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Morandi S, Cremonesi P, Capra E, Silvetti T, Decimo M, Bianchini V, Alves AC, Vargas AC, Costa GM, Ribeiro MG, Brasca M. Molecular typing and differences in biofilm formation and antibiotic susceptibilities among Prototheca strains isolated in Italy and Brazil. J Dairy Sci 2016; 99:6436-6445. [PMID: 27236754 DOI: 10.3168/jds.2016-10900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/19/2016] [Indexed: 11/19/2022]
Abstract
Bovine mastitis caused by Prototheca is a serious and complex problem that accounts for high economic losses in the dairy industry. The main objective of this study was to identify and characterize at genetic level different Prototheca strains and provide the most complete data about protothecal antibiotic resistance. The study involves 46 isolates from Italian (13 strains) and Brazilian (33 strains) mastitic milk. These strains were identified by multiplex PCR and single strand conformation polymorphism analysis and characterized by randomly amplified polymorphic DNA (RAPD)-PCR. Moreover, biofilm production and antibiotic susceptibility were evaluated. Forty-two strains resulted as Prototheca zopfii genotype 2, whereas 4 isolates could belong to a potential new Prototheca species. The RAPD-PCR, performed with 3 primers (M13, OPA-4, and OPA-18), showed a notable heterogeneity among isolates and grouped the strains according to the species and geographical origin. Biofilm production was species-dependent and P. zopfii genotype 2 strains were classified as strong biofilm producers. In vitro antibiotic susceptibility tests indicated that Prototheca strains were susceptible to antibacterial drugs belonging to aminoglycosides group; the highest activity against Prototheca strains was observed in the case of colistin sulfate, gentamicin, and netilmicin (100% of susceptible strains). It is interesting to note that all the Italian P. zopfii genotype 2 strains showed lower minimum inhibitory concentration values than the Brazilian ones. Nisin showed more efficacy than lysozyme and potassium sorbate, inhibiting 31% of the strains. Results obtained in this study confirmed that RAPD-PCR is a rapid, inexpensive, and highly discriminating tool for Prototheca strains characterization and could give a good scientific contribution for better understanding the protothecal mastitis in dairy herd.
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Affiliation(s)
- S Morandi
- Institute of Sciences of Food Production, Italian National Research Council, 20133 Milan, Italy.
| | - P Cremonesi
- Institute of Agricultural Biology and Biotechnology, National Research Council, 26900 Lodi, Italy
| | - E Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council, 26900 Lodi, Italy
| | - T Silvetti
- Institute of Sciences of Food Production, Italian National Research Council, 20133 Milan, Italy
| | - M Decimo
- Institute of Sciences of Food Production, Italian National Research Council, 20133 Milan, Italy
| | - V Bianchini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), 26900 Lodi, Italy
| | - A C Alves
- Department of Veterinary Hygiene and Public Health, Universidade Estadual Paulista (UNESP), 18618-970 Botucatu, SP, Brazil
| | - A C Vargas
- Department of Preventive Veterinary Medicine, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
| | - G M Costa
- Department of Veterinary Medicine, Universidade Federal de Lavras, 37200000, Larvas, MG, Brazil
| | - M G Ribeiro
- Department of Veterinary Hygiene and Public Health, Universidade Estadual Paulista (UNESP), 18618-970 Botucatu, SP, Brazil
| | - M Brasca
- Institute of Sciences of Food Production, Italian National Research Council, 20133 Milan, Italy
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Emami K, Hack E, Nelson A, Brain CM, Lyne FM, Mesbahi E, Day JG, Caldwell GS. Proteomic-based biotyping reveals hidden diversity within a microalgae culture collection: An example using Dunaliella. Sci Rep 2015; 5:10036. [PMID: 25963242 PMCID: PMC4650328 DOI: 10.1038/srep10036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/24/2015] [Indexed: 11/16/2022] Open
Abstract
Accurate and defendable taxonomic identification of microalgae strains is vital for culture collections, industry and academia; particularly when addressing issues of intellectual property. We demonstrate the remarkable effectiveness of Matrix Assisted Laser Desorption Ionisation Time of Flight Mass Spectrometry (MALDI-TOF-MS) biotyping to deliver rapid and accurate strain separation, even in situations where standard molecular tools prove ineffective. Highly distinctive MALDI spectra were obtained for thirty two biotechnologically interesting Dunaliella strains plus strains of Arthrospira, Chlorella, Isochrysis, Tetraselmis and a range of culturable co-occurring bacteria. Spectra were directly compared with genomic DNA sequences (internal transcribed spacer, ITS). Within individual Dunaliella isolates MALDI discriminated between strains with identical ITS sequences, thereby emphasising and enhancing knowledge of the diversity within microalgae culture collections. Further, MALDI spectra did not vary with culture age or growth stage during the course of the experiment; therefore MALDI presents stable and accurate strain-specific signature spectra. Bacterial contamination did not affect MALDI’s discriminating power. Biotyping by MALDI-TOF-MS will prove effective in situations wherein precise strain identification is vital, for example in cases involving intellectual property disputes and in monitoring and safeguarding biosecurity. MALDI should be accepted as a biotyping tool to complement and enhance standard molecular taxonomy for microalgae.
