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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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Moldes AB, Álvarez-Chaver P, Vecino X, Cruz JM. Purification of lipopeptide biosurfactant extracts obtained from a complex residual food stream using Tricine-SDS-PAGE electrophoresis. Front Bioeng Biotechnol 2023; 11:1199103. [PMID: 37346790 PMCID: PMC10280073 DOI: 10.3389/fbioe.2023.1199103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/29/2023] [Indexed: 06/23/2023] Open
Abstract
Protocols to identify lipopeptide biosurfactant extracts contained in complex residual streams are very important, as fermented agri-food matrices are potential sources of these valuable compounds. For instance, corn steep liquor (CSL), a secondary stream of the corn wet-milling industry, is composed of a mixture of microbial metabolites, produced during the corn steeping process, and other natural metabolites released from corn, that can interfere with the purification and analysis of lipopeptides. Electrophoresis could be an interesting technique for the purification and further characterization of lipopeptide biosurfactant extracts contained in secondary residual streams like CSL, but there is little existing literature about it. It is necessary to consider that lipopeptide biosurfactants, like Surfactin, usually are substances that are poorly soluble in water at acidic or neutral pH, forming micelles what can inhibit their separation by electrophoresis. In this work, two lipopeptide biosurfactant extracts obtained directly from CSL, after liquid-liquid extraction with chloroform or ethyl acetate, were purified by applying a second liquid extraction with ethanol. Following that, ethanolic biosurfactant extracts were subjected to electrophoresis under different conditions. Lipopeptides on Tricine-SDS-PAGE (polyacrylamide gels) were better visualized and identified by fluorescence using SYPRO Ruby dye than using Coomassie blue dye. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of lipopeptide isoforms separated by electrophoresis revealed the presence of masses at 1,044, 1,058, and 1,074 m/z, concluding that Tricine-SDS-PAGE electrophoresis combined with MALDI-TOF-MS could be a useful tool for purifying and identifying lipopeptides in complex matrices.
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Affiliation(s)
- A. B. Moldes
- CINTECX (Research Center in Technologies, Energy and Industrial Processes), Chemical Engineering Department, University of Vigo, Vigo, Spain
| | - P. Álvarez-Chaver
- CACTI (Centro de Apoyo Científico y Tecnológico a la Investigación), Structural Determination and Proteomics Service, University of Vigo, Vigo, Spain
| | - X. Vecino
- CINTECX (Research Center in Technologies, Energy and Industrial Processes), Chemical Engineering Department, University of Vigo, Vigo, Spain
| | - J. M. Cruz
- CINTECX (Research Center in Technologies, Energy and Industrial Processes), Chemical Engineering Department, University of Vigo, Vigo, Spain
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Platt GA, Davis KJ, Schweitzer HD, Smith HJ, Fields MW, Barnhart EP, Gerlach R. Algal amendment enhances biogenic methane production from coals of different thermal maturity. Front Microbiol 2023; 14:1097500. [PMID: 36970672 PMCID: PMC10036379 DOI: 10.3389/fmicb.2023.1097500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/12/2023] Open
Abstract
The addition of small amounts of algal biomass to stimulate methane production in coal seams is a promising low carbon renewable coalbed methane enhancement technique. However, little is known about how the addition of algal biomass amendment affects methane production from coals of different thermal maturity. Here, we show that biogenic methane can be produced from five coals ranging in rank from lignite to low-volatile bituminous using a coal-derived microbial consortium in batch microcosms with and without algal amendment. The addition of 0.1 g/l algal biomass resulted in maximum methane production rates up to 37 days earlier and decreased the time required to reach maximum methane production by 17–19 days when compared to unamended, analogous microcosms. Cumulative methane production and methane production rate were generally highest in low rank, subbituminous coals, but no clear association between increasing vitrinite reflectance and decreasing methane production could be determined. Microbial community analysis revealed that archaeal populations were correlated with methane production rate (p = 0.01), vitrinite reflectance (p = 0.03), percent volatile matter (p = 0.03), and fixed carbon (p = 0.02), all of which are related to coal rank and composition. Sequences indicative of the acetoclastic methanogenic genus Methanosaeta dominated low rank coal microcosms. Amended treatments that had increased methane production relative to unamended analogs had high relative abundances of the hydrogenotrophic methanogenic genus Methanobacterium and the bacterial family Pseudomonadaceae. These results suggest that algal amendment may shift coal-derived microbial communities towards coal-degrading bacteria and CO2-reducing methanogens. These results have broad implications for understanding subsurface carbon cycling in coal beds and the adoption of low carbon renewable microbially enhanced coalbed methane techniques across a diverse range of coal geology.
