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Foraminiferal assemblages on sediment and reef rubble at conch reef, florida usa

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Foraminiferal assemblages on sediment and reef rubble at conch reef, florida usa
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Stephenson, Christy Michelle
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Benthic Communities
Concentration Ratio
Coral Reef
Environmental Indicators
Foram Index
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ABSTRACT: ABSTRACT Foraminiferal Assemblages on Sediments and Reef Rubble at Conch Reef, Florida USA Christy Stephenson Benthic foraminiferal assemblages are widely used to interpret responses of the benthic communities to environmental stresses. This study compares epibiotic foraminiferal assemblages, collected from reef rubble, with those from reef sediments. The study site, Conch Reef, is the site of the Aquarius Underwater Habitat research facility and includes protected areas used only for scientific studies. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract, no projects have focused on the assemblages that occur at Conch Reef. Sediment and reef rubbles samples were collected via SCUBA from a depth range of 13 to 26 m during October 2008. Foraminiferal assemblages were assessed and compared between the two sample types. A total of 117 foraminiferal species, representing 72 genera, 37 families, and 8 orders were identified in 13 sediment samples and 21 rubble samples. In the rubble samples, 70 genera were identified, including 12 symbiont-bearing genera representing 20% of the total assemblage, 12 stress-tolerant genera representing 6%, planktic foraminifers representing 1%, and 46 other smaller foraminiferal genera representing 73% of the total foraminiferal assemblage. The rubble samples were quite homogenous. The mean (+SD) Fisher alpha α diversity of genera in these samples was 12.9 + 1.4. Sediment samples included 60 of the same genera. The 12 symbiont-bearing genera represented 41% of the total assemblage, 10 stress-tolerant genera represented 3%, planktic taxa represented 2%, and 40 other smaller foraminiferal genera represented 54% of the total assemblage. Overall, the taxonomic assemblages were very similar between the sample types, with sediment assemblages clearly representing the local and regional reef foraminiferal assemblage. The mean (+SD) Fisher alpha α for sediment samples was 11.4 + 2.3, which is not significantly different from that found for the rubble samples. A concentration ratio comparing relative abundances in sediment vs. rubble samples revealed that shells of larger, symbiont-bearing taxa were about 2.5-5.5 times more concentrated in the sediment, indicating winnowing of smaller taxa. Shells of Siphonatera, an agglutinated miliolid, and Textularia, an agglutinated textularid, were more abundant in sediments than in rubble, indicating high preservation potential. The concentration ratio provides a new taphonomic index that reflects the size and durability of foraminiferal taxa. The mean FORAM Index (FI) for the sediment samples (5.57 + 0.83) indicates that water quality at Conch Reef is suitable for calcifying symbioses. The most abundant symbiont-bearing genera were Amphistegina, Laevipeneroplis, Asterigerina, and Archaias.
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Thesis (M.S.)--University of South Florida, 2011.
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by Christy Michelle Stephenson.
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Foraminifera l Assemblages on Sediments and Reef Rubble at Conch Reef Florida USA by Christy Mc Ney Stephenson A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science College of Marine Science Unive rsity of South Florida Major Professor: Pamela Hallock Muller, Ph. D Kendra Dal y Ph.D Lisa Robbins Ph. D Date of Approval: April 11, 2011 Keywords: coral reef environmental indicators, benthic c ommunities, concentration ratio FORAM Index Copy right 2011, Christy McNey Stephenson

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DEDICATION with the living you are still a source of encouragement and inspiration to me throughout d to two strong women, whom never let the obstacles of life get in the way of personal success.

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ACKNOWLEDGEMENTS I would like to thank my advisor Dr. Pamela Hallock Muller for he r patience, support, and guidance throughout my graduate career I also acknowledge my committee members, Kendra Daly Ph.D. and Lisa Robbins Ph.D. for their critical reviews of my thesis. This research would not have been possible without field support from NOAA contract number to NURC UNCW: NA080AR4300863; subcontract to UNC Chapel Hill: ARB 2008 11 (PIs: C. Martens and N. Lindquist); subcontract to USF: 5 46147 (PIs: P. Hallock Muller and R. Byrne) Special thanks to J. Scott Fulcher for his invaluable help processing samples, photographic support and providing tremendous me ntal and moral support.

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i T ABLE OF CONTENTS LIST OF TABLES ................................ ................................ ................................ ............ iii LIST OF FIGURES ................................ ................................ ................................ ......... vii ABSTRACT ................................ ................................ ................................ .................... x INTRODUCTION ................................ ................................ ................................ ............. 1 Conch Reef ................................ ................................ ................................ ............. 1 Foraminifera ................................ ................................ ................................ ........... 4 Foraminifera as environmental i ndicators ................................ ............................. 5 Indices ................................ ................................ ................................ .................... 7 Controversy in foraminiferal r esearch ................................ ................................ 11 PROJECT OBJECT IVES ................................ ................................ ................................ 1 4 Major q uestions and h ypothesis ................................ ................................ ........... 1 5 METHODS ................................ ................................ ................................ .................. 1 6 Sample collection ................................ ................................ ................................ 1 6 Sample processing ................................ ................................ ............................... 1 7 Sediment samples ................................ ................................ ..................... 1 7 Grain size analysis ................................ ................................ ................... 1 8 Rubble samples ................................ ................................ ........................ 1 8 Foraminiferal assemblages ................................ ................................ ....... 1 9 Data analysis ................................ ................................ ................................ ........ 20 Grain size analysis ................................ ................................ ................... 20 Foraminiferal assembla ges ................................ ................................ ....... 20 Indices analysis ................................ ................................ ........................ 20 Multivariate analyse s of foraminiferal assemblages ................................ 2 4 RESULTS ................................ ................................ ................................ .................. 2 6 Grain size ................................ ................................ ................................ ............. 2 6 Foraminiferal assemblages in sediment samples ................................ ................. 2 8 Key genera ................................ ................................ ............................... 2 8 Indices analysis ................................ ................................ ........................ 2 9 Sample distribution ................................ ................................ .................. 3 4

