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Viver T, Conrad RE, Lucio M, Harir M, Urdiain M, Gago JF, Suárez-Suárez A, Bustos-Caparros E, Sanchez-Martinez R, Mayol E, Fassetta F, Pang J, Mădălin Gridan I, Venter S, Santos F, Baxter B, Llames ME, Cristea A, Banciu HL, Hedlund BP, Stott MB, Kämpfer P, Amann R, Schmitt-Kopplin P, Konstantinidis KT, Rossello-Mora R. Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov. Syst Appl Microbiol 2023; 46:126416. [PMID: 36965279 DOI: 10.1016/j.syapm.2023.126416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.
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Affiliation(s)
- Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Mourad Harir
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Ana Suárez-Suárez
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Rodrigo Sanchez-Martinez
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Eva Mayol
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Federico Fassetta
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Jinfeng Pang
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Ionuț Mădălin Gridan
- Doctoral School of Integrative Biology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Stephanus Venter
- Department of Biochemistry, Genetics and Microbiology, and Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690, San Vicent del Raspeig, Alicante, Spain
| | - Bonnie Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, USA
| | - María E Llames
- Laboratorio de Ecología Acuática, Instituto Tecnológico Chascomús (INTECH)-CONICET-UNSAM, Escuela de Bio y Nanotecnologías -UNSAM, Buenos Aires, Argentina
| | - Adorján Cristea
- Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Horia L Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj‑Napoca, Romania; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj‑Napoca, Romania
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154-4004, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig Universität Giessen, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, 85764 Neuherberg, Germany; Chair of Analytical Food Chemistry, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Konstantinos T Konstantinidis
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; School of Civil & Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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Effects of the endophyte Epichloë coenophiala on the root microbial community and growth performance of tall fescue in different saline-alkali soils. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Esteves AM, Graça G, Peyriga L, Torcato IM, Borges N, Portais JC, Santos H. Combined transcriptomics-metabolomics profiling of the heat shock response in the hyperthermophilic archaeon Pyrococcus furiosus. Extremophiles 2018; 23:101-118. [PMID: 30430272 DOI: 10.1007/s00792-018-1065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrococcus furiosus is a remarkable archaeon able to grow at temperatures around 100 °C. To gain insight into how this model hyperthermophile copes with heat stress, we compared transcriptomic and metabolomic data of cells subjected to a temperature shift from 90 °C to 97 °C. In this study, we used RNA-sequencing to characterize the global variation in gene expression levels, while nuclear magnetic resonance (NMR) and targeted ion exchange liquid chromatography-mass spectrometry (LC-MS) were used to determine changes in metabolite levels. Of the 552 differentially expressed genes in response to heat shock conditions, 257 were upregulated and 295 were downregulated. In particular, there was a significant downregulation of genes for synthesis and transport of amino acids. At the metabolite level, 37 compounds were quantified. The level of di-myo-inositol phosphate, a canonical heat stress solute among marine hyperthermophiles, increased considerably (5.4-fold) at elevated temperature. Also, the levels of mannosylglycerate, UDP-N-acetylglucosamine (UDPGlcNac) and UDP-N-acetylgalactosamine were enhanced. The increase in the pool of UDPGlcNac was concurrent with an increase in the transcript levels of the respective biosynthetic genes. This work provides the first metabolomic analysis of the heat shock response of a hyperthermophile.
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Affiliation(s)
- Ana M Esteves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Gonçalo Graça
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Lindsay Peyriga
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Inês M Torcato
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Nuno Borges
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal
| | - Jean-Charles Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31077, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.,Université Paul Sabatier, Université de Toulouse, 31062, Toulouse, France
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-127, Oeiras, Portugal.