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Affiliation(s)
- George A. Platt
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Chemical and Biological Engineering, Montana State University-Bozeman, Bozeman, MT, United States
| | - Katherine J. Davis
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Chemical and Biological Engineering, Montana State University-Bozeman, Bozeman, MT, United States
| | - Hannah D. Schweitzer
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Microbiology and Immunology, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Heidi J. Smith
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
| | - Matthew W. Fields
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Microbiology and Immunology, Montana State University-Bozeman, Bozeman, MT, United States
| | - Elliott P. Barnhart
- United States Geological Survey, Montana Water Science Center, Helena, MT, United States
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- Department of Chemical and Biological Engineering, Montana State University-Bozeman, Bozeman, MT, United States
- *Correspondence: Robin Gerlach,
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Combining OSMAC Approach and Untargeted Metabolomics for the Identification of New Glycolipids with Potent Antiviral Activity Produced by a Marine Rhodococcus. Int J Mol Sci 2021; 22:ijms22169055. [PMID: 34445761 PMCID: PMC8396431 DOI: 10.3390/ijms22169055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 11/22/2022] Open
Abstract
Natural products of microbial origin have inspired most of the commercial pharmaceuticals, especially those from Actinobacteria. However, the redundancy of molecules in the discovery process represents a serious issue. The untargeted approach, One Strain Many Compounds (OSMAC), is one of the most promising strategies to induce the expression of silent genes, especially when combined with genome mining and advanced metabolomics analysis. In this work, the whole genome of the marine isolate Rhodococcus sp. I2R was sequenced and analyzed by antiSMASH for the identification of biosynthetic gene clusters. The strain was cultivated in 22 different growth media and the generated extracts were subjected to metabolomic analysis and functional screening. Notably, only a single growth condition induced the production of unique compounds, which were partially purified and structurally characterized by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). This strategy led to identifying a bioactive fraction containing >30 new glycolipids holding unusual functional groups. The active fraction showed a potent antiviral effect against enveloped viruses, such as herpes simplex virus and human coronaviruses, and high antiproliferative activity in PC3 prostate cancer cell line. The identified compounds belong to the biosurfactants class, amphiphilic molecules, which play a crucial role in the biotech and biomedical industry.
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Draft genome sequence and potential identification of a biosurfactant from Brevibacterium casei strain LS14 an isolate from fresh water Loktak Lake. 3 Biotech 2021; 11:326. [PMID: 34194910 DOI: 10.1007/s13205-021-02867-9] [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: 10/24/2020] [Accepted: 05/31/2021] [Indexed: 10/21/2022] Open
Abstract
This study reports the whole-genome sequencing and sequence analysis of a bacterial isolate Brevibacterium casei strain LS14, isolated from Loktak Lake, Imphal, India. The de novo assembled genome reported in this paper featured a size of 3,809,532 bp, has GC content of 68% and contains 3602 genomic features, including 3551 protein-coding genes, 46 tRNA and 5rRNA. A biosurfactant biosynthesis gene cluster in the genome of the isolated strain was identified using AntiSMASH online tool V3.0.5 and KAAS (KEGG Automatic Annotation Server). The presence of biosurfactant was demonstrated by drop collapse, oil displacement and emulsification index. Subsequent chemical characterization using FTIR and LC-MS analyses revealed surfactin and terpene containing biosurfactant moieties. Also, the presence of genes involved in terpenoid synthesis pathway in the genome sequence may account for biosurfactant terpenoid backbone, but genes for later-stage conversion of terpenoid to biosurfactant were not ascertained. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02867-9.