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ii Foraminiferal assemblages in rubbl e samples ................................ ..................... 41 Key genera ................................ ................................ ............................... 41 Indices analysis ................................ ................................ ........................ 41 Sample distribution ................................ ................................ .................. 4 5 Comparison of foraminiferal assemblages with sediment and rubble samples ................................ ................................ ......................... 5 3 Key genera ................................ ................................ ............................... 53 Indices analysis ................................ ................................ ........................ 53 Sample distribution ................................ ................................ .................. 55 Concentration ratio ................................ ................................ ................... 62 Comparison of live v ersus dead foraminiferal assemblages .................... 6 4 Langer Morphotypes ................................ ................................ ................ 64 DISCUSSION ................................ ................................ ................................ .................. 69 History of previous studies ................................ ................................ ................. 69 Sample homogeneity and distribution ................................ ................................ 70 Concentration ratio ................................ ................................ ............................... 71 Faunal assemblage s ................................ ................................ .............................. 74 Total assemblage controversy ................................ ................................ .............. 75 Comparison of live versus dead fora miniferal assemblages ................................ 7 6 Within sample versus within site variability ................................ ........................ 78 Indices ................................ ................................ ................................ .................. 79 CONCLUSION ................................ ................................ ................................ ................ 82 REFERENCES ................................ ................................ ................................ ................ 8 5 APPENDICES ................................ ................................ ................................ ................. 9 6 Appendix A : Raw data from sediment samples ................................ .................. 9 7 Appendix B : Raw SIMPER results from sediment samples .............................. 101 Appendix C : Raw dat a from rubble samples ................................ ..................... 10 7 Appendix D : Raw SIMPER results from rubble samples ................................ .. 111 Appendix E : Foraminiferal Species list for Conch Reef, Florida ...................... 120 Appendix F : Raw SIMPER results on the combined data set by Clusters ........ 12 6 Appendix G: Raw SIMPER results on th e combined data set to sample type ................................ ................................ .............................. 134

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iii LIST OF TABLES Table 1: Calculation of the FORAM Index ................................ ............................... 2 3 Table 2 : Weight percent for each grain size class for the 17 sediment samples from Conch Reef, collected in October 2008 ................................ ............. 2 7 Table 3 : Distribut ion of median grain size in 17 sediment samples from Conch Reef, collected in October 2008 ................................ ...................... 2 7 Table 4 : All foraminiferal genera identified in samples collected at Conch Reef in October 2008. ................................ ................................ ................ 30 Table 5 : Summary of foraminiferal assemblage data and ind ices in sediment samples collected at Conch Reef, October 2008 ................................ ........ 3 3 Table 6 : Summary of ANOSIM and SIMPER results for sediment samples by clusters ................................ ................................ ................................ ........ 3 7 Table 7 : ANOSIM pairwise test of the sediment samples to FI groupings .............. 3 8 Table 8 : Summary of the foram iniferal as semblage data and indices in rubble samples collected at Conch Reef, October 2008 ................................ ....... 4 2 Table 9 : Summary of ANOSIM and SIMPER results for rubble samples by Clusters ................................ ................................ ................................ ....... 50 Table 10 : ANOSIM pairwise test of the rubble samples to FI group ing s ................... 50

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iv T able 11 : ANOSIM and SIMPER pairwise tests by cluster groups on the foraminiferal clusters ................................ ................................ .................. 5 5 Table 12 : Summary of ANOSIM and SIMPER results of foraminiferal assemblages by sample type ................................ ................................ ....... 57 Table 13 : ANOSIM pairwise test of the combined data set (sediment and rubble) to FI group ing s ................................ ................................ ............... 60 Table 14 : Relative abundances of the 20 most common genera used to calculate a Concentration Ratio (S/R) for each genus. ............................... 6 2 Table 15 : Percentage of live foraminifers found in sediment and rubble with Langer Morphotype and colored accordi ng to functional categories ........ 6 5 Table 16 : Langer Morphotype c omparison of foraminiferal relative abundances in sediment and rubble samples from Conch Reef, October 2008 ............. 6 6 Table 17 : Relative abundances and Langer Morphotype of foramin iferal genera by order in sediment and rubble samples from Conch Reef, October 2 008 ................................ ................................ ................................ ............. 6 7 Table A1 : Foraminiferal abundances (#/gm) in sediment samples collected in October 2008 at Conch Reef, Florida ................................ ......................... 9 7 Table A2 : Summary of sediment foraminiferal data of samples collected in October 2008 at Conch Reef, Florida from the table above. .................... 100 Table B1 : SIMPER similarity results on se diment samples by Cluster 1 ................ 101 Table B2 : SIMPER similarity results on sediment samples by Cluster 2 ................ 102 Table B3 : SIM PER similarity results on sediment samples by Cluster 3 ............... 10 3

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v Table B4 : SIMPER dissimilarity results on sediment samples by Clusters 1 & 2 .... 104 Table B5 : SIMPER dissimilarity results o n sediment samples by Clusters 2 & 3 .... 105 Table B6 : SIMPER dissim ilarity results on sediment sampl es by Clusters 1 & 3 .... 106 Table C1 : Foraminiferal abundance ( #/ 100cm 2 ) in rubble samples collected in October 2008 at Conch Reef, Florida ................................ ....................... 107 Table C2 : Summary of rubble foraminiferal data of samples collected in Octob er 2008 at Conch Reef, Florida from the table above. .................... 110 Table D1 : SIMPER similarity results on rubble samples by Cluster 1 ...................... 1 11 Table D2 : SIMPER similarity results on rubble samples by Cluster 2 ...................... 1 12 Table D3 : S IMPER similarity results on rubble sa mples by Cluster 3 ...................... 1 13 Table D4 : SIMPER dissimilarity results on rubble samples by Clusters 2 & 1 ...... 11 4 Table D5 : SIMPER dissimilarity results on rubble samples by Clusters 2 & 3 ........ 11 6 Table D6 : SIMPER dissimilarity results on rubble samples by Cluste rs 3 & 1 ........ 11 8 Table E1 : Foraminiferal species identified in samples collected at Conch Reef in October 2008. ................................ ................................ ........................ 120 Table F1 : SIMPER similarity results on the comparison of sediment and rubble samples by Cluster 1 ................................ ................................ ................. 12 6 Table F2 : SIMPER similarity result s on the comparison of sediment and rubble samples by C luster 2 ................................ ................................ ................. 12 7