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Wienhausen G, Noriega-Ortega BE, Niggemann J, Dittmar T, Simon M. The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites. Front Microbiol 2017; 8:1985. [PMID: 29075248 PMCID: PMC5643483 DOI: 10.3389/fmicb.2017.01985] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/27/2017] [Indexed: 12/04/2022] Open
Abstract
Recent studies applying Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) showed that the exometabolome of marine bacteria is composed of a surprisingly high molecular diversity. To shed more light on how this diversity is generated we examined the exometabolome of two model strains of the Roseobacter group, Phaeobacter inhibens and Dinoroseobacter shibae, grown on glutamate, glucose, acetate or succinate by FT-ICR-MS. We detected 2,767 and 3,354 molecular formulas in the exometabolome of each strain and 67 and 84 matched genome-predicted metabolites of P. inhibens and D. shibae, respectively. The annotated compounds include late precursors of biosynthetic pathways of vitamins B1, B2, B5, B6, B7, B12, amino acids, quorum sensing-related compounds, indole acetic acid and methyl-(indole-3-yl) acetic acid. Several formulas were also found in phytoplankton blooms. To shed more light on the effects of some of the precursors we supplemented two B1 prototrophic diatoms with the detected precursor of vitamin B1 HET (4-methyl-5-(β-hydroxyethyl)thiazole) and HMP (4-amino-5-hydroxymethyl-2-methylpyrimidine) and found that their growth was stimulated. Our findings indicate that both strains and other bacteria excreting a similar wealth of metabolites may function as important helpers to auxotrophic and prototrophic marine microbes by supplying growth factors and biosynthetic precursors.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Beatriz E Noriega-Ortega
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jutta Niggemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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He G, Wu C, Huang J, Zhou R. Metabolic response of Tetragenococcus halophilus under salt stress. BIOTECHNOL BIOPROC E 2017. [DOI: 10.1007/s12257-017-0015-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Favre L, Ortalo-Magné A, Greff S, Pérez T, Thomas OP, Martin JC, Culioli G. Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters. J Proteome Res 2017; 16:1962-1975. [PMID: 28362105 DOI: 10.1021/acs.jproteome.6b01027] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC-MS metabolomics approach of marine biofilm-forming bacterial strains was developed. Four marine bacteria, Persicivirga (Nonlabens) mediterranea TC4 and TC7, Pseudoalteromonas lipolytica TC8, and Shewanella sp. TC11, were used as model organisms. The main objective was to search for some strain-specific bacterial metabolites and to determine how culture parameters (culture medium, growth phase, and mode of culture) may affect the cellular metabolism of each strain and thus the global interstrain metabolic discrimination. LC-MS profiling and statistical partial least-squares discriminant analyses showed that the four strains could be differentiated at the species level whatever the medium, the growth phase, or the mode of culture (planktonic vs biofilm). A MS/MS molecular network was subsequently built and allowed the identification of putative bacterial biomarkers. TC8 was discriminated by a series of ornithine lipids, while the P. mediterranea strains produced hydroxylated ornithine and glycine lipids. Among the P. mediterranea strains, TC7 extracts were distinguished by the occurrence of diamine derivatives, such as putrescine amides.
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Affiliation(s)
- Laurie Favre
- Université de Toulon , MAPIEM, EA 4323, La Garde Cedex 83130, France
| | | | - Stéphane Greff
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France
| | - Thierry Pérez
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France
| | - Olivier P Thomas
- CNRS, Aix Marseille Univ , IRD, Avignon Univ. Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Station marine d'Endoume, Marseille 13007, France.,National University of Ireland Galway , School of Chemistry, Marine Biodiscovery, Galway, Ireland
| | | | - Gérald Culioli
- Université de Toulon , MAPIEM, EA 4323, La Garde Cedex 83130, France
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Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Rattray NJW, Goodacre R. Metabolomics Analysis Reveals the Participation of Efflux Pumps and Ornithine in the Response of Pseudomonas putida DOT-T1E Cells to Challenge with Propranolol. PLoS One 2016; 11:e0156509. [PMID: 27331395 PMCID: PMC4917112 DOI: 10.1371/journal.pone.0156509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/16/2016] [Indexed: 02/07/2023] Open
Abstract
Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden addition of 0.2, 0.4 and 0.6 mg mL-1 of this β-blocker to several strains of P. putida, including the wild type DOT-T1E and the efflux pump knockout mutants DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the efflux pump TtgABC plays a more important role than the TtgGHI pump in strain tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a rapid, high-throughput screening tool to investigate any phenotypic changes resulting from exposure to varying levels of propranolol. Multivariate statistical analysis of these MIR data revealed gradient trends in resultant ordination scores plots, which were related to the concentration of propranolol. MIR illustrated phenotypic changes associated with the presence of this drug within the cell that could be assigned to significant changes that occurred within the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during the growth of bacteria following toxic perturbation with the same concentration levels of propranolol. Metabolic profiling revealed that ornithine, which was only produced by P. putida cells in the presence of propranolol, presents itself as a major metabolic feature that has important functions in propranolol stress tolerance mechanisms within this highly significant and environmentally relevant species of bacteria.