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Ibrahim S, Abdul Khalil K, Zahri KNM, Gomez-Fuentes C, Convey P, Zulkharnain A, Sabri S, Alias SA, González-Rocha G, Ahmad SA. Biosurfactant Production and Growth Kinetics Studies of the Waste Canola Oil-Degrading Bacterium Rhodococcus erythropolis AQ5-07 from Antarctica. Molecules 2020; 25:E3878. [PMID: 32858796 PMCID: PMC7503493 DOI: 10.3390/molecules25173878] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/26/2022] Open
Abstract
With the progressive increase in human activities in the Antarctic region, the possibility of domestic oil spillage also increases. Developing means for the removal of oils, such as canola oil, from the environment and waste "grey" water using biological approaches is therefore desirable, since the thermal process of oil degradation is expensive and ineffective. Thus, in this study an indigenous cold-adapted Antarctic soil bacterium, Rhodococcus erythropolis strain AQ5-07, was screened for biosurfactant production ability using the multiple approaches of blood haemolysis, surface tension, emulsification index, oil spreading, drop collapse and "MATH" assay for cellular hydrophobicity. The growth kinetics of the bacterium containing different canola oil concentration was studied. The strain showed β-haemolysis on blood agar with a high emulsification index and low surface tension value of 91.5% and 25.14 mN/m, respectively. Of the models tested, the Haldane model provided the best description of the growth kinetics, although several models were similar in performance. Parameters obtained from the modelling were the maximum specific growth rate (qmax), concentration of substrate at the half maximum specific growth rate, Ks% (v/v) and the inhibition constant Ki% (v/v), with values of 0.142 h-1, 7.743% (v/v) and 0.399% (v/v), respectively. These biological coefficients are useful in predicting growth conditions for batch studies, and also relevant to "in field" bioremediation strategies where the concentration of oil might need to be diluted to non-toxic levels prior to remediation. Biosurfactants can also have application in enhanced oil recovery (EOR) under different environmental conditions.
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Affiliation(s)
- Salihu Ibrahim
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.I.); (K.N.M.Z.)
| | - Khalilah Abdul Khalil
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam, Selangor 40450, Malaysia;
| | - Khadijah Nabilah Mohd Zahri
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.I.); (K.N.M.Z.)
| | - Claudio Gomez-Fuentes
- Department of Chemical Engineering, Universidad de Magallanes, Avda. Bulnes 01855, Punta Arenas, Región de Magallanes y Antártica Chilena, Chile;
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of system Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama 337-8570, Japan;
| | - Suriana Sabri
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Siti Aisyah Alias
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
- Institute of Ocean and Earth Sciences, Universiti Malaya, B303 Level 3, Block B, Lembah Pantai, Kuala Lumpur 50603, Malaysia
| | - Gerardo González-Rocha
- Laboratorio de Investigacion en Agentes Antibacterianos, Facultad de Ciencias Biologicas, Universidad de Concepcion, Concepcion 4070386, Chile;
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.I.); (K.N.M.Z.)
- National Antarctic Research Centre, B303 Level 3, Block B, IPS Building, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
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Habib S, Ahmad SA, Wan Johari WL, Abd Shukor MY, Alias SA, Smykla J, Saruni NH, Abdul Razak NS, Yasid NA. Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus. Int J Mol Sci 2020; 21:ijms21176138. [PMID: 32858859 PMCID: PMC7504157 DOI: 10.3390/ijms21176138] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/19/2022] Open
Abstract
Rhodococci are renowned for their great metabolic repertoire partly because of their numerous putative pathways for large number of specialized metabolites such as biosurfactant. Screening and genome-based assessment for the capacity to produce surface-active molecules was conducted on Rhodococcus sp. ADL36, a diesel-degrading Antarctic bacterium. The strain showed a positive bacterial adhesion to hydrocarbon (BATH) assay, drop collapse test, oil displacement activity, microplate assay, maximal emulsification index at 45% and ability to reduce water surface tension to < 30 mN/m. The evaluation of the cell-free supernatant demonstrated its high stability across the temperature, pH and salinity gradient although no correlation was found between the surface and emulsification activity. Based on the positive relationship between the assessment of macromolecules content and infrared analysis, the extracted biosurfactant synthesized was classified as a lipopeptide. Prediction of the secondary metabolites in the non-ribosomal peptide synthetase (NRPS) clusters suggested the likelihood of the surface-active lipopeptide production in the strain’s genomic data. This is the third report of surface-active lipopeptide producers from this phylotype and the first from the polar region. The lipopeptide synthesized by ADL36 has the prospect to be an Antarctic remediation tool while furnishing a distinctive natural product for biotechnological application and research.