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Affiliation(s)
- Kaveh Emami
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ethan Hack
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST
| | - Chelsea M Brain
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Fern M Lyne
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ehsan Mesbahi
- Faculty of Science, Agriculture and Engineering (SAgE), Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - John G Day
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, PA37 1QA, UK
| | - Gary S Caldwell
- School of Marine Science and Technology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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González MA, Pröschold T, Palacios Y, Aguayo P, Inostroza I, Gómez PI. Taxonomic identification and lipid production of two Chilean Chlorella-like strains isolated from a marine and an estuarine coastal environment. AOB PLANTS 2013; 5:plt020. [PMCID: PMC4104639 DOI: 10.1093/aobpla/plt020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/26/2013] [Indexed: 06/06/2023]
Abstract
This paper emphasizes the value of knowing the correct identity of microalgal strains that may have biotechnological potential. Here, two Chilean small green coccoid referred as Chlorella-like strains were identified using a polyphasic approach. Only one of them corresponded to the genus Chlorella (C. vulgaris); the other belonged to the recently amended genus Chloroidium (C. saccharophilum). Lipids characterization of the biomass obtained from these strains showed that Chlorella vulgaris (Baker strain) appeared to be suitable as raw material for biodiesel production, while Chloroidium saccharophilum (Coliumo strain) would be more appropriate for animal nutrition. The genus Chlorella was the first microalga to be massively cultured as food, feed and as a source of nutraceuticals. More recently, some species have been suggested as candidates for biodiesel production. One of the most difficult tasks in studying the systematics of green coccoids is the identification of species assigned to the genus Chlorella. In the context of several projects carried out by our research group we isolated two Chlorella-like strains from a marine and an estuarine coastal environment in Chile (Coliumo strain and Baker strain, respectively). The main objectives of this research were to identify these Chilean strains—at the species level—and determine and compare their lipid production when cultured under identical conditions. Cell size and shape, autospore number and sizes, and chloroplast and pyrenoid ultrastructure were considered as taxonomic descriptors, and 18S rDNA sequences and internal transcribed spacer ITS-1 + ITS-2 sequences and secondary structure were adopted as phylogenetic tools. The combined use of these morphological, ultrastructural and molecular attributes revealed that only the Baker strain belongs to the genus Chlorella (C. vulgaris), while the Coliumo strain corresponds to the recently amended genus Chloroidium (C. saccharophilum). Lipid characterization of the biomass obtained from these strains showed that Chlorella vulgaris (Baker strain) appears to be suitable as a raw material for biodiesel production, while Chloroidium saccharophilum (Coliumo strain) would be more appropriate for animal nutrition.
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Affiliation(s)
- Mariela A. González
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Thomas Pröschold
- Department of Applied Ecology,University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Yussi Palacios
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Paula Aguayo
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Ingrid Inostroza
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Patricia I. Gómez
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
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Preetha K, John L, Subin CS, Vijayan KK. Phenotypic and genetic characterization of Dunaliella (Chlorophyta) from Indian salinas and their diversity. AQUATIC BIOSYSTEMS 2012; 8:27. [PMID: 23114277 PMCID: PMC3598838 DOI: 10.1186/2046-9063-8-27] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 10/16/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND The genus Dunaliella (Class - Chlorophyceae) is widely studied for its tolerance to extreme habitat conditions, physiological aspects and many biotechnological applications, such as a source of carotenoids and many other bioactive compounds. Biochemical and molecular characterization is very much essential to fully explore the properties and possibilities of the new isolates of Dunaliella. In India, hyper saline lakes and salt pans were reported to bloom with Dunaliella spp. However, except for the economically important D. salina, other species are rarely characterized taxonomically from India. Present study was conducted to describe Dunaliella strains from Indian salinas using a combined morphological, physiological and molecular approach with an aim to have a better understanding on the taxonomy and diversity of this genus from India. RESULTS Comparative phenotypic and genetic studies revealed high level of diversity within the Indian Dunaliella isolates. Species level identification using morphological characteristics clearly delineated two strains of D. salina with considerable β-carotene content (>20 pg/cell). The variation in 18S rRNA gene size, amplified with MA1-MA2 primers, ranged between ~1800 and ~2650 base pairs, and together with the phylogeny based on ITS gene sequence provided a pattern, forming five different groups within Indian Dunaliella isolates. Superficial congruency was observed between ITS and rbcL gene phylogenetic trees with consistent formation of major clades separating Indian isolates into two distinct clusters, one with D. salina and allied strains, and another one with D. viridis and allied strains. Further in both the trees, few isolates showed high level of genetic divergence than reported previously for Dunaliella spp. This indicates the scope of more numbers of clearly defined/unidentified species/sub-species within Indian Dunaliella isolates. CONCLUSION Present work illustrates Indian Dunaliella strains phenotypically and genetically, and confirms the presence of not less than five different species (or sub-species) in Indian saline waters, including D. salina and D. viridis. The study emphasizes the need for a combined morphological, physiological and molecular approach in the taxonomic studies of Dunaliella.
