Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics: = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
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| Main Author: | |
|---|---|
| Format: | Thesis Book |
| Language: | English |
| Published: |
Würzburg
March 2017
|
| Subjects: | |
| Online Access: | Volltext Volltext Inhaltsverzeichnis |
| Physical Description: | xiii, 131 Blätter Illustrationen CD-ROM (12 cm): Appendix |
| Format: | Langzeitarchivierung gewährleistet, LZA |
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| 245 | 1 | 0 | |a Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics |b = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |c submitted by Beate Magdalena Slaby from München |
| 246 | 1 | 1 | |a Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| 264 | 1 | |a Würzburg |c March 2017 | |
| 300 | |a xiii, 131 Blätter |b Illustrationen |e CD-ROM (12 cm): Appendix | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |b Dissertation |c Julius-Maximilians-Universität Würzburg |d 2017 | ||
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| 546 | |a Zusammenfassung in deutscher und englischer Sprache | ||
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| 650 | 0 | 7 | |a Mikroorganismus |0 (DE-588)4039226-0 |2 gnd |9 rswk-swf |
| 653 | |a metagenomics | ||
| 653 | |a single-cell genomics | ||
| 653 | |a sponge microbiome | ||
| 653 | |a differential coverage binning | ||
| 653 | |a PacBio sequencing | ||
| 653 | |a Illumina HiSeq | ||
| 653 | |a hybrid assembly | ||
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Record in the Search Index
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| adam_text | TABLE OF CONTENTS
AFFIDAVIT.........................................................................................................................
ILL
ACKNOWLEDGEMENTS................................................................................................
IV
TABLE OF
CONTENTS......................................................................................................V
LIST OF
FIGURES............................................................................................................VII
LIST OF
TABLES...............................................................................................................
IX
SUMMARY............................................................................................................................X
ZUSAMMENFASSUNG...................................................................................................
XII
1
INTRODUCTION.........................................................................................................14
1.1 SPONGES (PHYLUM
PORIFERA)...................................................................................14
1.2 SPONGE-MICROBE
SYMBIOSIS...................................................................................17
1.2.1 MICROBIAL
DIVERSITY..........................................................................................17
1.2.2 MICROBIAL
FUNCTION...........................................................................................18
1.3 APLYSINA
AEROPHOBA................................................................................................19
1.3.1 GEOGRAPHIC DISTRIBUTION AND PHYSICAL
PROPERTIES.............................................19
1.3.2 THE
A. AEROPHOBA MICROBIOME
......................................................................
20
1.4 SEQUENCE-BASED ANALYSES OF MICROBIOMES
..........................................................
21
1.4.1 RECENT DEVELOPMENTS IN SEQUENCING
TECHNOLOGIES..........................................22
1.4.2 WHY SHORT-READS FALL
SHORT...............................................................................24
1.4.3 LONG-READ SEQUENCING IN METAGENOMICS
........................................................
24
2 MATERIAL AND
METHODS...................................................................................
26
2.1 RESEARCH QUESTIONS AND AIM
S..............................................................................
26
2.2 SPONGE COLLECTION AND ENRICHMENT OF PROKARYOTIC CELLS
....................................
27
2.3 SEQUENCING AND ANALYSIS OF CYANOBACTERIAL SPONGE SYMBIONTS
.........................
28
2.3.1 LABORATORY METHODS: FROM SAMPLE TO SEQUENCE
............................
28
2.3.2 BIOINFORMATIC METHODS: FROM SEQUENCING READS TO GENOME COMPARISON
.....
30
2.4 DEVELOPMENT OF A HYBRID ASSEMBLY PIPELINE FOR PACBIO LONG-READS AND
ILLUMINA
SHORT-READS........................................................................................................
32
2.4.1 SIMULATING SEQUENCING READS FOR A TEST DATASET
........
.
...................
32
2.4.2 TESTING ASSEMBLERS AND SETTINGS
.
.......
33
2.4.3 COMPARING AND EVALUATING OF ASSEMBLIES AND BINS............... 34
2.5 APYLSINA AEROPHOBA
METAGENOMICS.....................................................................
36
2.5.1 LABORATORY METHODS: DNAE EXTRACTION AND
SEQUENCING.......................... 36
2.5.2 BIOINFORMATIC METHODS: FROM ASSEMBLY TO ANNOTATION
............
.
.............
36
2.5.3 STATISTICAL ANALYSIS: COMPARISON TO REFERENCES AND WITHIN
SYMBIONTS
............
37
3
RESULTS......................................................................................................................40
3.1 ASSESSING THE GENOME OF THE *CA. SYNECHOCOCCUS SPONGIARUM* GROUP
...........
40
3.1.1 ASSESSMENT OF CLADE F GENOMES FROM
A. AEROPHOBA
.....................................
40
3.1.2 COMPARISON WITHIN THE *CA. SYNECHOCOCCUS SPONGIARUM* GROUP AND TO
FREE-
LIVING
REFERENCES.............................................................................................................
44
3.2 PACBIO-ILLUMINA HYBRID ASSEMBLY PIPELINE DEVELOPMENT
.................................
63
3.2.1 STATISTICS OF THE TESTED ASSEMBLY STRATEGIES
.....................................................
63
3.2.2 COMPARISON BACK TO ORIGINAL REFERENCE GENOMES
...........................................
64
3.2.3 REFERENCE-INDEPENDENT BINNING
.....................................................................
65
3.3 BINNING 37 SYMBIONT GENOMES FROM THE METAGENOME OF A. AEROPHOBA
...........