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Affiliation(s)
- Ali Sayqal
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Yun Xu
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Drupad K. Trivedi
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Najla AlMasoud
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - David I. Ellis
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicholas J. W. Rattray
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Royston Goodacre
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- * E-mail:
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Metabolic Fingerprinting of Pseudomonas putida DOT-T1E Strains: Understanding the Influence of Divalent Cations in Adaptation Mechanisms Following Exposure to Toluene. Metabolites 2016; 6:metabo6020014. [PMID: 27128955 PMCID: PMC4931545 DOI: 10.3390/metabo6020014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas putida strains can adapt and overcome the activity of toxic organic solvents by the employment of several resistant mechanisms including efflux pumps and modification to lipopolysaccharides (LPS) in their membranes. Divalent cations such as magnesium and calcium play a crucial role in the development of solvent tolerance in bacterial cells. Here, we have used Fourier transform infrared (FT-IR) spectroscopy directly on cells (metabolic fingerprinting) to monitor bacterial response to the absence and presence of toluene, along with the influence of divalent cations present in the growth media. Multivariate analysis of the data using principal component-discriminant function analysis (PC-DFA) showed trends in scores plots, illustrating phenotypic alterations related to the effect of Mg(2+), Ca(2+) and toluene on cultures. Inspection of PC-DFA loadings plots revealed that several IR spectral regions including lipids, proteins and polysaccharides contribute to the separation in PC-DFA space, thereby indicating large phenotypic response to toluene and these cations. Finally, the saturated fatty acid ratio from the FT-IR spectra showed that upon toluene exposure, the saturated fatty acid ratio was reduced, while it increased in the presence of divalent cations. This study clearly demonstrates that the combination of metabolic fingerprinting with appropriate chemometric analysis can result in practicable knowledge on the responses of important environmental bacteria to external stress from pollutants such as highly toxic organic solvents, and indicates that these changes are manifest in the bacterial cell membrane. Finally, we demonstrate that divalent cations improve solvent tolerance in P. putida DOT‑T1E strains.
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Sayqal A, Xu Y, Trivedi DK, AlMasoud N, Ellis DI, Muhamadali H, Rattray NJW, Webb C, Goodacre R. Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry. Metabolomics 2016; 12:112. [PMID: 27398079 PMCID: PMC4916193 DOI: 10.1007/s11306-016-1054-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/04/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION An exceptionally interesting stress response of Pseudomonas putida strains to toxic substances is the induction of efflux pumps that remove toxic chemical substances from the bacterial cell out to the external environment. To exploit these microorganisms to their full potential a deeper understanding of the interactions between the bacteria and organic solvents is required. Thus, this study focuses on investigation of metabolic changes in P. putida upon exposure to toluene. OBJECTIVE Investigate observable metabolic alterations during interactions of three strains of P. putida (DOT-T1E, and its mutants DOT-T1E-PS28 and DOT-T1E-18) with the aromatic hydrocarbon toluene. METHODS The growth profiles were measured by taking optical density (OD) measurement at 660 nm (OD660) at various time points during incubation. For fingerprinting analysis, Fourier-transform infrared (FT-IR) spectroscopy was used to investigate any phenotypic changes resulting from exposure to toluene. Metabolic profiling analysis was performed using gas chromatography-mass spectrometry (GC-MS). Principal component-discriminant function analysis (PC-DFA) was applied to the FT-IR data while multiblock principal component analysis (MB-PCA) and N-way analysis of variance (N-way ANOVA) were applied to the GC-MS data. RESULTS The growth profiles demonstrated the effect of toluene on bacterial cultures and the results suggest that the mutant P. putida DOT-T1E-18 was more sensitive (significantly affected) to toluene compared to the other two strains. PC-DFA on FT-IR data demonstrated the differentiation between different conditions of toluene on bacterial cells, which indicated phenotypic changes associated with the presence of the solvent within the cell. Fifteen metabolites associated with this phenotypic change, in P. putida due to exposure to solvent, were from central metabolic pathways. Investigation of MB-PCA loading plots and N-way ANOVA for condition | strain × time blocking (dosage of toluene) suggested ornithine as the most significant compound that increased upon solvent exposure. CONCLUSION The combination of metabolic fingerprinting and profiling with suitable multivariate analysis revealed some interesting leads for understanding the mechanism of Pseudomonas strains response to organic solvent exposure.
