Mireille Consalvey PhD Thesis - University of St Andrews

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ii . p. -'I;? I Sediment surfau-ýý -VIVA Figure 6.10: Change in taxonomic composition at the surface of the Point Clear biofilm (1999) (A) 06: 00 No cells evident at the sediment surface but sub-surface cells visible (B) 12: 00 One cell layer of diatoms, surface dominated by larger cells e. g. Pleurosigma sp. (C) (D) Assemblage still dominated by larger forms but some smaller cells evident in between cells and a well developed matrix of EPS (E) 18: 00 Surface still dominated by larger diatoms and also patches of cyanobacteria are evident (F) 20: 00 Surface dominated by larger forms but sub-surface cells evident. Scale bar in tim. -, . Oý &. ", rF, , -. 0, --. w -, qg -
volt W%ýq 001 Figure 6.11: It is essential to measure microphytobenthic b1ofilms at an appropriate scale (A) Large scale fracture face of biofilm does not fully reveal the fine scale detail (B) shows the size variation of the microphytobenthos (C) Cells are intimately associated and position within the biofilm is highly dynamic (D) Cyanobacteria sometimes form sheets. Scale bar in [tm
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42 =>
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Table of Contents Declaration ii Ac
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4 Laboratory investigation into mic
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temperatures on fluorescence parame
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always been real sweeties. Also tha
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Chl Chlorophyll Chl a Chlorophyll a
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CHAPTER ONE GENERAL INTRODUCTION Wo
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(, 'I, I 1)CI ii I lU RH araphid (n
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dpl. II (I c I) cIq 111 I-Itro-ducJ
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c 11 cIa 11 (T-oduct-Ioll integrate
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( lapRl Wilclul IfInOdik 11011 impo
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Chdpt(1111 1. -, -- I--, -- -- I, -
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(-Jlaptýýr j( rcllcj-ý11 ý: - o
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1.3.2. The Photosynthetic carbon re
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( CflCI iii I TI )dU( t Zingmark 19
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( lidptLI ( ft fln JI flU UII Di wh
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Cha ter I (iclicl-al IntroiftwOoll
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whilst cells minimise their exposur
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1. Pigments Introduction Chlorophyl
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Spectral reflectance studies examin
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(-'Ilaptcýr J, I, -, --, --, --, -
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( anci JII )tI( )(Jtk IO) which buf
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( ! p1'1 -- -1 -ý T-( ý 1)era J-1
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Uh Temporal changes in the microsca
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(I (rcI IpuiE't, cells as they emer
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( hap'wv -1 ( ýI II ntrodt 1ý t I
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( hapi"T 1 11 1- 11 1- ---- -- -- 1
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(A lal )te II- iý; 11 11 1 1- IIIJ
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( 1ý lv-ý ý12, -) -, - -- - -- -
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2.1.3. The Colne Estuary "VIt"utc-1
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(I --- -- "I'l- I -11-1--l- -I--"--
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E I I Uneven surface topography ma]
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2.4. Wet bulk density (Equation 2.2
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('liapti 2- 2.5.4. Cell identificat
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( hapt )- acetone and DMF do not di
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Chapter 2 Materials and Nlethocts P
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Prior to a run all solvents were ge
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(h1ft 'ý, I (I ', tý7! ýI)iI"Iý
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QLapteLi2 2.6.6. Troubleshooting th
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---- ------ at 486.5 nm on a Cecil
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Figure 2.10. A) The fibre optic mea
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tcl -1 Materials jnd 'Mclho(k attac
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Chapt r2 Materials mid Methods A hi
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2 2.9.2. Fluorescence parameters Fl
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CHAPTER THREE ! i()fi1I1I 1]lILli\L
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- -I ii-ofj) II 1- 1-() 111 llatim
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Biofilill follllýltioll ailki de,
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I Fresh sea water 0 inflow Petri di
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" V. 74ý IkIftill AV Ali 4ft llý
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CD 70 60 50 40 30 20 02468 10 12 14
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'I) 3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0
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Aiil- . -, ý'. 4 ý.. , lo "CJ U r
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70 65 60 55 50 -m 45 0 C) cu E 40 3
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3.1. There was a significant differ