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Affiliation(s)
- Syahir Habib
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Wan Lutfi Wan Johari
- Department of Environment, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Mohd Yunus Abd Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308 Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Jerzy Smykla
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120 Kraków, Poland;
| | - Nurul Hani Saruni
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Syafiqah Abdul Razak
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
- Correspondence: ; Tel.: +603-9769-8297
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Exploiting the Natural Diversity of RhlA Acyltransferases for the Synthesis of the Rhamnolipid Precursor 3-(3-Hydroxyalkanoyloxy)Alkanoic Acid. Appl Environ Microbiol 2020; 86:AEM.02317-19. [PMID: 31924623 PMCID: PMC7054101 DOI: 10.1128/aem.02317-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
While rhamnolipids of the Pseudomonas aeruginosa type are commercially available, the natural diversity of rhamnolipids and their origin have barely been investigated. Here, we collected known and identified new rhlA genes encoding the acyltransferase responsible for the synthesis of the lipophilic rhamnolipid precursor 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA). Generally, all homologs were found in Betaproteobacteria and Gammaproteobacteria A likely horizontal gene transfer event into Actinobacteria is the only identified exception. The phylogeny of the RhlA homologs from Pseudomonas and Burkholderia species is consistent with the organism phylogeny, and genes involved in rhamnolipid synthesis are located in operons. In contrast, RhlA homologs from the Enterobacterales do not follow the organisms' phylogeny but form their own branch. Furthermore, in many Enterobacterales and Halomonas from the Oceanospirillales, an isolated rhlA homolog can be found in the genome. The RhlAs from Pseudomonas aeruginosa PA01, Pseudomonas fluorescens LMG 05825, Pantoea ananatis LMG 20103, Burkholderia plantarii PG1, Burkholderia ambifaria LMG 19182, Halomonas sp. strain R57-5, Dickeya dadantii Ech586, and Serratia plymuthica PRI-2C were expressed in Escherichia coli and tested for HAA production. Indeed, except for the Serratia RhlA, HAAs were produced with the engineered strains. A detailed analysis of the produced HAA congeners by high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) highlights the congener specificity of the RhlA proteins. The congener length varies from 4 to 18 carbon atoms, with the main congeners consisting of different combinations of saturated or monounsaturated C10, C12, and C14 fatty acids. The results are discussed in the context of the phylogeny of this unusual enzymatic activity.IMPORTANCE The RhlA specificity explains the observed differences in 3-(3-hydroxyalkanoyloxy)alkanoic acid (HAA) congeners. Whole-cell catalysts can now be designed for the synthesis of different congener mixtures of HAAs and rhamnolipids, thereby contributing to the envisaged synthesis of designer HAAs.
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Novel PCB-degrading Rhodococcus strains able to promote plant growth for assisted rhizoremediation of historically polluted soils. PLoS One 2019; 14:e0221253. [PMID: 31437185 PMCID: PMC6705854 DOI: 10.1371/journal.pone.0221253] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/04/2019] [Indexed: 12/28/2022] Open
Abstract
Extended soil contamination by polychlorinated biphenyls (PCBs) represents a global environmental issue that can hardly be addressed with the conventional remediation treatments. Rhizoremediation is a sustainable alternative, exploiting plants to stimulate in situ the degradative bacterial communities naturally occurring in historically polluted areas. This approach can be enhanced by the use of bacterial strains that combine PCB degradation potential with the ability to promote plant and root development. With this aim, we established a collection of aerobic bacteria isolated from the soil of the highly PCB-polluted site “SIN Brescia-Caffaro” (Italy) biostimulated by the plant Phalaris arundinacea. The strains, selected on biphenyl and plant secondary metabolites provided as unique carbon source, were largely dominated by Actinobacteria and a significant number showed traits of interest for remediation, harbouring genes homologous to bphA, involved in the PCB oxidation pathway, and displaying 2,3-catechol dioxygenase activity and emulsification properties. Several strains also showed the potential to alleviate plant stress through 1-aminocyclopropane-1-carboxylate deaminase activity. In particular, we identified three Rhodococcus strains able to degrade in vitro several PCB congeners and to promote lateral root emergence in the model plant Arabidopsis thaliana in vivo. In addition, these strains showed the capacity to colonize the root system and to increase the plant biomass in PCB contaminated soil, making them ideal candidates to sustain microbial-assisted PCB rhizoremediation through a bioaugmentation approach.
