Affiliation(s)
- Anna C. Lienkamp
- Microbial Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
| | - Jan Burnik
- X-Ray Structure Analysis of Proteins, Ruhr-Universität Bochum, Bochum, Germany
| | - Thomas Heine
- Environmental Microbiology, TU Bergakademie Freiberg, Freiberg, Germany
| | - Eckhard Hofmann
- X-Ray Structure Analysis of Proteins, Ruhr-Universität Bochum, Bochum, Germany
| | - Dirk Tischler
- Microbial Biotechnology, Ruhr-Universität Bochum, Bochum, Germany
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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.
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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.
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16
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Yun J, Crombie AT, Ul Haque MF, Cai Y, Zheng X, Wang J, Jia Z, Murrell JC, Wang Y, Du W. Revealing the community and metabolic potential of active methanotrophs by targeted metagenomics in the Zoige wetland of the Tibetan Plateau. Environ Microbiol 2021; 23:6520-6535. [PMID: 34390603 DOI: 10.1111/1462-2920.15697] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023]
Abstract
The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity and metabolism at the molecular level can guide the isolation of the uncultured microorganisms and inform strategy-making decisions and policies to counteract global warming in this unique ecosystem. Here we applied DNA stable isotope probing using 13 C-labelled methane to label the genomes of active methanotrophs, examine the methane oxidation potential and recover metagenome-assembled genomes (MAGs) of active methanotrophs. We found that gammaproteobacteria of type I methanotrophs are responsible for methane oxidation in the wetland. We recovered two phylogenetically novel methanotroph MAGs distantly related to extant Methylobacter and Methylovulum. They belong to type I methanotrophs of gammaproteobacteria, contain both mxaF and xoxF types of methanol dehydrogenase coding genes, and participate in methane oxidation via H4 MPT and RuMP pathways. Overall, the community structure of active methanotrophs and their methanotrophic pathways revealed by DNA-SIP metagenomics and retrieved methanotroph MAGs highlight the importance of methanotrophs in suppressing methane emission in the wetland under the scenario of global warming.
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Affiliation(s)
- Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Andrew T Crombie
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, Jiangsu Province, 210008, China
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 10049, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 10049, China
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Hawkes CV, Kjøller R, Raaijmakers JM, Riber L, Christensen S, Rasmussen S, Christensen JH, Dahl AB, Westergaard JC, Nielsen M, Brown-Guedira G, Hestbjerg Hansen L. Extension of Plant Phenotypes by the Foliar Microbiome. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:823-846. [PMID: 34143648 DOI: 10.1146/annurev-arplant-080620-114342] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.
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Affiliation(s)
- Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Jesper Cairo Westergaard
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service and Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
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18
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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.
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19
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Sharma M, Khurana H, Singh DN, Negi RK. The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 280:111744. [PMID: 33280938 DOI: 10.1016/j.jenvman.2020.111744] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.
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Affiliation(s)
- Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Durgesh Narain Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.
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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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21
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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.
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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
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22
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Gibson L, Larke-Mejía NL, Murrell JC. Complete Genome of Isoprene Degrading Nocardioides sp. WS12. Microorganisms 2020; 8:microorganisms8060889. [PMID: 32545487 PMCID: PMC7355492 DOI: 10.3390/microorganisms8060889] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 01/20/2023] Open
Abstract
Isoprene is a climate-active gas whose wide-spread global production stems mostly from terrestrial plant emissions. The biodegradation of isoprene is carried out by a number of different bacteria from a wide range of environments. This study investigates the genome of a novel isoprene degrading bacterium Nocardioides sp. WS12, isolated from soil associated with Salix alba (Willow), a tree known to produce high amounts of isoprene. The Nocardioides sp. WS12 genome was fully sequenced, revealing the presence of a complete isoprene monooxygenase gene cluster, along with associated isoprene degradation pathway genes. Genes associated with rubber degradation were also present, suggesting that Nocardioides sp. WS12 may also have the capacity to degrade poly-cis-1,4-isoprene.
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23
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Carrión O, Gibson L, Elias DMO, McNamara NP, van Alen TA, Op den Camp HJM, Supramaniam CV, McGenity TJ, Murrell JC. Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation. MICROBIOME 2020; 8:81. [PMID: 32493439 PMCID: PMC7271495 DOI: 10.1186/s40168-020-00860-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/11/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees. RESULTS DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere. CONCLUSION This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas. Video abstract.
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Affiliation(s)
- Ornella Carrión
- 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
| | - Dafydd M O Elias
- UK Centre of Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Niall P McNamara
- UK Centre of Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ, Nijmegen, The Netherlands
| | - Christina Vimala Supramaniam
- School of Biosciences, Nottingham Centre of Sustainable Palm Oil, University of Nottingham-Malaysia, Jalan Broga, 43500, Semenyih, Selangor Darul Ehsan, Malaysia
| | | | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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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.
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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
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Dawson RA, Larke-Mejía NL, Crombie AT, Ul Haque MF, Murrell JC. Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11. Microorganisms 2020; 8:E349. [PMID: 32121431 PMCID: PMC7143210 DOI: 10.3390/microorganisms8030349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 01/19/2023] Open
Abstract
Plant-produced isoprene (2-methyl-1,3-butadiene) represents a significant portion of global volatile organic compound production, equaled only by methane. A metabolic pathway for the degradation of isoprene was first described for the Gram-positive bacterium Rhodococcus sp. AD45, and an alternative model organism has yet to be characterised. Here, we report the characterisation of a novel Gram-negative isoprene-degrading bacterium, Variovorax sp. WS11. Isoprene metabolism in this bacterium involves a plasmid-encoded iso metabolic gene cluster which differs from that found in Rhodococcus sp. AD45 in terms of organisation and regulation. Expression of iso metabolic genes is significantly upregulated by both isoprene and epoxyisoprene. The enzyme responsible for the initial oxidation of isoprene, isoprene monooxygenase, oxidises a wide range of alkene substrates in a manner which is strongly influenced by the presence of alkyl side-chains and differs from other well-characterised soluble diiron monooxygenases according to its response to alkyne inhibitors. This study presents Variovorax sp. WS11 as both a comparative and contrasting model organism for the study of isoprene metabolism in bacteria, aiding our understanding of the conservation of this biochemical pathway across diverse ecological niches.
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Affiliation(s)
- Robin A. Dawson
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK; (R.A.D.); (N.L.L.-M.)
| | - Nasmille L. Larke-Mejía
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK; (R.A.D.); (N.L.L.-M.)
| | - Andrew T. Crombie
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK;
| | - Muhammad Farhan Ul Haque
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54000, Pakistan;
| | - J. Colin Murrell
- School of Environmental Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK; (R.A.D.); (N.L.L.-M.)
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