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vi T able F3 : SIMPER similarity results on the comparison of sediment and rubble samples by Cluster 3 ................................ ................................ ................ 12 8 T able F4 : SIMPER dissimilarity results on the comparison of sediment and rubble samples by Clusters 1 & 2 ................................ ............................ 12 9 Table F5 : SIMPER dissimilarity results on the comparison of sediment and rubble samples by Clusters 3 & 2 ................................ ............................ 1 31 Table F6 : SIMPER dissimilarity results on the comparison of sediment and rubble samples by Clusters 1 & 3 ................................ ............................. 1 32 Table G1 : SIMPER similarity results of sediment samples using combined data set by sample type. ................................ ................................ ................... 13 4 Table G2 : SIMPER similarity results of rubble samples using combined data set by sample type. ................................ ................................ ................... 13 5 Table G3 : SIMPER dissimilarity results on th e comparison of sediment and rubble samples using the combined data set ................................ ............. 13 6

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vii LIST OF FIGURES Figure 1: Florida Keys National Marine Sanctuary ................................ ..................... 2 Figure 2 : Conch Reef Sanctuary Preserve within the Aquarius Underwater Research Habitat ................................ ................................ ........................... 3 Figure 3 : Langer (1993) categorization of foraminiferal morphotypes occurring on phytal substrates ................................ ................................ ...... 9 Figure 4 : Conch Reef sites where sediment and rubble samples were collected ....... 1 6 Figure 5 : Rubble sample with AxioV ision area (cm 2 ) measurements indicated ........ 1 9 Fig ure 6: Foram Index [FI] representing the three functional groupings. .................. 22 Figure 7 : Randomized accumulation plot for genera in sediment samples from Conch Reef October 2008 indicating that 90% of the genera are found in about 10 samples. ................................ ................................ ......... 31 Figure 8 : Tw enty most abundant genera in sediment samples collected in Oc tober 2008 at Conch Reef; the 44 less abundant genera are included under remaining ................................ ................................ ....... 3 2 Figure 9 : Sediment cluster analysis of foraminiferal assemblages by station at Conch Reef, October 2008 ................................ ................................ .......... 3 5 Figure 10 : Bray Curtis Multidimensional Scaling (MDS) plot of similarities of foraminiferal assemblages, in sediment samples from Conch Reef, October 2008 ................................ ................................ ............................... 3 6

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viii Figure 11 : Cluster analysis of genera in sediment samples collected at Conch Reef, October 2008 ................................ ................................ ..................... 3 9 Figure 1 2 : Bray Curtis MDS plot of foraminifers in the sediment samples by FI groupings ................................ ................................ ................................ ..... 40 Figure 13 : Randomized accumulation plot f or genera of rubble samples from Conch Reef in October 2008 indicating that 90% of the genera are found in about 7 samples ................................ ................................ ............ 4 3 Figure 1 4 : Twenty most abundant genera in rubble samples collected in Oc tober 2008 at Conch Reef; the 55 less common genera are included under ................................ ................................ ................................ 4 4 Figure 1 5 : Cluster analysi s of rubble samples, based on foraminiferal assemblage s, with depth range of sampling site s indicated ........................ 4 7 Figure 1 6 : Bray Curtis MDS plot of rubble samples based on foraminiferal assemblages at Conch Reef ................................ ................................ ......... 4 8 Figure 1 7 : Cluster diagram by foraminiferal genera from rubble samples collected at Conch Reef ................................ ................................ .............. 51 Figure 1 8 : Bray Curtis (r mode) MDS plot of rubble samples by FI group ing s .......... 5 2 Figure 1 9 : Spe cies richness by foraminiferal order of samples collected at Conch Reef, October 2008 ................................ ................................ .......... 5 4 Figure 20 : Cluster analysi s of the combined data set (sediment and rub ble samples) noting sample types at Conch Reef October 2008 ...................... 5 8 Figur e 21 : Bray Curtis MDS plot of all samples, based on relative abundances of foraminifers ................................ ................................ ........................... 5 9

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ix Figure 2 2 : Cluster analysi s of foraminiferal genera using the combined (sediment and rubble ) data set ................................ ................................ .... 61 Figure 2 3 : Concentration ratio of the 20 most common genera, calculated by dividing the average relative abundance of each genus in the sediment by its relative abundance in the rubble ................................ ........ 6 3

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x ABSTRACT Benthic foraminiferal assembla ges are widely used to interpret responses of the benthic communities to environmental stresses. This study compares epibiotic foraminiferal assemblages collected from reef rubble with those from sediments at Conch Reef, Florida reef tract, USA. Conch Reef is the site of the Aquarius Underwater Habitat research facility and includes protected areas used only for scientific studies. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract, no projects have focused on the asse mblages that occur at Conch Reef. Sediment and reef rubbles samples were collected via SCUBA from a depth range of 13 to 26 m at Conch Reef, Florida, during October 2008. F oraminiferal assemblages were assessed and compared between the two sample types One hundred and seventeen foraminiferal speci es, representing 72 genera, 37 families, and 8 o rders were identified in 17 sediment samples and 21 rubble samples Seventy genera were identified in the rubble samples, including 12 symbiont bearing genera r epresenting 20% of the total assemblage, 12 stress tolerant genera representing 6%, planktic foraminifers representing 1%, and 46 other smaller foraminiferal genera representing 73% of the total foraminiferal assemblage. The rubble samples were quite homo genous The mean ( + SD) Fisher alpha [ ] diversity of genera in these samples was 12.9 1 + 1.4 1