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Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
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Tischler D, van Berkel WJH, Fraaije MW. Editorial: Actinobacteria, a Source of Biocatalytic Tools. Front Microbiol 2019; 10:800. [PMID: 31040839 PMCID: PMC6477052 DOI: 10.3389/fmicb.2019.00800] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dirk Tischler
- Microbial Biotechnology, Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Marco W Fraaije
- Molecular Enzymology, University of Groningen, Groningen, Netherlands
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Waghmode S, Suryavanshi M, Dama L, Kansara S, Ghattargi V, Das P, Banpurkar A, Satpute SK. Genomic Insights of Halophilic Planococcus maritimus SAMP MCC 3013 and Detail Investigation of Its Biosurfactant Production. Front Microbiol 2019; 10:235. [PMID: 30863371 PMCID: PMC6399143 DOI: 10.3389/fmicb.2019.00235] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/28/2019] [Indexed: 01/02/2023] Open
Abstract
Moderate halophilic bacteria thrive in saline conditions and produce biosurfactant (BS) which facilitates the oil scavenging activity in the oil polluted surroundings. Production of such unusual bioactive molecules plays a vital role for their survival in an extreme and adverse environment. Current research deals with isolation of Planococcus maritimus strain SAMP MCC 3013 from Indian Arabian coastline sea water for BS production. The bacterium tolerated up to 2.7 M NaCl demonstrating osmotic stress bearable physiological systems. We used integrated approach to explore the genomic insight of the strain SAMP and displayed the presence of gene for BS biosynthesis. The genome analysis revealed this potential to be intrinsic to the strain. Preliminary screening techniques viz., surface tension (SFT), drop collapse (DC) and oil displacement (OD) showed SAMP MCC 3013 as a potent BS producer. BS reduced SFT of phosphate buffer saline (PBS) pH: 7.0 from 72 to 30 mN/m with a critical micelle concentration (CMC) value of 1.3 mg/mL. Subsequent investigation on chemical characterization, using thin layer chromatography (TLC), Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (1H NMR and 13C NMR) and liquid chromatography mass spectrometry (LC-MS) revealed terpene containing BS having sugar, lipid moieties. The genomic sequence analysis of P. maritimus SAMP showed complete genes in the pathway for the synthesis of terpenoid. Probably terpenoid is the accountable backbone molecule for the BS production, but the later stages of terpenoid conversion to the BS could not be found. Moreover, it is important to highlight that till today; no single report documents the in-detailed physico-chemical characterization of BS from Planococcus sp. Based on genomic and functional properties, the term terpene containing BS is denoted for the surfactant produced by P. maritimus.
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Affiliation(s)
- Samadhan Waghmode
- Department of Microbiology, Elphinstone College, University of Mumbai, Mumbai, India
| | - Mangesh Suryavanshi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Laxmikant Dama
- Department of Zoology, DBF Dayanand College, University of Solapur, Solapur, India
| | - Shraddha Kansara
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Vikas Ghattargi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Parijat Das
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Arun Banpurkar
- Department of Physics, Savitribai Phule Pune University, Pune, India
| | - Surekha K. Satpute
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
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Patel S, Homaei A, Patil S, Daverey A. Microbial biosurfactants for oil spill remediation: pitfalls and potentials. Appl Microbiol Biotechnol 2018; 103:27-37. [DOI: 10.1007/s00253-018-9434-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
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14
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Bernardin-Souibgui C, Barraud S, Bourgeois E, Aubin JB, Becouze-Lareure C, Wiest L, Marjolet L, Colinon C, Lipeme Kouyi G, Cournoyer B, Blaha D. Incidence of hydrological, chemical, and physical constraints on bacterial pathogens, Nocardia cells, and fecal indicator bacteria trapped in an urban stormwater detention basin in Chassieu, France. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:24860-24881. [PMID: 29931635 DOI: 10.1007/s11356-018-1994-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
The nature and fate of urban contaminants washed by stormwater events and accumulating in a detention basin (DB) were investigated. Relations between bacterial and chemical contaminants of trapped urban sediments, and field parameters were analyzed. Fecal indicators and some pathogens known to be environmentally transmitted (Nocardia, Pseudomonas aeruginosa, and Aeromonas caviae) were tracked, and their persistence investigated. Six sampling campaigns were carried out over 3 years, using five sites including a settling chamber (SC). Aerosolized bacteria at these sites were also monitored. Deposits in the basin were made of fine particles and their content in chemical pollutants was found highly variable. High polycyclic aromatic hydrocarbon (PAH) contents were measured but only three pesticides, over 22, were detected. Deposits were significantly contaminated by fecal indicator bacteria (FIB), P. aeruginosa, A. caviae, and by Nocardia. Only A. caviae showed significant numbers in aerosolized particles recovered over the detention basin. Nocardia spp. cells heavily contaminated the SC. The efficacy of the detention basin at reducing bacterial counts per rain event and over time were estimated. A slight drop in the counts was monitored for fecal indicators but not for the other bacterial groups. Hydrodynamic parameters had a strong impact on the distribution and features of the deposits. Multiple factors impacted the fate of FIB, P. aeruginosa, A. caviae, and Nocardia cells, but in a group dependent manner. Nocardia counts were found positively correlated with volatile organic matter. FIB appeared highly efficient colonizers of the DB.
