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Li J, Dong C, Sen B, Lai Q, Gong L, Wang G, Shao Z. Lignin-oxidizing and xylan-hydrolyzing Vibrio involved in the mineralization of plant detritus in the continental slope. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158714. [PMID: 36113801 DOI: 10.1016/j.scitotenv.2022.158714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A large amount of terrigenous organic matter (TOM) is constantly transported to the deep sea. However, relatively little is known about the microbial mineralization of TOM therein. Our recent in situ enrichment experiments revealed that Vibrio is especially enriched as one of the predominant taxa in the cultures amended with natural plant materials in the deep sea. Yet their role in the mineralization of plant-derived TOM in the deep sea remains largely unknown. Here we isolated Vibrio strains representing dominant members of the enrichments and verified their potential to degrade lignin and xylan. The isolated strains were closely related to Vibrio harveyi, V. alginolyticus, V. diabolicus, and V. parahaemolyticus. Extracellular enzyme assays, and genome and transcriptome analyses revealed diverse peroxidases, including lignin peroxidase (LiP), catalase-peroxidase (KatG), and decolorizing peroxidase (DyP), which played an important role in the depolymerization and oxidation of lignin. Superoxide dismutase was found to likely promote lignin oxidation by supplying H2O2 to LiP, DyP, and KatG. Interestingly, these deep-sea Vibrio strains could oxidize lignin and hydrolyze xylan not only through aerobic pathway, but also through anaerobic pathway. Genome analysis revealed multiple anaerobic respiratory mechanisms, including the reductions of nitrate, arsenate, tetrathionate, and dimethyl sulfoxide. The strains showed the potential to anaerobically reduce sulfite and metal oxides of iron and manganese, in contrast the non-deep-sea Vibrio strains were not retrieved of genes involved in reduction of metal oxides. This is the first report about the lignin oxidation mechanisms in Vibrio and their role in TOM mineralization in anoxic and oxic environments of the marginal sea.
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Affiliation(s)
- Jianyang Li
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China; Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300387, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361005, PR China; State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China.
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Thiour-Mauprivez C, Dayan FE, Terol H, Devers M, Calvayrac C, Martin-Laurent F, Barthelmebs L. Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:9932-9944. [PMID: 36068455 DOI: 10.1007/s11356-022-22801-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.
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Affiliation(s)
- Clémence Thiour-Mauprivez
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Franck Emmanuel Dayan
- Agricultural Biology Department, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hugo Terol
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Marion Devers
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Christophe Calvayrac
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Fabrice Martin-Laurent
- Agroécologie, INRAE, Institut Agro, Unv. Bourgogne, University Bourgogne Franche-Comté, F-21000, Dijon, France
| | - Lise Barthelmebs
- University Perpignan Via Domitia, Biocapteurs-Analyses-Environnement, 66860 Perpignan, France; Laboratoire de Biodiversité et Biotechnologies Microbiennes, USR 3579 Sorbonne Universités (UPMC) Paris 6 et CNRS Observatoire Océanologique, 66650, Banyuls-sur-Mer, France.
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Zhao S, Liu R, Lai Q, Shao Z. Muricauda aurea sp. nov. and Muricauda profundi sp. nov., two marine bacteria isolated from deep sea sediment of Pacific Ocean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005217] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, aerobic, rod-shaped, carotenoid-pigmented and non-flagellated bacteria, designated BC31-1-A7T and BC31-3-A3T, were isolated from polyethylene-terephthalate-degrading bacterial consortia enriched from deep-sea sediment collected in the Pacific Ocean. Optimal growth of both strains was observed at 28–32 °C, at pH 7.5 and in the presence of 3–4% (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strains BC31-1-A7T and BC31-3-A3T were closely related to
Muricauda aquimarina
JCM 11811T,
Muricauda lutimaris
KCTC 22173T,
Muricauda ruestringensis
DSM 13258T,
Muricauda zhangzhouensis
DSM 25030T,
Muricauda oceani
JCM 33902T and
Muricauda oceanensis
KCTC 72200T with 96.8–98.9% sequence similarity. The 16S rRNA gene sequence similarity between strains BC31-1-A7T and BC31-3-A3T was 97.5%. The genomic G+C contents of strains BC31-1-A7T and BC31-3-A3T were 42.1 and 41.6 mol%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain BC31-3-A3T, strain BC31-1-A7T and their six closely related type strains were 77.6–84.3% and 20.5–27.9%, respectively. Menaquinone-6 was detected as the major isoprenoid quinone in all strains. Their major fatty acids were iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH. The major polar lipids of strains BC31-1-A7T and BC31-3-A3T were identified as one phosphatidylethanolamine, some unidentified polar lipids and one aminolipid. Based on their distinct taxonomic characteristics, strains BC31-1-A7T and BC31-3-A3T represent two novel species in the genus
Muricauda
. The names proposed to accommodate these two strains are Muricauda aurea sp. nov. and Muricauda profundi sp. nov., and the type strains are BC31-1-A7T (=MCCC M23246T=KCTC 82569T) and BC31-3-A3T (=MCCC M23216T=KCTC 82302T), respectively.