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xi Sediment samples included 60 of the same genera as the rubble samples. The same 12 symbiont bearing genera represented 41% of the total assemblage, 10 stress tolerant gen era represented 3%, planktic taxa represented 2%, and 40 other smaller foraminiferal genera represented 54% of the total assemblage. A ssemblages were somewhat more variable between sediment samples because several samples contained very few ( <100) specimens per grams. Overall, th e taxonomic assemblages were similar between the sample types, with sediment assemblage s alone adequately representing th e local foraminiferal assemblage The mean ( + SD) Fisher alpha for sediment samples was 11.37 + 2.27 which is not significantly different from that found for the rubble samples A concentration ratio comparing relative abundances in sediment vs. rubble samples (S/R) was developed. It revealed that smaller taxa were more abundant in the rubble, while shells of larger, symbiont bearing taxa were about 2.5 5.5 times more concentrated in the sediment, indicating winnowing of smaller taxa. Shells of Siphonatera, an agglutinated miliolid, and Textularia an agglutinated textularid, were more abundant in sediments than in rubble, indicating high preservation potential. The concentration ratio provides a new taphonomic index that reflects the size and durability of foraminiferal taxa. The mean FORAM Index [FI] for the sediment samples (5. 57 + 0.8 3 ) indicates that water quality at Conch Reef is suitable for calcifying symbioses. The most abundant symbiont bearing genera were Amphistegina, Laevipeneroplis, Asterigerina and Archaias.

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1 INTRODUCTION Conch Reef Conch Reef, located within t he Florida Keys National Marine Sanctuary, has been a focus of research activities since the site was chosen for placement of the Aquarius Underwater Habitat in 1991 by NOAA/NURC (National Oceanic and Atmospheric Administration/National Undersea Research C enter) ( Figure 1 ) ( www.floridakeys.noaa.gov.com ). Located approximately 14.5 km south of Key Largo, Conch Reef considered a bank reef, with a shallow platform inshore and deeper spur and groove formations found to depths of approximately 35m. A special surrounds the Aquarius Underwater Research Laboratory ( Figure 2 ) ( ww w.uncw.edu/aquarius ), is where the samples for this study were collected. The boundary zone for the Aquarius facility A detailed bathymetric map of the site is available on t he Aquarius Research Facility website ( www.uncw.edu/aquarius )

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2 Figure 1 Florida Keys National Marine Sanctuary www.floridakeys.noaa.gov.com

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3 Figure 2 Conch Reef Sanctuary Preserve within the Aquarius Underwater Research Ha bitat

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4 Foraminiferal research began at Conch Reef in 1991 with the discovery of bleaching in Amphistegina gibbosa (Hallock and Tal ge 1993 b ). This foraminifera l population was intensively studied through out the 1990 s (Hallock et al. 1995) and sporadically since (Hallock et al. 2006a, 2006b ). Baker et al. (2009) expanded the research focus to include other symbiont bearing foraminife rs. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract (Bock 1971 ; Culver and Buzas 1982; Martin 1986 ; Cockey et al. 1996 ), no projects have focused on the assemblages that occur at Conch Reef. F oraminifera Fora m inifera are a class of protists in the Phylum Granuloreticulosea and are characterized by their tests ( i.e., shell s ) which can be single or multiple chambered organic agglutinated or calcareous ( e.g., Sen Gupta 1999). Though foraminifera are unicell ular, the cytoplasm has t wo apparent components with different functions. The ectoplasm found in the outermost portion of the shell, is abundant in microt ubules a nd is the location where the reticulopodia are produced, enabling foraminifers to feed, mov e, and grow new chambers. The endoplasm, found within the shell, contains the nucleus (or many nuclei) and functions to accumulate the organic mat ter required for reproduction ( Hallock 1999). O f the 150 families of Foraminifera fewer than 10 % include me mbers that host algal endosymbionts (Lee and Anderson 1991). Most symbiont bearing benthic

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5 foraminifers grow larger than non symbiont benthic foraminifers and as such are known as (Hallock 1999). Taxa of benthic Foramin ifera that host algal endosymbionts, particularly the LBF, are characteristic of warm shallow shelf environments where they are important contributors to shelf sediments Hallock (1988) noted that shells of LBF, along with physically eroded, identifiabl e coral fragments, are characteristic in oligotrophic waters conducive to reef health and accretion (Hallock 1988, 2000b; Cockey et al. 1996). Symbiont bearing benthic foraminifers require similar water quality parameters as corals and are normally abunda nt on healthy coral reefs. There are advantages and disadvantages to symbioses with algae. The major advantage occurs when the host lives in shallow, clear waters where there is plenty of sunlight and the algae photosynthesize and provide the host with carbohydrates or lipids. However if dissolved nutrients are plentiful, the symbionts can use the products of photosynthesis to grow and reproduce themselves without providing photosynthate to the host ( e.g., Hallock 2000 a; Wooldridge 2009 ). Foraminife ra as environmental i ndicators Benthic foraminiferal assemblages are known to respond rapidly t o environmental changes. They have been found in the geologic record since the Cambrian Pe riod, and are used as bi oindicators of countless global change events in the geologic record, from mass extinctions to more subtle local events like volcanism ( e.g., Sen Gupta 1999). Foramini fers are useful bioindicators of pollution increases, the more sensitive taxa are

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6 eliminated, whereas the most tolerant genera are gen erally among the last organism to disappear from an impacted site (Schafer 2000; Carnahan et al. 2008). Environments containing excess organic carbon, nutrients or sunlight can cause physiological stress to the host ( Hallock 19 99 ; Hallock et al. 2006a ; Wo oldridge 2009 ). Due to their rela tively short life cycles, which range from a pproximately a few weeks up to one year, and their sensitivity to environmental conditions, the foraminiferal assemblage s react faster than corals to changes in water quality (Ha llock 2000b; Hallock et al. 2003). While water samples may indicate normal nutrient concentrations, the effect of increased nutrient flux into an ecosystem typically results in a community change ( e.g., Hallock 1988) known as a phase shift (Done 1992 ; McM anus and Polsenberg 2004 ; Palandro et al. 2008 ). Reef recovery potential following an acute event is dependent on water quality (Hallock et al. 2006b). Foraminiferal assemblages may indicate whether water quality can support healthy coral reefs and allow them to recover after a mortality event. How benthic foraminifers recover and colonize an area following a disturbance also depends on the hydrodynamics of the area. Small infaunal species are among the first and most successful colonizers of the soft b ottom habitats (Alve 1999; Buzas et al. 2002). The LBF lose dominance to those small, fast growing herbivorous and detritivorous species, when increased nutrient l oads from coastal land areas are introduced into the environment (Hallock 2000a; Carnahan et al. 2009). The short lifespan and large numbers of foraminifers within an assemblage allows for a differentiation between chronic reef decline and acute mortality events (Cockey et al. 1996 ; Hallock et al. 2003 ).