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Affiliation(s)
- Krishna Preetha
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Lijo John
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Cherampillil Sukumaran Subin
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Koyadan Kizhakkedath Vijayan
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
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Isolation and Characterization of Dunaliella Species from Sambhar Lake (India) and its Phylogenetic Position in the Genus Dunaliella Using 18S rDNA. NATIONAL ACADEMY SCIENCE LETTERS-INDIA 2012. [DOI: 10.1007/s40009-012-0038-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Jayappriyan KR, Rajkumar R, Rengasamy R. Unusual occurrence of non carotenogenic strains of Dunaliella bardawil and Dunaliella parva in India. J Basic Microbiol 2011; 51:473-83. [DOI: 10.1002/jobm.201000384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 02/04/2011] [Indexed: 11/11/2022]
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Hejazi MA, Barzegari A, Gharajeh NH, Hejazi MS. Introduction of a novel 18S rDNA gene arrangement along with distinct ITS region in the saline water microalga Dunaliella. SALINE SYSTEMS 2010; 6:4. [PMID: 20377865 PMCID: PMC2867797 DOI: 10.1186/1746-1448-6-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 04/08/2010] [Indexed: 11/10/2022]
Abstract
Comparison of 18S rDNA gene sequences is a very promising method for identification and classification of living organisms. Molecular identification and discrimination of different Dunaliella species were carried out based on the size of 18S rDNA gene and, number and position of introns in the gene. Three types of 18S rDNA structure have already been reported: the gene with a size of ~1770 bp lacking any intron, with a size of ~2170 bp consisting one intron near 5' terminus, and with a size of ~2570 bp harbouring two introns near 5' and 3' termini. Hereby, we report a new 18S rDNA gene arrangement in terms of intron localization and nucleotide sequence in a Dunaliella isolated from Iranian salt lakes (ABRIINW-M1/2). PCR amplification with genus-specific primers resulted in production of a ~2170 bp DNA band, which is similar to that of D. salina 18S rDNA gene containing only one intron near 5' terminus. Whilst, sequence composition of the gene revealed the lack of any intron near 5' terminus in our isolate. Furthermore, another alteration was observed due to the presence of a 440 bp DNA fragment near 3' terminus. Accordingly, 18S rDNA gene of the isolate is clearly different from those of D. salina and any other Dunaliella species reported so far. Moreover, analysis of ITS region sequence showed the diversity of this region compared to the previously reported species. 18S rDNA and ITS sequences of our isolate were submitted with accesion numbers of EU678868 and EU927373 in NCBI database, respectively. The optimum growth rate of this isolate occured at the salinity level of 1 M NaCl. The maximum carotenoid content under stress condition of intense light (400 mumol photon m-2 s-1), high salinity (4 M NaCl) and deficiency of nitrate and phosphate nutritions reached to 240 ng/cell after 15 days.
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Affiliation(s)
- Mohammad A Hejazi
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
| | - Abolfazl Barzegari
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
| | - Nahid Hosseinzadeh Gharajeh
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
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Metfies K, Medlin L. Ribosomal RNA probes and microarrays: their potential use in assessing microbial biodiversity. Methods Enzymol 2005; 395:258-78. [PMID: 15865972 DOI: 10.1016/s0076-6879(05)95016-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The awareness that global biological diversity is affected by numerous, mostly human-made threats has made biodiversity assessment an important scientific issue for decades. Biodiversity includes different levels of complexity, such as community diversity, habitat diversity, genetic diversity, and species diversity. The application of molecular methods to answer ecological questions permits issues of biodiversity to be addressed at all levels. Microorganisms dominate global biological diversity in terms of their species numbers. However, their small size and limited morphological features make it challenging to obtain a comprehensive view of their biodiversity. The application of ribosomal RNA (rRNA) probes contributes significantly to the assessment of biodiversity at the molecular level. DNA microarrays offer a great potential to facilitate the application of molecular probes and other DNA analytical methods to answer ecological and biodiversity questions. We provide an introduction into the application of rRNA probes and DNA microarrays for the assessment of microbial biodiversity, as well as protocols for the implementation of DNA microarrays.
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Affiliation(s)
- Katja Metfies
- Alfred Wegener Institute, D-27570 Bremerhaven, Germany
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