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(F5,12ý1.48, p=O. 266). The colloi
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ý-Jofilj I I,, Corn I, atio IIoIId
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100- 80- 60- 40- 20- 01 0 100-1 80
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6) 5 4 3 2 I 01111 40 45 50 55 7- 6
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llaptýýl 3 Riof-11111 f6l matioll
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C, ý E z 6 5- 4 3- 6- 2- 5- _0 4-
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13i(, )flllll f'ormatioll alld (]C\
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Colloidal carbohydrates 13iof-11111
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- ------ J i of -11 d 11 -i dd and
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! )f]llfl 101 IfliltIoll l1l(l1l de
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The presence of grazers in the fiel
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Table 3.4: Correlative relationship
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I. ahoratory investiLalion iln-lo-
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Chapici 4 Laborator\ hivest' jgauml
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11 tei 41 ahora ao I% tigallon -- i
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"' 0 . C13 CIS m 1 1 ; -10 --1 5 -0
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u r . mu tu Q) Q) P. Q) C) 2 ý- ý
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liapiý,, i 4 iilvý: Ajt III()[) l
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. ..... ..... kihorator wo Inicrol)
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Water level 00 High tide Low 10 tid
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Chapter 4 4.2.4. Pigment determinat
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IIa lit ei--" -aborutorv II III to,
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LO (n CD 0 140 120 100 80 =3 i; --
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C: 0.5 0.4 0.3 0.2 0.1 .2o. o4 0 co
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0.88 0.86 LO Eý 0.84 LLý 0.82 0.8
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-C 100 200 300 400 500 PPFD (ý, mo
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( li-, tp-lci 4_-, -- -, -1, aho_r
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C: E 1.2 1.0 0.8 0.6 2 c:: 0.4 (D c
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0.90 E 0.88 U- Li 0.86 0.84 Low tid
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-. 1-Aho-ratory i 11-1ý1, -Clýtj
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0 CL (D Cl) 0 CL x 0 w -0 21 G) cm
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Rates of change (Eden April) 1) Ove
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liapl, cr 4 1.. ahoray III%: (, 1:
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0.82 'ý' 0.81 LL. . 2) 0.80 0.79 0
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ce Cd -a gý- -+ Um (n " -C. , m CI
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( hapt I ahorator u on ns1r / in wa
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(11ýqjtý2i 4 I. abon'tiolvimc, .
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J-1a Ii 1--c i oll Itil'o tll'! rw
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( ! q)1 II CtRdtIO(I Ito flhII 01)h
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In ýiw mw Ll->illýg CHAPTER FIVE
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%im illvestiLalion into micronfivto
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( /11 /Iu The following day the tan
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Figure 5.2: (A) Experimental set-up
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f- Ii 7-f .r- 1« Figure 5.3: (A) T
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Table 5.5: Sampling schedules in si
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Changes in Fluorescence parameters
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5.3.2. Colne Estuary (U. K. ) Day 1
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hi . ýilll jtlvý: SliLatiorl lilt
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0 0- 0- C 0) 0- 2000 1500 )6 42 c:
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ýifu ilivcSit'. 'alion ilito 1111c
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5.3.3. Eden Estuary (U. K. ) Physic
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300- 275- 250- 225- c 200- 0 :3 = 1
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1.6 1.4 E 1.2 =3 D 0 1.0 0.8 0.6 0.
Page 216 and 217: 1'-1 wa 1wation 111to 1111cl YI In
Page 218 and 219: ct C) 1: 1 ý, c r- 00 kf) a c) t)b
Page 220 and 221: ( hcqici Iii situ n Ito 1 ICI Oph\
Page 222 and 223: Cý, ýZlt]Oll 111to l! llCloDl)vLo
Page 224 and 225: n Sim Into Jlqý: loj! hyw be I Ith
Page 226 and 227: n wif Im iý ýI Im Ill to III 11ý
Page 228 and 229: hapler 5- In sill Iin vcstjý, a Ii
Page 230 and 231: ha In ýim ilm CS11,2anorl into --p
Page 232 and 233: 'hapt in I'l II cl-w II rl I,, CHAP
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Page 236 and 237: ( hdpir ( 1)ici iition in rlI]cIopl
Page 238 and 239: (--- 1)cI \ ai 1JI? )fl fl rfliL to
Page 240 and 241: Chapici 6 Dwl \ariatioriý, m biol-
Page 242 and 243: 11c1j)ft () I )1 ai a in iiioiJIi t
Page 244 and 245: (-J Table 6.2: Sampling schedule Ye
Page 246 and 247: 0 DI-cl (B) Sampling schedule March
Page 248 and 249: hajll(! l 0 \arij1jorv, -jn cc and
Page 250 and 251: CD C) CD 0 CD (D 000C, C> CD 0 LO N
Page 252 and 253: (D CD CD 000 06 0 C, C, 0 CD CD 00
Page 254 and 255: = - $: I. Ln -tj 03 9b 03 1=1 0 rq
Page 256 and 257: C> 00 (D CD- CD ci -02Q CD 2m -0 e
Page 258 and 259: 0 co "' - (A) 90- 80- 70-- ý() z-
Page 260 and 261: C) (Z 0- cu to o .=Vý E5 C> 7ý 4.