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7 Cockey et al. (1996) assessed f oraminifer al assemblages from sediments collected in 1991 and 1992 along the Florida reef tract at sites originally sampled by Rose and Lidz (1977) in the 19 60s and published in 1989 ( Lidz and Rose 1989 ) to determine if biotic changes had occurred. Assemblage cha nges were consistent with increased nutrient flux from coastal sources Indications of nutrient flux occurring to a system include the presence of smaller foraminiferal shells unidentifiable carbonate grains, and abundant calcareous algal fragments (Hall ock 1988, 2000b ; Cockey et al. 1996). Cockey et al. (1996) found that family level identification s were sufficient to detect decadal scale changes in foraminiferal assemblages on the reef tract. I ndices A variety of ecological assemblage indices are co mmonly used in benthic foraminiferal research including Taxonomic Richness [S], Shannon [H], Fisher Simpson [D] and Evenness [E] (Hayek and Buzas 1997 2006 ). Taxonomic richness [S] is defined as the number of different taxa of interest ( e.g., specie s or genera ) identified from a sample or set of sample s The Shannon diversity [H] measure s the order (or disorder) obse rved within a particular system, with maximum values occurring when species are evenly distributed. index measures t he biodiversity within a particular area, community, or ecosystem The alpha index is based on the ratio of the number of species to the number of individuals Simpson index of diversity [D] calculates the probabilities of picking two specimens at random that are different species, and thus ranges from 0 to 1. Evenness [E] quantifies how equal ly

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8 distributed the species are in the assemblage Evenness is calculated by using the Shannon diversity and the T axonomic R ichness values. Evenness values range f ro m 0 to 1, the higher the value the more evenly distributed the taxa are, while lower values indicate dominance by one or more taxa All of these measures are evaluated as a function of the number of individuals in the sample ( Hayek and Buzas 2010 ). Vari ous other parameters of foraminiferal assemblages have been used to define en vironments. Severin (1983 ) and Hallock and Glen n (1986), among others, use d test morphology to determine biofaces Langer (1993 ) subsequently develop ed a classification for epip hytic foraminifers Morphotypes are used as indicators to interpret epiphytic habit ats in which foraminifers live ( Figure 3 ) The diversity of specific assemblages is controlled by independent factors related to temporal availability of substrates and sp ace (substrate geometry) For each species, in variable environments different factors may be limiting distributions both temporally and spatially (Murray 2001)

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9 Figure 3. Langer (1993) categorization of foraminiferal morphotypes occurring on phytal substrates.

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10 A ) Morphotype A ( e.g., Planorbulina ) are permane ntly attached, sessile species with a typical life span of about one year, they have relatively large or multiple aper a tures. Chambers are commonly added in an orbitoidal or similar pattern for rapid growth in response to competiton for space. These benthic foraminifers secrete a subs tance, termed glycoglue, between the test and the substrate to give them the ability to stay in position. B ) Morphotype B ( e.g., Rosalina ) are temporarily attached but can bec ome motile with a typical life span of 2 5 months The aperatural faces are wide and interiomarginal (facing the substrate) and shell shapes are low or high trochospiral. Attachment and detachment is possible, allowing the individual to free themselves from the substrate when searching for food or for sexual reproduction. Morpho type B individuals have been known to free themselves from a substrate in response to changing environmental condition or when threatened with overgrowth by a more rapidly growing organism C ) Morphotype C ( e.g., Elphidium ) are motile suspension or filte r feeders with a typical life span of 3 4 months. They are characterized by presence of a canal system th r ough which they extrude pseudopods, and they have mu lti ple aperatures. Most of these taxa prefer structurally dense algal substrates, which are ide al microhabitats for suspension feeders. D ) Morphotype D ( e.g., Quinqueloculina ) are permanently motile, grazing epiphytes, and include the majorit y of the species most of which have short life span s of weeks The apertures are narrow to bottle neck, w ith the most common feature being

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11 their method of locomotion. They all move in an upright postion on the ape a rtural face by extending pseudopods in the direction of movement (Langer 1993). The FORAM Index (Foraminifera in Reef A ssessment and Monitoring) is "intended to provide resource managers with a measure, which is independent of coral populations, to determine whether water quality in the environment is sufficient to Hallock et al. 2003 p 222 ). The FORAM Index [FI ] is based upon observations that sediments on healthy re efs have a larger proportion of symbiont bearing foraminifers shells compared to other smaller foraminifers and stress tolerant foraminifers (Hallock 1988; Hallock et al. 200 3 ). The FI focuses on as semblage changes within foraminiferal populations as reflected in reef sedimen ts. Controversy in foraminiferal research An ongoing controversy in foraminiferal research is the practical application of live versus dead versus total assemblages. Studies of live assemblages in reef associated sediment samples have typically i dentified relatively few taxa living in the sediments ( e.g., Martin 1986 ; Cockey et al. 1996 ), which is why researchers ( e.g., Hallock et al. 1986 b ; Hallock et al. 1993a; Hallock et al. 2006a) have focused on sampling reef rubble and phytal substrates when assessing live populations. foraminifers living in the sediments at the time of sampling may be overreprese nted. This is of serious concern in siliclastic or organic rich sediments where dead shells may quickly dissolve (Aller 1982), but generally not in carbonate sediments (Martin and

