Kültürden bağımsız metotlarla aydın ili ve çevresindeki sıcak su kaynaklarında siyanobakteri çeşitliliğin belirlenmesi

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dc.contributor.advisor	Başbülbül, Gamze
dc.contributor.author	Phiri, Ruth Maseko
dc.date.accessioned	2021-11-26T07:21:03Z
dc.date.available	2021-11-26T07:21:03Z
dc.date.issued	2021-11-04
dc.date.submitted	2021-09-14
dc.identifier.citation	Phiri, R. M. (2021) Kültürden bağımsız metotlarla aydın ili ve çevresindeki sıcak su kaynaklarında siyanobakteri çeşitliliğin belirlenmesi (yayınlanmamış yüksek lisans tezi) Aydın Adnan Menderes Üniversitesi Fen Bilimleri Enstitüsü, Aydın	tr_TR
dc.identifier.uri	http://hdl.handle.net/11607/4500
dc.description.abstract	Amaç: Bu tezin amacı, Aydın ili ve çevresindeki kaplıcalardan kültürden bağımsız yöntemlerle siyanobakteri çeşitliliğini belirlemektir. Materyal ve Metodlar: Toplam genomik DNA'lar su, çamur veya toprak örneklerinden izole edildi ve ekstrakte edilmiş çevresel DNA'lardan 16S rDNA genleri PCR yöntemi ile amplifiye edildi. Amplikonlar daha sonra E.coli hücrelerine klonlandı, mavi-beyaz koloniler arasından transforme olmuş beyaz koloniler seçildi ve M13 primerleri kullanılarak PCR reaksiyonları yapıldı. M13 PCR ile elde edilen amplikonlar dizilendi ve GenBank veri tabanında BLAST analizine göre diğer bakteriyal gruplar ile olan homolojiler belirlendi. Bulgular: Klonlama sonucu elde edilen fragmanların toplam sayısı 298 olup, yapılan sekans analizi sonucunda 201 tanesinin siyanobakteriler ile, 97 tanesinin ise diğer bakteriyal filumlar ile en yüksek homolojileri gösterdikleri belirlenmiştir. BLAST analizi sonucu bulunan yüzde özdeşlik %78 ila %100 aralığındadır. En sık tespit edilen taksonlar, Planktothricoides raciborskii, Trichocoleus desertorum, Spirulina subsalsa, Gleobacter violaceus, Leptolyngbya laminosa, Synechococcus sp. ve Alkalima pantanalense olarak belirlenmiştir. Sonuç: Çalışmamız, Türkiye'de Aydın İli ve çevresindeki termal ortamlardan termofilik siyanobakterilerin belirlenmesinde kültürden bağımsız bir yaklaşım içermesi açısından önemlidir ve ekstrem habitatlardaki siyanobakteri araştırmalarına yeni bakış açıları sağlayabilir	tr_TR
dc.description.abstract	Objectives: The thesis’s objectives were to determine the cyanobacterial diversity from hot springs around Aydın province and surrounding using culture independent methods. Material and Methods: Total genomic DNAs were isolated from water, mud or soil samples and 16S rDNA genes were amplified from extracted environmental DNAs. Amplicons were then cloned into E.coli cells, transformed cells were chosen and PCR reactions were done using M13 primers. Amplicons obtained by M13 PCR, were sequenced and according to BLAST analyses homologies were determined in GenBank database. Results: In this study we highlighted the Cyanobacterial diversity of hot springs in Aydın and its surroundings using culture independent methods as well as cloning of PCR amplified fragments of 16S rRNA genes. The total number of cloned colonies were 298 of which 201 belonged to Cyanobacteria phylum while 97 other phylum and the percentage identity found were in the range of 78% to 100%. Most abundant species detected were, Planktothricoides raciborskii, Trichocoleus desertorum, Spirulina subsalsa, Gleobacter violaceus, Leptolyngbya laminosa, Synechococcus sp. and Alkalinema pantanalense. Conclusion: Our study is important for being first culture- independent approach to determine thermophilic cyanobacteria from thermal environments in Aydın Province and surrounding area, Turkey and may provide new insights into the Cyanobacteria researches from extreme habitats.	tr_TR
dc.description.tableofcontents	TABLE OF CONTENTS KABUL VE ONAY ....................................................................................................................i ACKNOWLEDGEMENTS .......................................................................................................ii LIST OF SYMBOLS AND ABBREVAITIONS.......................................................................v LIST OF FIGURES..................................................................................................................vii LIST OF PICTURES.................................................................................................................ix LIST OF TABLE........................................................................................................................x ÖZET.........................................................................................................................................xi ABSTRACT .............................................................................................................................xii 1. INTRODUCTION..................................................................................................................1 2. LITERATURE REVIEW.......................................................................................................3 2.1. Extremophiles......................................................................................................................3 2.2. Background of Thermophilic Cyanobacteria ......................................................................4 2.3. Cyanobacteria Taxonomy/Classification.............................................................................6 2.4. The Mechanism of Adaptation in Thermophiles...............................................................12 2.5. Thermophilic Habitats.......................................................................................................13 2.6. Thermal Areas in Aydın and Surrounding places. ............................................................15 2.7. The Importance of Thermophilic Cyanobacteria in Biotechnology..................................16 2.8. 