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Affiliation(s)
- Sufang Zhao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Fisheries and life, Shanghai Ocean University, Shanghai 201306, PR China
| | - Renju Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Xiamen 361005, PR China
- School of Fisheries and life, Shanghai Ocean University, Shanghai 201306, PR China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, PR China
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Mustila H, Kugler A, Stensjö K. Isobutene production in Synechocystis sp. PCC 6803 by introducing α-ketoisocaproate dioxygenase from Rattus norvegicus. Metab Eng Commun 2021; 12:e00163. [PMID: 33552898 PMCID: PMC7856465 DOI: 10.1016/j.mec.2021.e00163] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Cyanobacteria can be utilized as a platform for direct phototrophic conversion of CO2 to produce several types of carbon-neutral biofuels. One promising compound to be produced photobiologically in cyanobacteria is isobutene. As a volatile compound, isobutene will quickly escape the cells without building up to toxic levels in growth medium or get caught in the membranes. Unlike liquid biofuels, gaseous isobutene may be collected from the headspace and thus avoid the costly extraction of a chemical from culture medium or from cells. Here we investigate a putative synthetic pathway for isobutene production suitable for a photoautotrophic host. First, we expressed α-ketoisocaproate dioxygenase from Rattus norvegicus (RnKICD) in Escherichia coli. We discovered isobutene formation with the purified RnKICD with the rate of 104.6 ± 9 ng (mg protein)-1 min-1 using α-ketoisocaproate as a substrate. We further demonstrate isobutene production in the cyanobacterium Synechocystis sp. PCC 6803 by introducing the RnKICD enzyme. Synechocystis strain heterologously expressing the RnKICD produced 91 ng l−1 OD750−1 h−1. Thus, we demonstrate a novel sustainable platform for cyanobacterial production of an important building block chemical, isobutene. These results indicate that RnKICD can be used to further optimize the synthetic isobutene pathway by protein and metabolic engineering efforts. Photosynthetic isobutene production is demonstrated in a cyanobacterium. A Synechocystis strain capable of continuous direct conversion of CO2 to isobutene. α-ketoisocaproate dioxygenase from R. norvegicus (RnKICD) is determined to form isobutene. RnKICD can convert α-ketoisocaproate to isobutene both in vitro and in vivo.
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Affiliation(s)
- Henna Mustila
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Amit Kugler
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, SE-751 20, Uppsala, Sweden
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Seo D, Choi KY. Heterologous production of pyomelanin biopolymer using 4-hydroxyphenylpyruvate dioxygenase isolated from Ralstonia pickettii in Escherichia coli. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Characterization of 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione resistance in pyomelanogenic Pseudomonas aeruginosa DKN343. PLoS One 2017; 12:e0178084. [PMID: 28570601 PMCID: PMC5453437 DOI: 10.1371/journal.pone.0178084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 05/07/2017] [Indexed: 01/11/2023] Open
Abstract
Pyomelanin is a reddish-brown pigment that provides bacteria and fungi protection from oxidative stress, and is reported to contribute to infection persistence. Production of this pigment can be inhibited by the anti-virulence agent 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC). The Pseudomonas aeruginosa clinical isolate DKN343 exhibited high levels of resistance to NTBC, and the mechanism of pyomelanin production in this strain was uncharacterized. We determined that pyomelanin production in the clinical Pseudomonas aeruginosa isolate DKN343 was due to a loss of function in homogentisate 1,2-dioxygenase (HmgA). Several potential resistance mechanisms were investigated, and the MexAB-OprM efflux pump is required for resistance to NTBC. DKN343 has a frameshift mutation in NalC, which is a known indirect repressor of the mexAB-oprM operon. This frameshift mutation may contribute to the increased resistance of DKN343 to NTBC. Additional studies investigating the prevalence of resistance in pyomelanogenic microbes are necessary to determine the future applications of NTBC as an anti-virulence therapy.
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Complete Genome Sequence of Alteromonas stellipolaris LMG 21856, a Budding Brown Pigment-Producing Oligotrophic Bacterium Isolated from the Southern Ocean. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00137-16. [PMID: 27013039 PMCID: PMC4807228 DOI: 10.1128/genomea.00137-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the complete genome sequence of Alteromonas stellipolaris LMG 21856, which was isolated from seawater collected from the Southern Ocean. A. stellipolaris LMG 21856 is a budding, psychrotrophic, brown pigment-producing, and oligotrophic bacterium. The complete genome of this bacterium contains 4,686,200 bp, with a G+C content of 43.6%.
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