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12 Wright 1988). Some researchers have argued that assessment of the accumul ation of foraminiferal shells in the sediment integrates information about the general conditions more effectively than that of living assemblages ( Scott and Medioli 1980; Hallock et al. 2003; Carnahan 2009 ). To form a temporal perspective on a wider comm unity, one would need a view of the dead assemblage, which has not had substantial and selective taphonomic loss An understanding of how a fossil assemblage might differ from the living assemblage is essential fo r paleoecologic reconstructions. How well the total assemblage of tests in the sediments reflects the assemblage of foraminifers living in the area is an ongoing question (Martinez Colon et al. 2009). There are differing opinions on the reliability and usefulness of total foraminiferal assemblag es as environmental indicators. Some researchers (Murray and Alve 1999a 1999 b ; Patterson et al. 1999 ; Murray and Pudsey 2004) have argued forcefully that only live and dead assemblages provide a sound ecological foundation for interpretation (Shifflett 1 961). Hallock et al. (2003) and Martinez Colon et al. ( 2009) suggested that the choice of assemblages (as well as the lowest taxonomic level to assess) depends upon the questions being addressed and the resources available to address those questions. Num erous investigations have shown seasonal changes in living assemblages ( e.g., Lynts 1966 ; Lee et al. 1969 ; Scott and Medioli 1980), but most one time or decadal interval assessment s have focused on associated total assemblages ( e.g., Bock 1971; Martin and Wright 1988 ; Cockey et al. 1996 ; Carnahan et al. 2009 ). Scott and Medioli (1980) found that in a marsh system in Nova Scotia, living populations and assemblages were highly variable resulting from micro environmental changes. However, the total assembla ges

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13 did not change significan tly over the same period Buzas et al. ( 2002) reported similar dead and total assemblages more consistently depicted modern environments, while the li ve assemblage as described by Buzas et al. ( 2002 ). Samples in which live assemblages differ substantially from the dead assemblages can represent local blooms, especially of taxa with fragile or readily soluble shells that are lost from the assemblage soon after death and therefore cannot contribute a representative amount to the total assemblages (Scott and Medioli 1980). While dead shells can be found in plankton tows, transport by suspension is not considered a common means of dispersal of live benthic foraminifers (Murray et al. 1982). A brasion, hydraulic sorting, and removal of smaller foraminifers may result in under representation in th e sediments as compared to the occurrence of liv ing fracti ons of the assemblage (Greenstein 2003) T hose t axa associated with fluffy sediments, (phytodetritus) have a higher dispersion potential (Alve 1999).

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14 P ROJECT OBJECTIVES A sample set collected at Conch Reef in October 2008 provide d the opportunity to examine differences between total foraminiferal assemblages from sediment and rubble samples collected from the same sites and the variability of similar samples collect ed within a general reef area. Foraminiferal assemblages were evaluated using thir teen sets of samples which included sediments and reef rubble The goals were to evaluate inter si t e assemblage vari ability and to determine how assemblage s isolated from sediment samples differed from assemblages isolated from rubble samples at the same locations. The sediment ru bble assemblage comparison contribute s data to the ongoing debate concerning whether assemblages from sediment samples are representative of live assemblages in an area and specifically what taxa tend to be under represented in reef sand samples In addition, this sample set provided the opportunity to compile a species list of common Foraminifera at Conch Reef near t he Aquarius Underwater Habitat. The species list will be useful to other scientist s planning future research as well as contributing to the biodiversity assessments for this active research location.

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15 Major Questions and Hypothes e s 1. Are there inter site differences in the foraminiferal assemblages on the rubble samples from Conch Reef? H o : No sign ificant differ ences will be evident in assemblages between thirteen sites Differences in assemblages on the rubble between sites are not significantly greater than differences between samples from the same site. H 1: Differences in assemblages between sites are signifi cantly greater than differences between samples from the same sites. 2 Do the foraminiferal assemblages from rubble samples differ from assemblages in the sediment samples ? H o : N o difference s will be seen in the foraminiferal assembla ges from the rubble o r sediment samples. H 1 : D iffere nt assemblages will be seen in different substrate s 3. Do any taxa correlate to depth or sediment texture ? H o : N o difference related to depth or sediment texture will be detected H 1 : Differences will be observed with depth or sediment texture.

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16 METHODS Sample c ollection Thirteen sites were sampled during October 2008 at Conch Reef. The sample sites were primarily along transect line intersections and were chosen to facilitate future sampling from the same locations ( Figu re 4 ) The reef area over which the samples were collected was approximately 0.13 km 2 SCUBA divers haphazardly ( i.e., with no a priori knowledge of what foraminifers might be found in any sample) (Hayek and Buzas 1997) collected one 30ml vi al of F igure 4 Conch Reef sites where sediment and rubbles samples were collected. 2008.

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17 sediment and three fist sized pieces of reef rubble from each site Each rubble sample was placed into a re sealable plastic bag at depth and then brought to the surface. All samples were then frozen to preserve color of those collected live ( e.g., Hallock 2006a ). Sample p rocessing Sediment s amples Each sediment sample was placed into a 63 m sieve fitted with a container below to catch mud fractions. Deionized water was sprayed from a squirt bottle o n the sediments until they were washed clean of mu ds The sand sized sediments (>63 m) were washed into a small beaker (100 ml), water was extracted from the beaker usin g a thingamagigy and the sample was placed into a drying oven ~45 o C The dried sample was then weighed. Th e suspended mud fraction was p laced in a beaker and allowed to settle until the water was clear (typically overnight) ; the water was then decanted The remaining mud sample was placed into a smaller beaker (250 ml) and allowed to settle again, overnight. Once s ettled, the remaining w ater was removed and the sample was dried and weighed. The sand sized fraction (>63 m) was divided using a sample splitter. One half of each sand sized fraction w as used in grain size analysis and the other half examined to assess the foraminiferal asse mblages S ubsamples were analyzed for two shallower sites (5 b and 6 b ) and two deeper sites (15 b and 16 b ) to determine variability within and between samples