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Affiliation(s)
- Ali Sayqal
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Drupad K. Trivedi
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Najla AlMasoud
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - David I. Ellis
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Nicholas J. W. Rattray
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Carole Webb
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN UK
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Exo-metabolome of Pseudovibrio sp. FO-BEG1 analyzed by ultra-high resolution mass spectrometry and the effect of phosphate limitation. PLoS One 2014; 9:e96038. [PMID: 24787987 PMCID: PMC4008564 DOI: 10.1371/journal.pone.0096038] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 04/02/2014] [Indexed: 02/03/2023] Open
Abstract
Oceanic dissolved organic matter (DOM) is an assemblage of reduced carbon compounds, which results from biotic and abiotic processes. The biotic processes consist in either release or uptake of specific molecules by marine organisms. Heterotrophic bacteria have been mostly considered to influence the DOM composition by preferential uptake of certain compounds. However, they also secrete a variety of molecules depending on physiological state, environmental and growth conditions, but so far the full set of compounds secreted by these bacteria has never been investigated. In this study, we analyzed the exo-metabolome, metabolites secreted into the environment, of the heterotrophic marine bacterium Pseudovibrio sp. FO-BEG1 via ultra-high resolution mass spectrometry, comparing phosphate limited with phosphate surplus growth conditions. Bacteria belonging to the Pseudovibrio genus have been isolated worldwide, mainly from marine invertebrates and were described as metabolically versatile Alphaproteobacteria. We show that the exo-metabolome is unexpectedly large and diverse, consisting of hundreds of compounds that differ by their molecular formulae. It is characterized by a dynamic recycling of molecules, and it is drastically affected by the physiological state of the strain. Moreover, we show that phosphate limitation greatly influences both the amount and the composition of the secreted molecules. By assigning the detected masses to general chemical categories, we observed that under phosphate surplus conditions the secreted molecules were mainly peptides and highly unsaturated compounds. In contrast, under phosphate limitation the composition of the exo-metabolome changed during bacterial growth, showing an increase in highly unsaturated, phenolic, and polyphenolic compounds. Finally, we annotated the detected masses using multiple metabolite databases. These analyses suggested the presence of several masses analogue to masses of known bioactive compounds. However, the annotation was successful only for a minor part of the detected molecules, underlining the current gap in knowledge concerning the biosynthetic ability of marine heterotrophic bacteria.
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Metabolomic characterization of halophilic bacterial isolates reveals strains synthesizing rare diaminoacids under salt stress. Biochimie 2014; 102:102-11. [PMID: 24636996 DOI: 10.1016/j.biochi.2014.02.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 02/26/2014] [Indexed: 11/23/2022]
Abstract
Metabolomics-based approaches to study stress responses in bacteria have received much attention in recent years. In the present study, a metabolomic analysis of the representative halophilic bacterial isolates (Halomonas hydrothermalis VITP9, Bacillus aquimaris VITP4, Planococcus maritimus VITP21 and Virgibacillus dokdonensis VITP14) from a saltern region in India was performed using nuclear magnetic resonance spectroscopy. Chemometric analysis of (1)H NMR spectra revealed salt-dependent increase in the levels of metabolites, mainly from the aspartate and glutamate family, that are directed from the glycolytic pathway, pentose phosphate pathway and citric acid cycle. The composition of the metabolites was found to be different with respect to the species and the type of growth medium. Analysis of the two dimensional NMR data revealed accumulation of two rare diaminoacids, Nε-acetyl-α-lysine and Nδ-acetylornithine (by VITP21 and VITP4 strains respectively) apart from other well known solutes such as ectoine, proline, glutamate and glycine betaine. Metabolite profiles of strains capable of synthesizing Nε-acetyl-α-lysine and Nδ-acetylornithine suggested their biosynthesis from lysine and ornithine using aspartate and glutamate as their precursors, respectively. Further, the cells in moderate salinity (5% w/v NaCl) showed an increase in growth rate along with increase in the levels of nucleotides, whereas at higher salinity (10% w/v NaCl), the levels of aromatic and hydrophobic metabolites dropped, accompanied with a decrease in growth rate, rightly suggesting that at any salt-stress condition provided, cellular homeostasis was favored over growth.