68
3.3.1 ASSESSMENT OF METAGENOMIC DNA EXTRACTION AND SEQUENCING
......................
68
3.3.2 COMPARISON OF ILLUMINA-ONLY AND PACBIO-ILLUMINA HYBRID ASSEMBLIES
........
69
3.3.3 BACTERIAL GENOMES BINNED FROM HYBRID ASSEMBLY
..........................................
72
3.3.4 SYMBIONT-REFERENCE COMPARISON
....................................................................
78
3.3.5 WITHIN-SYMBIONT COMPARISON
.........................................................................
84
4
DISCUSSION...............................................................................................................
88
4.1 *CO. SYNECHOCOCCUS SPONGIARUM* GROUP - CLOSELY RELATED BUT DIFFERENT
IN GENE
CONTENT...............................................................................................................................
88
4.1.1 AN OPTIMAL CANDIDATE FOR *MINI-METAGENOMICS*
............................................
88
4.1.2 LIFESTYLE EVOLUTION IN CYANOBACTERIAL SYMBIONTS OF SPONGES
..........................
89
4.2 PACBIO-ILLUMINA HYBRID ASSEMBLY PIPELINE DEVELOPMENT
.................................
97
4.3 METAGENOMIC BINS FROM THE MICROBIOME OF A. AEROPHOBA REVEAL UNITY IN
DEFENSE BUT METABOLIC SPECIALIZATION
..............................................................................
98
4.3.1 BREAKING NEW GROUND IN ASSEMBLY STRATEGY AND CHOICE OF REFERENCES
............
98
4.3.2 UNITY IN
DEFENSE.............................................................................................
99
4.3.3 METABOLIC
SPECIALIZATION...............................................................................100
4.3.4
CONCLUSIONS...................................................................................................100
4.4 GENERAL CONCLUSIONS AND FUTURE
DIRECTIONS.......................................................101
5 BIBLIOGRAPHY___________________________________________________ 107
6 APPENDIX
________________________________________________________
128
7 PUBLICATIONS LIST
______________________________________________
129
8 CURRICULUM VITAE
______________________________________________
130
|
| any_adam_object | 1 |
| author | Slaby, Beate |
| author_GND | (DE-588)108842354X |
| author_facet | Slaby, Beate |
| author_role | aut |
| author_sort | Slaby, Beate |
| author_variant | b s bs |
| building | Verbundindex |
| bvnumber | BV044456831 |
| collection | ebook |
| ctrlnum | (OCoLC)1159326678 (DE-599)DNB1137836040 |
| dewey-full | 579 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 579 - Microorganisms, fungi & algae |
| dewey-raw | 579 |
| dewey-search | 579 |
| dewey-sort | 3579 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| format | Thesis Book |
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| spelling | Slaby, Beate Verfasser (DE-588)108842354X aut Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik Würzburg March 2017 xiii, 131 Blätter Illustrationen CD-ROM (12 cm): Appendix txt rdacontent n rdamedia nc rdacarrier Dissertation Julius-Maximilians-Universität Würzburg 2017 Langzeitarchivierung gewährleistet, LZA Zusammenfassung in deutscher und englischer Sprache Metagenom (DE-588)7635820-3 gnd rswk-swf Aplysina aerophoba (DE-588)4778447-7 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf metagenomics single-cell genomics sponge microbiome differential coverage binning PacBio sequencing Illumina HiSeq hybrid assembly (DE-588)4113937-9 Hochschulschrift gnd-content Aplysina aerophoba (DE-588)4778447-7 s Mikroorganismus (DE-588)4039226-0 s Metagenom (DE-588)7635820-3 s DE-604 Erscheint auch als Online-Ausgabe, PDF urn:nbn:de:bvb:20-opus-151869 https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-151869 Resolving-System kostenfrei Volltext http://d-nb.info/1137836040/34 Langzeitarchivierung Nationalbibliothek kostenfrei Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029857615&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Slaby, Beate Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik Metagenom (DE-588)7635820-3 gnd Aplysina aerophoba (DE-588)4778447-7 gnd Mikroorganismus (DE-588)4039226-0 gnd |
| subject_GND | (DE-588)7635820-3 (DE-588)4778447-7 (DE-588)4039226-0 (DE-588)4113937-9 |
| title | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| title_alt | Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| title_auth | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| title_exact_search | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| title_full | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München |
| title_fullStr | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München |
| title_full_unstemmed | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München |
| title_short | Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics |
| title_sort | exploring the microbiome of the mediterranean sponge aplysina aerophoba by single cell and metagenomics untersuchungen am mikrobiom des mittelmeerschwamms aplysina aerophoba mittels einzelzell und metagenomik |
| title_sub | = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik |
| topic | Metagenom (DE-588)7635820-3 gnd Aplysina aerophoba (DE-588)4778447-7 gnd Mikroorganismus (DE-588)4039226-0 gnd |
| topic_facet | Metagenom Aplysina aerophoba Mikroorganismus Hochschulschrift |
| url | https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-151869 http://d-nb.info/1137836040/34 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029857615&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT slabybeate exploringthemicrobiomeofthemediterraneanspongeaplysinaaerophobabysinglecellandmetagenomicsuntersuchungenammikrobiomdesmittelmeerschwammsaplysinaaerophobamittelseinzelzellundmetagenomik AT slabybeate untersuchungenammikrobiomdesmittelmeerschwammsaplysinaaerophobamittelseinzelzellundmetagenomik |