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Affiliation(s)
- Claire Bernardin-Souibgui
- Université de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France
| | - Sylvie Barraud
- Université de Lyon, Lyon, France
- DEEP, INSA Lyon, 34 avenue des Arts, 69621, Villeurbanne cedex, France
| | - Emilie Bourgeois
- Université de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France
| | - Jean-Baptiste Aubin
- Université de Lyon, Lyon, France
- DEEP, INSA Lyon, 34 avenue des Arts, 69621, Villeurbanne cedex, France
- Institut Camille-Jordan UMR CNRS 5208, INSA Lyon - Bâtiment Léonard de Vinci, 69621, Villeurbanne cedex, France
| | - Celine Becouze-Lareure
- Université de Lyon, Lyon, France
- DEEP, INSA Lyon, 34 avenue des Arts, 69621, Villeurbanne cedex, France
| | - Laure Wiest
- Institut des Sciences Analytiques, CNRS 5280, Université Lyon 1, ENS Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Laurence Marjolet
- Université de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France
| | - Celine Colinon
- Université de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France
| | - Ghislain Lipeme Kouyi
- Université de Lyon, Lyon, France
- DEEP, INSA Lyon, 34 avenue des Arts, 69621, Villeurbanne cedex, France
| | - Benoit Cournoyer
- Université de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France
| | - Didier Blaha
- Université de Lyon, Lyon, France.
- UMR Ecologie Microbienne, CNRS 5557, INRA 1418, VetAgro Sup, Research group on "Bacterial Opportunistic Pathogens and Environment", Université Lyon I, 8 avenue Rockefeller, 69373, Lyon, France.
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15
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Lamilla C, Braga D, Castro R, Guimarães C, V. A. de Castilho L, Freire DMG, Barrientos L. Streptomyces luridus So3.2 from Antarctic soil as a novel producer of compounds with bioemulsification potential. PLoS One 2018; 13:e0196054. [PMID: 29684071 PMCID: PMC5912782 DOI: 10.1371/journal.pone.0196054] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/05/2018] [Indexed: 11/18/2022] Open
Abstract
The present study aimed to identify novel microbial producers of bioemulsificant compounds from Antarctic soils. Fifty-nine microbial strains were isolated from five different locations at South Shetland Islands, Antarctica, and screened for biosurfactant production by β-hemolytic activity. Strain So 3.2 was determined as bioemulsifier-producer and identified by phenotypic and molecular characterization as Streptomyces luridus. Emulsification activity, oil displacement method and drop-collapsing test were performed to evaluate the biosurfactant activity with different oils and hydrocarbons using two different culture media (Luria Bertani and Bushnell Haas in the presence of different carbon sources: glucose, glycerol, olive oil and n-Hexadecane). Cell free supernatant of Bushnell Haas culture supplemented with n-Hexadecane showed the best results for all tests. Emulsification of hydrocarbons exceeded 60%, reaching up to 90% on oil with high API grade, while displacement tests ranged from 8 cm to 4 cm in diameter according the culture media and tested oils. Our results revealed that Streptomyces luridus So3.2 is able to produce bioemulsifiers capable of emulsifying hydrocarbons and oils, which could be used in different biotechnological applications, particularly for bioremediation of environments contaminated by oil leaks.