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Ma B, Gong J. A meta-analysis of the publicly available bacterial and archaeal sequence diversity in saline soils. World J Microbiol Biotechnol 2013; 29:2325-34. [DOI: 10.1007/s11274-013-1399-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 06/03/2013] [Indexed: 10/26/2022]
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Antón J, Lucio M, Peña A, Cifuentes A, Brito-Echeverría J, Moritz F, Tziotis D, López C, Urdiain M, Schmitt-Kopplin P, Rosselló-Móra R. High metabolomic microdiversity within co-occurring isolates of the extremely halophilic bacterium Salinibacter ruber. PLoS One 2013; 8:e64701. [PMID: 23741374 PMCID: PMC3669384 DOI: 10.1371/journal.pone.0064701] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/17/2013] [Indexed: 11/29/2022] Open
Abstract
Salinibacter ruber is an extremely halophilic member of the Bacteroidetes that thrives in crystallizer ponds worldwide. Here, we have analyzed two sets of 22 and 35 co-occurring S. ruber strains, newly isolated respectively, from 100 microliters water samples from crystalizer ponds in Santa Pola and Mallorca, located in coastal and inland Mediterranean Spain and 350 km apart from each other. A set of old strains isolated from the same setting were included in the analysis. Genomic and taxonomy relatedness of the strains were analyzed by means of PFGE and MALDI-TOF, respectively, while their metabolomic potential was explored with high resolution ion cyclotron resonance Fourier transform mass spectrometry (ICR-FT/MS). Overall our results show a phylogenetically very homogeneous species expressing a very diverse metabolomic pool. The combination of MALDI-TOF and PFGE provides, for the newly isolated strains, the same scenario presented by the previous studies of intra-specific diversity of S. ruber using a more restricted number of strains: the species seems to be very homogeneous at the ribosomal level while the genomic diversity encountered was rather high since no identical genome patterns could be retrieved from each of the samples. The high analytical mass resolution of ICR-FT/MS enabled the description of thousands of putative metabolites from which to date only few can be annotated in databases. Some metabolomic differences, mainly related to lipid metabolism and antibiotic-related compounds, provided enough specificity to delineate different clusters within the co-occurring strains. In addition, metabolomic differences were found between old and new strains isolated from the same ponds that could be related to extended exposure to laboratory conditions.
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Affiliation(s)
- Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Marianna Lucio
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Arantxa Peña
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ana Cifuentes
- Marine Microbiology Group, Departament of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Jocelyn Brito-Echeverría
- Marine Microbiology Group, Departament of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Franco Moritz
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Dimitrios Tziotis
- Helmholtz Zentrum Munich, German Research Center for Environmental Health, Analytical BioGeoChemistry, Neuherberg, Germany
| | - Cristina López
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Departament of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Philippe Schmitt-Kopplin
- Marine Microbiology Group, Departament of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Illes Balears, Spain
- Technische Universität München, Chair of Analytical Food Chemistry, Freising-Weihenstephan, Germany
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Departament of Ecology and Marine Resources, Institut Mediterrani d’Estudis Avançats IMEDEA (CSIC-UIB), Esporles, Illes Balears, Spain
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Oren A. Salinibacter: an extremely halophilic bacterium with archaeal properties. FEMS Microbiol Lett 2013; 342:1-9. [PMID: 23373661 DOI: 10.1111/1574-6968.12094] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 12/17/2022] Open
Abstract