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18 Grain size a nalysis To determ ine grain size distribution, each dried subsample was weighed, t hen placed in a tower of seven previously weighed sieves ( > 2 mm, 1 2 mm, 0.5 1 mm, 0.25 0.50 mm, 0.125 0.250 mm, 0.125 mm, and shaken for 10 minutes. After 10 minutes on the shaker, each sieve with sediments was weighed and recorded. Any sedi ment that passed through the 63 m sieve was weighed and recorded. The weight percent of each g rain size was calculated, including the mud fraction, corrected for the weight of the mud fraction originally removed by wet sieving. Rubble samples Each piece of rubble was thawed and carefully scrubbed with a toothbrush and rinsed with fresh water to remove foraminifers from the rock surface. Because many foraminifers adhered to tube worms, filamentous algae and algal mats a sonicator was used to dislodge those foraminifers attached to larger pieces. The sediment slurry r emoved from each rubble sample was then dried ~45 o C and weighe d All t hree reef rubble samples were analyzed for two shallower sites (5 _1, 5_2, 5_3 and 6 _1, 6_2, 6_3 ) and two deeper sites ( 15_1, 15_2, 15_3, and 16 _1, 16_2, 16_3 ) to determine variability between and within sites The total seafloor area represented by the three rubble pieces colle cted per station was computed using Carl Zeiss AxioV ison 4.4 software (2002 2004) which calculated area directly from a digital image taken of the reef rubble pieces ( Figure 5 ). Using the rubble seafloor areas sampled, the number of foraminiferal shells/cm 2 was calculated.

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19 Foraminife ral a ssemblages To extract foraminifers from the samples a weighed subsample was sprinkled over a gridded tray and examined under a stereomicrosco pe. The weighed subsample was picked manually with a fine paintbrush to extract approximately 150 200 foraminifers Additional aliquots of the sub sample were weighed and picked until 150 200 specimens were isolated or until 1 gram of sediment was examined All f oraminiferal specimens were picked onto a micropaleontological faunal slide coated with water soluble glue (Ramirez 2008 ). Foraminifers were then sorted and identified to gen us using characteristics defined by Loeblich and Tappan ( 198 7 ). The abundances o f each taxon were calculated using weights of the picked fraction compared to the total Figure 5 Rubble sample with AxioV ision area (cm 2 ) measurem ents indicated. 2008.

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20 weight of the subsamples (Hallock et al. 2003). To compile the species list for the samples, the faunal slides were examined and species identified. D ata Analysis G ra in size a nalysis For each grain size class the raw weights were converted to weight percent for e ach sample using standard procedures called the scale ( Wentworth 1922; Blatt et al. 1972 ) Percent weights of each of the following size fractions (p hi) were determined: > 2mm ( 1), 1 2 mm (0), 0.5 1 mm (1), 0.25 0.50 mm (2), 0.125 0.250mm (3), Median gra in size for each sample was then calculated Foraminiferal a ssemblages Foraminiferal data can be represented in either relative or absolute abundance. Relative abundance expresses each genus as a percenta ge of total foraminifers counted Absolute abundance accounts for the number of foraminifers per unit mass, in grams of bulk sediment sorted, or for rubble sampl es, number of foraminifers per unit area of seafloor sampled. In this study data compared between sediment samples (#/g) and reef rubble samples ( #/100 cm 2 ) are reported and analyzed as relative abundance s Indices a nalysis Several assemblage indices that a re widely used in ecological research are comm only used in foraminiferal research including Taxonomic Richness [S], Shannon [H], Fisher and Evenness [E] (Hayek and Buzas 1997) These indices were calculated for each sample. In add ition, two indices specific to foraminiferal

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21 research the Langer M orphotype Index described previously (Langer 1993 ) and the FORAM Index [FI] ( Hallock et al. 2003 ; Carnahan et al. 2009 ) were also used in analysis of each sample Each genus identified wa s assign ed to one of the four Langer Morphotypes: A) permanently attached, B) t emporarily motile C) m otile and D) p ermanently motile ( Figure 3 ) To calculate the FI ( Table 1 ) the genera of foraminifers wer e placed in one of three functional categories ba sed on their ecological role in warm water environments, which includes : A ) Symbiont bearing taxa: benthic taxa that host algal endosymbionts and are generally relatively large B ) Stress tolerant taxa: smaller benthic taxa commonly found in naturally or a nthropogenically stressed environments such as euryhaline estuaries, intermittently hypoxic environments, or environments subjected to chemical pollution. C ) Other smaller taxa: small benthic taxa that are heterotrophic and therefore bloom with abundan t food sources in otherwise normal marine environments. The percent abundance of each of these groups was used to calculate the FORAM Index (Hallock et al. 2003 ; Carnahan et al. 2009 ) ( Table 1 ).

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22 Figure 6 FORAM Index (FI) representing the three functional groupings. Photos: by Christy McNey Stephenson

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23 et al. (2003 Paper (Yanko et al. 1999; Carnahan 2005 ; Carnahan et al. 2009 ) The FORAM Index resultant values can be interpreted as follows (Hallock et al. 2003) : Values of <2 would result from the presence of stress tolerant tax a w ith the remaining being other smaller foraminifers This indicates heterotrophic processes dominating the reef wher e environmental conditions are unsuitable for reef growth and recovery. Values of 2 4 would result from the presence of <25% some symbiont bearin g species indicating an environment that supports calcifying mixotrophs a lthough not optimal for them Values of >4 would result when >25% of the foraminiferal assemblage is symbiont bearing taxa, indicating environments suitable for reef g rowth and for recovery following a mortality event

