University of Groningen

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University of Groningen

The sponge as a hypothesis pump Chaib De Mares, Maryam

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2018

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Chaib De Mares, M. (2018). The sponge as a hypothesis pump: A multi-omics overview of a sponge- microbe symbiosis. University of Groningen.

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The sponge as a hypothesis pump

A multi-omics overview of a sponge-microbe symbiosis

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The sponge as a hypothesis pump

A multi-omics overview of a sponge-microbe symbiosis

PhD thesis

to obtain the degree of PhD at the University of Groningen

on the authority of the Rector Magnificus Prof. E. Sterken

and in accordance with

the decision by the College of Deans.

This thesis will be defended in public on Friday September 7

^th

2018 at 12.45 hours

by

Maryam Chaib De Mares

born on February 10

^th

1989

in Armenia, Colombia

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Supervisors Prof. J.D. van Elsas Prof. D. Sipkema

Assessment Committee Prof. U. Hentschel Humeida Prof. L.J. Stal

Prof. B.D.H.K. Eriksson

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Summary

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Samenvatting

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Chapter 1

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General Introduction

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Chapter 1

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Chapter 1

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Chapter 1

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Chapter 1

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Chapter 1

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Chapter 1

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Chapter 2

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Three-domain microbial communities in Aplysina and Dysidea sponges

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Chapter 2

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Chapter 2

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Chapter 2

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Sample Name Abbrev. Sponge genus

No. of bacterial

reads No. of archaea l reads

No. of fungal reads (ITS2)

Total no. of microeukary a reads

No. of microeukary a reads not Porifera

bacterial reads archaeal reads fungal reads microeukarya reads

Observe d OTUs

Expected OTUs (Chao1)^a

Observe d OTUs

Expecte d OTUs (Chao1)^a

Observe d OTUs

Mediterranean Sea

A. aerophoba 1 Aa1 Aplysina 34209 178947

7 27921

0 395294 2173 1197 12425 ±

227 213 264 ± 23 135 242 ± 40 70 100 ± 16

2 35217

2 402403 3106 1302 12621 ±

160 160 207 ± 30 167 237 ± 24 53 91 ± 22

7 33421

6 447478 7626 1226 12939 ±

225 219 248 ± 12 112 158 ± 20 70 101 ± 18

D. avara 1 Da1 Dysidea 46412 201717

2 20691

4 447676 5376 681 3397 ± 69 349 373 ± 11 193 292 ± 31 91 107 ± 9

0 18129

5 436855 88166 876 4386 ± 114 235 263 ± 11 244 358 ± 32 100 118 ± 10

8 14230

2 464741 9693 1208 4032 ± 63 192 205 ± 7 27 49 ± 17 107 130 ± 13

Seawater

Mediterranean 1 SWM1 116282 262589

8 22426

1 535350 499579 719 14548 ±

225 394 401 ± 6 328 515 ± 48 159 159 ± 0

Seawater

0 30822

7 469621 466658 707 14029 ±

235 390 399 ± 7 393 575 ± 41 158 168 ± 10

Seawater

8 20097

5 471441 465064 745 14543 ±

192 399 407 ± 6 338 491 ± 36 159 159 ± 1

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Chapter 2

Caribbean Sea

A. cauliformis 1 Ac1 Aplysina 318385 14984 56727

8 1196853 83779 1147 14942 ±

232 238 255 ± 6 103 138 ± 15 25 31 ± 7

A. cauliformis 2 Ac2 Aplysina 385282 18047 50756

7 835488 417744 1226 15639 ±

231 367 374 ± 3 87 178 ± 42 27 27 ± 0

A. cauliformis 3 Ac3 Aplysina 149375

0 249426 9971 149481 8969 781 17258 ±

109 370 452 ± 23 72 126 ± 28 86 104 ± 13

D. etheria 1 De1 Dysidea 8450 84252 16081

8 155462 137611 837 1980 ± 90 292 309 ± 9 77 146 ± 29 49 55 ± 5

6 123956 44040 832 4031 ± 18 268 3 ± 2 77 114 ± 16 65 73 ± 6

7 131040 13050 866 2056 ± 87 2 305 ± 17 100 223 ± 48 62 73 ± 6

Seawater

Caribbean 1 SWC1 0 230048

2 196 350760 334212 542 598 ± 19 16 26 ± 11 66 77 ± 10

Seawater

9 10197

8 252887 252868 443 501 ± 19 222 378 ± 43 30 31 ± 1

Seawater

3 15629 284003 274362 563 632 ± 22 62 147 ± 44 70 73 ± 3

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Chapter 2

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Chapter 2

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Chapter 2

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Chapter 2

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Chapter 2

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Chapter 2

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Chapter 3

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Sample processing strongly affects identified diversity in A. aerophoba microbiome

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Chapter 3

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Chapter 3

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Chapter 4

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Metaproteomics of bacterial symbionts of A. aerophoba

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Chapter 4

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Chapter 5

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Combined bacterial omics in A. aerophoba: food, friend or foe?

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Chapter 5

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Chapter 5

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Chapter 6

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The multi-omics promise in context: From sequence to microbial isolate

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Chapter 6

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Chapter 6

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Chapter 6

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Chapter 6

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Chapter 6

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Chapter 6

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Chapter 7

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General Discussion

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Chapter 7

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General Discussion