The existence of large number of a member of the Bacteroidetes in NaCl-saturated brines in saltern crystallizer ponds was first documented in 1999 based on fluorescence in situ hybridization studies. Isolation of the organism and its description as Salinibacter ruber followed soon. It is a rod-shaped, red-orange pigmented, extreme halophile that grows optimally at 20-30% salt. The genus is distributed worldwide in hypersaline environments. Today, the genus Salinibacter includes three species, and a somewhat less halophilic relative, Salisaeta longa, has also been documented. Although belonging to the Bacteria, Salinibacter shares many features with the Archaea of the family Halobacteriaceae that live in the same habitat. Both groups use KCl for osmotic adjustment of their cytoplasm, both mainly possess salt-requiring enzymes with a large excess of acidic amino acids, and both contain different retinal pigments: light-driven proton pumps, chloride pumps, and light sensors. Salinibacter produces an unusual carotenoid, salinixanthin that forms a light antenna and transfers energy to the retinal group of xanthorhodopsin, a light-driven proton pump. Other unusual features of Salinibacter and Salisaeta include the presence of novel sulfonolipids (halocapnine derivatives). Salinibacter has become an excellent model for metagenomic, biogeographic, ecological, and evolutionary studies.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Goulitquer S, Potin P, Tonon T. Mass spectrometry-based metabolomics to elucidate functions in marine organisms and ecosystems. Mar Drugs 2012; 10:849-880. [PMID: 22690147 PMCID: PMC3366679 DOI: 10.3390/md10040849] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/13/2012] [Accepted: 03/21/2012] [Indexed: 01/01/2023] Open
Abstract
Marine systems are very diverse and recognized as being sources of a wide range of biomolecules. This review provides an overview of metabolite profiling based on mass spectrometry (MS) approaches in marine organisms and their environments, focusing on recent advances in the field. We also point out some of the technical challenges that need to be overcome in order to increase applications of metabolomics in marine systems, including extraction of chemical compounds from different matrices and data management. Metabolites being important links between genotype and phenotype, we describe added value provided by integration of data from metabolite profiling with other layers of omics, as well as their importance for the development of systems biology approaches in marine systems to study several biological processes, and to analyze interactions between organisms within communities. The growing importance of MS-based metabolomics in chemical ecology studies in marine ecosystems is also illustrated.
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Affiliation(s)
- Sophie Goulitquer
- Plate-forme MetaboMER, CNRS & UPMC, FR2424, Station Biologique, 29680 Roscoff, France
| | - Philippe Potin
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UMR 7139 Marine Plants and Biomolecules, UPMC Univ Paris 6, Station Biologique, 29680 Roscoff, France; (P.P.); (T.T.)
- UMR 7139 Marine Plants and Biomolecules, CNRS, Station Biologique, 29680 Roscoff, France
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Rosselló-Móra R. Towards a taxonomy of Bacteria and Archaea based on interactive and cumulative data repositories. Environ Microbiol 2012; 14:318-34. [PMID: 21958017 DOI: 10.1111/j.1462-2920.2011.02599.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Taxonomy in the second decade of the 21st century is benefiting from technological advances in molecular microbiology, especially those related to genomics. Gene and genome databases are significantly increasing due to intense research activities in the field of molecular ecology and genomics. Taxa, and especially species, are tailored by means of the recognition of a phylogenetic, genomic and phenotypic coherence that reveal their uniqueness in the classification schema. Phylogenetic coherence is mainly revealed by means of 16S rRNA gene analyses for which curated databases such as EzTaxon and LTP provide a valuable tool for tree reconstruction to taxonomy users. On the other hand, in silico full or partial genomic sequence comparisons are called on to substitute cumbersome techniques such as DNA-DNA hybridization (DDH) to genomically circumscribe species. DDH similarity values around 70% would be equivalent to ANI values of 96%. Finally, finding an exclusive phenotypic property for the taxa to be classified is of paramount relevance to producing an operative and predictive classification system. The current methods used for taxonomic classification require significant laboratory experimentation, and generally will not produce interactive databases. The new high-throughput metabolomic technologies, such as ICR-FT and MALDI-TOF mass spectrometry methods, open the door to the construction of metabolic databases for taxonomic purposes. It is to be foreseen that, in the future, taxonomists will benefit significantly from public databases speeding up the classification process. However, serious effort will be needed to harmonize them and to prevent inaccurate material.
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Affiliation(s)
- Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Ecology and Marine Resources, Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), C/Miquel Marqués 21, Esporles, Illes Balears, Spain.
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