Page 262 and 263: a C 0 N N >1 m R (D r _0 c cu I -X:
Page 264 and 265: - - 7-2.1 ': --. ... .......... _t.
Page 268 and 269: E 75 E =L 7ý5 .. 0 1400 - 1200- 10
Page 270 and 271: E E LLI 24- 22- 20- 18- 16- 14- 12-
Page 272 and 273: PPFD lam CD s 03 0 -1Z) N V (-) 0 4
Page 274 and 275: 0 Cl) I- 0 CD r4 cq ý2 9 CD co C)
Page 276 and 277: 1'1 1' 1 1" 1" I 040 VA "0 o' U. MS
Page 278 and 279: ( ldJ)t1 (I )i ii Predicted and mea
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Page 282 and 283: significantly higher in the top 0-2
Page 284 and 285: Chapter 6 Diel variations in microp
Page 286 and 287: ohic hioiihn-, sediment surface, oc
Page 288 and 289: ( () -I -- -- --- I---, - ---I, - -
Page 290 and 291: increasing PPFD; first an apparent
Page 292 and 293: Lj1)I ( i)icl dl ItR)fl Ii tfl)LI)J
Page 294 and 295: 6---- - -- , --- -- ---- -- -Dicl h
Page 296 and 297: ý w pwr-- 111 I I- CHAPTERSEVEN k_
Page 298 and 299: vs, iioil--mi ratorv -,, bioiflins
Page 300 and 301: ato I-V Vý11,11011-111! the total
Page 302 and 303: E LZ -0 5 L4 ý7- 'ol r a- 0I 00 CM
Page 304 and 305: ( hatei \1 'IcLtU1 S. iig a1or hiln
Page 306 and 307: cm E7 -*-Cover - Hole for probe Lid
Page 308 and 309: (A) rrr Uk Ilmol ms) Temperature Da
Page 310 and 311: C ulorv \ S. lloll-ml, ýrworv Nigh
Page 312 and 313: N-liý-, ralol v hiol-11111"', Tabl
Page 314 and 315: N1111 ý, ral ol-I -V--\ ". alorv -
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weeq 5upjr4es 6ulinp plalA eoueosaj
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( llaptcl- -; " -1 -I", ý -, l, '
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700 m (D ýo 0) 600 .2 03 U) 500 't
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('11a -, - Pl(ýT I--I-- ,t, III ý
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E -0 (ID 0 0 (ID 0 C 0 c-) -g H ,z
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ý'Ilap! c 7 MI oratory vs. nop-miu
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('haPltcT 7 -Migiatoiv \. -,. tion-
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( iaptl 121 alory s l1o1iiflldtory
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Hypothesis 5: NPQ will be highest a
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minimum and maximum fluorescence yi
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Cha )1(: r 'Vii--latorv ý-, -1 A I
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v vs. 11011-IT . ratory hiolilms -M
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Chapter 7 MiLlatorv v. ". lioll-lim
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Chapt(j 7 s, non-im ratory biot-ilm
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0 E H Cl. 0 -Izý "0 $n. -0 CA 7ý
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( 'llapt c I'll" - 11 - -11,1 1111-
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( llcpk'i_ ( rencral living on, as
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cral I )isctv, -, jon Hythe showed
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ý cKS -1-la-IM, -- (lencral Di-scu
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Cha ici 8 Oencral Di-scussion large
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Chaplet 8 I- I (-. Tciwr, al may th
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( liapRi - ( icnerl I )! ', tR)II D
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hapter ( cncra I )i ii in smaller t
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8.4. Summary -( ic w ra 11, ) ISC L
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9) LTS-EM analysis provided evidenc
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9. Reference List PA , )ý ý, 1j,
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photosynthesis and chlorophyll in t
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Fauvel, P. and Bohn, G. (1907). Le
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Blackwell scientific publications,
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Kilhl, M., Glud, R. N., Ploug, H. a
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Palmer, J. D. and Round, F. E. (196
Page 379 and 380:
Pinckney, J., Piceno, Y. and Lovell
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Ser6dio, J., Marques da Silva, J. a
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Wessels, N. K. and Hopson, J. L. (1
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Mireille Consalvey PhD Thesis - University of St Andrews

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