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Affiliation(s)
- Claudio Lamilla
- Laboratory of Applied Molecular Biology, Center of Excellence in Translational Medicine, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Douglas Braga
- Laboratório de Biotecnologia Microbiana, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro RJ, Brasil
| | - Rui Castro
- Laboratório de Biotecnologia Microbiana, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro RJ, Brasil
| | - Carolina Guimarães
- Laboratório de Biotecnologia Microbiana, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro RJ, Brasil
| | - Livia V. A. de Castilho
- Laboratório de Biotecnologia Microbiana, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro RJ, Brasil
| | - Denise M. G. Freire
- Laboratório de Biotecnologia Microbiana, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro RJ, Brasil
- * E-mail: (LB); (DMGF)
| | - Leticia Barrientos
- Laboratory of Applied Molecular Biology, Center of Excellence in Translational Medicine, Temuco, Chile
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
- * E-mail: (LB); (DMGF)
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16
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Götze S, Herbst-Irmer R, Klapper M, Görls H, Schneider KRA, Barnett R, Burks T, Neu U, Stallforth P. Structure, Biosynthesis, and Biological Activity of the Cyclic Lipopeptide Anikasin. ACS Chem Biol 2017; 12:2498-2502. [PMID: 28846366 DOI: 10.1021/acschembio.7b00589] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The class of cyclic lipopeptide natural products consists of compounds with a diverse range of bioactivities. In this study, we elucidated the structure of the cyclic lipopeptide anikasin using X-ray crystallography, analyzed its biosynthetic gene cluster, and investigated its natural role in the interaction between the producer strain Pseudomonas fluorescens HKI0770 and protozoal predators. These results led to the conclusion that anikasin has dual functionality enabling swarming motility and acting as a niche amoebicide, which effectively inhibits the social amoeba Polysphondylium violaceum and protects the producer strain from protozoal grazing.
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Affiliation(s)
- Sebastian Götze
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Regine Herbst-Irmer
- Universität Göttingen, Insitute of Inorganic Chemistry, Tammannstraße 4, 37077 Göttingen, Germany
| | - Martin Klapper
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Helmar Görls
- Friedrich-Schiller-Universität Jena, Institute for Inorganic and Analytical
Chemistry, Humboldtstraße
8, 07743 Jena, Germany
| | - Kilian R. A. Schneider
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Robert Barnett
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Thomas Burks
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ursula Neu
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Arnimallee 22, 14195 Berlin, Germany
| | - Pierre Stallforth
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Junior Research Group Chemistry of Microbial Communication, Beutenbergstraße 11a, 07745 Jena, Germany
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17
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Rahman PKSM, Randhawa KKS. Editorial: Microbiotechnology Based Surfactants and Their Applications. Front Microbiol 2015; 6:1344. [PMID: 26648924 PMCID: PMC4664617 DOI: 10.3389/fmicb.2015.01344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Affiliation(s)
- Pattanathu K S M Rahman
- School of Science and Engineering, Technology Futures Institute, Teesside University Middlesbrough, UK
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18
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Kügler JH, Muhle-Goll C, Hansen SH, Völp AR, Kirschhöfer F, Kühl B, Brenner-Weiss G, Luy B, Syldatk C, Hausmann R. Glycolipids produced by Rouxiella sp. DSM 100043 and isolation of the biosurfactants via foam-fractionation. AMB Express 2015; 5:82. [PMID: 26698314 PMCID: PMC4689721 DOI: 10.1186/s13568-015-0167-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/11/2015] [Indexed: 11/10/2022] Open
Abstract
Microorganisms produce a great variety of secondary metabolites that feature surface active and bioactive properties. Those possessing an amphiphilc molecular structure are also termed biosurfactant and are of great interest due to their often unique properties. Rouxiella sp. DSM 100043 is a gram negative enterobacter isolated from peat-bog soil and described as a new biosurfactant producing species in this study. Rouxiella sp. produces glycolipids, biosurfactants with a carbohydrate moiety in its structure. This study characterizes the composition of glycolipids with different hydrophobicities that have been produced during cultivation in a bioreactor and been extracted and purified from separated foam. Using two dimensional nuclear magnetic resonance spectroscopy, the hydrophilic moieties are elucidated as glucose with various acylation sites and as talose within the most polar glycolipids. The presence of 3′ hydroxy lauroleic acid as well as myristic and myristoleic acid has been detected.
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