16S Ribosomal RNA and Its Importance in Systematics..................................................18 2.9. Analysis of 16S rRNA.......................................................................................................19 3. MATERIAL AND METHODS ...........................................................................................23 3.1. Materials............................................................................................................................23 3.1.1. Water, Mat, and Debris Samples Were Used in This Study...........................................23 3.1.2. Types of Culture Media Used During The Study...........................................................27 iv 3.1.3. Solvents Used in the Study.............................................................................................27 3.1.4. Primers............................................................................................................................28 3.2. Method...............................................................................................................................30 3.2.1. Total Genomic DNA Isolation From Environmental Samples ......................................30 3.2.2. Amplification of Cyanobacterial 16S rRNA Genes Using PCR (Polymerase Chain Reaction). ........................................................................................................................31 3.2.3. Purification of PCR Amplicons......................................................................................31 3.3. Cloning of the 16S rRNA gene .........................................................................................32 3.3.1. pUC19 Plasmid Restriction ............................................................................................32 3.3.2. Amplicon Restriction......................................................................................................33 3.3.3. Forming of the TA Cloning Vector and TA Cloning .....................................................33 3.3.4 Making of TA Vector (Plasmid) By Adding of dTTP (deoxyThymidine Triphosphate) to Plasmid with Blunt Ends. ....................................................................33 3.3.5. Competent Cell Preparation and Chemical Transformation of Recombinant DNA ......34 3.3.6. Recombinant DNA Chemical Transformation...............................................................35 4. RESULTS.............................................................................................................................36 4.1 Total DNA isolation from Water samples..........................................................................36 4.2. Amplification of 16S rDNA with PCR .............................................................................36 4.3. Restriction of Amplicons and the Plasmid. .......................................................................37 4.4. TA cloning Vector.............................................................................................................37 4.5. Selection of Colonies and M13 PCR.................................................................................38 4.6. Sequence Analysis and Determination of Homologies. ....................................................44 5. DISCUSSION.......................................................................................................................58 6. CONCLUSION ....................................................................................................................62 REFERENCES.........................................................................................................................63 SCIENTIFIC ETHICAL STATEMENT..................................................................................70 CURRICULUM VITAE ..........................................................................................................71	tr_TR
dc.language.iso	eng	tr_TR
dc.publisher	Aydın Adnan Menderes Üniversitesi Fen Bilimleri Enstitüsü	tr_TR
dc.rights	info:eu-repo/semantics/openAccess	tr_TR
dc.subject	Siyanobakteriler, Kültürden Bağımsız Yöntem, Kaplıcalar ve 16S rDNA	tr_TR
dc.subject	Cyanobacteria, Culture Independent Method, Hot Springs and 16S rDNA	tr_TR
dc.title	Kültürden bağımsız metotlarla aydın ili ve çevresindeki sıcak su kaynaklarında siyanobakteri çeşitliliğin belirlenmesi	tr_TR
dc.title.alternative	Determination of cyanobacteria diversity from hot springs around aydin province by culture independent methods	tr_TR
dc.type	masterThesis	tr_TR
dc.contributor.department	Aydın Adnan Menderes Üniversitesi Fen Bilimleri Enstitüsü Biyoloji Ana Bilim Dalı	tr_TR