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24 Multivariate a nalyses of f oraminiferal a ssemblages Multivariate analyses of foraminiferal assemblages follow Carnahan et al. ( 2009). A nalyses were performed on sediment samples (absolute abundances), rubble samples (absolute abundances), and both sediment and rubble samples (relative abundances) to determine how sample sites grouped based on their similarity of foraminiferal assemblages (Q mode analysis), and how the variables (foraminiferal gen era) clustered (R mode analysis) PRIMER e v.6 (Plymouth Routines in Multivariate Ecological Research PRIMER E Ltd., Plymouth) was used to construct Bray Curtis similarity matrices on square root transformed data This transformation down weights the imp ortance of the highly abundant species, so that similarities depend not only on their (Clarke and Gorley 2006 ) Based on this similarity matrix c luster analys es were performed and Multidimensional S caling ( MD S ) plots were constructed For an MDS plot, the proximity between sites represented similarity and a stress level of <0.2 was considered to be a useful representation of relationships (Clarke and Warwick 2001). To further interpret the MDS plots, two a dditiona l analyses were applied The ANOSIM (analysis of similarity ) and SIMPER (sim ilarity percentages) routine s were performed in PRIMER The ANOSIM test determined if th ere is an assemblage difference among samples, between clusters and other factors. The A NOSIM test produces a Global R statistic between 1 and 1, where zero represents the null hypothesis or no difference amo ng samples. Pairwise tests were run as well with results indicating

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25 the degree of separation between groups as either indistinguishab le, or variation within groups is less tha n the variation between groups (Clarke and Warwick 2001 ). SIMPER determined the contributions of individual genera to the separation of the groups, either for an observed clustering pattern or for the differences among set s of samples SIMPER analysis was carried out on square root transformed data based on site groupings defined by cluster analysis. SIMPER outputs statistical parameters for each genus contributing to >90% similarity within each group or dissimil arity between groups ( Clarke and Gorley 2006 ). Outputs included average abundance, percent contribution, and cumulative percent contribution of each genus. Analyses were performed on the rubble data and the sediment data separately and combined Th e comparison of sediment and rubble samples analyses showed whether the sediment samples cluster ed separately from the rubble samples the ANOSIM analysis s howed if there was similarity between the samples, and the SIMPER analyses show ed which genera contr ibuted to the seperation in either type of sample. To determine which genera tend to co occur (i.e., R mode analyses), a Bray Curtis similarity matrix was constructed based on generic data for all taxa present in more than 5% of the samples. Cluster analy sis and MDS plots were constructed based on this similarity matrix

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26 R ESULTS Grain s ize Results of grain size analysis for each sample are reported as weight percent ( Table 2 ) Median grain size reported in phi ( ) revealed that the majority of site s were characterized by coarse sand (82%) and the rest were medium sand (18%). No sample contained more than 2% mud ( Table 3 )

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27

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28 Foramin iferal assemblages in sediment s amples In the 17 sediment samples examined, the shells of 62 foraminiferal genera were identified ( Table 4 ). Generic abundances by station and a summary of the foraminiferal data from sediment samples by station are provided (A ppendix A ) A taxon accumulation curve ( Figure 6 ) indicated that 90% of the genera could be found in ~10 samp les. The dominant genus was Laevipeneroplis representing 11 %, of foraminiferal shells identified, followed by Amphistegina at 9 %, Asterigerina and Quinqueloculina each at 8%, and Archaias Textularia and Rosalina each at 5 % ( Fig ure 7 ) Another 11 gener a each accounted for at least 2% of the total, while 44 genera made up the remainder of the assemblage. For PRIMER analyses of sediment data genera occu r ring in less than 5% of the samples, which were Abditodentrix, Rectobolivina, Fursenkoina, Cornuspiro ides Triloculinella, Cancris, and Cibicoide s were removed from data set, consistent with recommended procedures ( Clark and Warwick 2001; Parker and Arnold 2002 ) Key genera Symbiont bearing foraminifers dominated in four of the 17 samples the other samples were dominated by other small foraminifers Stress tolerant genera occurred sporadically and together never accounted for 10% of any sample. In f ive out of the 17 sediment samples fewer than 150 fora miniferal shells were found in a one gram sample S a mples 5 and 5b each had fewer than 50 shells per gram Across stations, shell abundance was quite variable, ranging from 38 to 678 foraminiferal shells per gram

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29 Indices analysis The Taxonomic Richness [S] for the sediment samples was 33.59 + 9.77 The mean ( + SD) Shannon Diversity [H] for the sediment samples was 2.9 5 + 0. 29 The mean Fisher alpha di ve rsity for these samples was 11.37 + 2.27 Diversity Index [D] was 0.9 3 + 0.0 3 The mean Evenness [E] for these samples was 0.6 0 + 0. 09 The mean FORAM Index [FI] was 5. 5 7 + 0.8 3 A summary of the data for the sediment samples including means and standard deviations for each assemblage parameter calculated is liste d in Table 5 Maximum values in Table 5 were calculated for the indices based on the total 62 genera of identified from all sediment samples.

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30

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31 Figure 7. Randomized accumulation plot for genera in sediment s amples from Conch Reef, October 2008, indicating that 90 % of the genera are found in about 10 samples

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32 F igure 8 Twenty most abundant genera in sediment samples collected in October 2008 at Conch Reef; the 4 4 less abundant genera are included under remaining

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33

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34 Sampl e distribution T h ree sample clusters were evident in cluster analyses ( Figure 8 ) and the associated MDS Plot ( Figure 9 ) ; the latter had a stress value of 0.07 which denotes a very useful representation of the data Cluster 1 included nine samples which e xhibited no significant differences amo ng them and another two samples (12, 18), that were more than 60% similar to the nine samples. All of the se samples had more other smaller foraminifers than symbiont bearing taxa T h e two samples that differed were primarily by higher overall abundances. Cluster 2 included two s amples (2, 6b) the deeper of which had more symbiont bearing foraminifers than other smaller taxa The shallower site was also notable for the unusual prevalence of Discorbis in greater qu antity than in all other sediment samples Cluster 3 included shallower sites (5, 5b, 6, 13) which had the least number of foraminiferal shells per gram of sediment, and was dominated by symbiont bearing foraminifers. The occurrence of sample 6 as an outlier com pared with sample 6b from the same site indicates that differences within sites can be as great as differences among sites.

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35 Figure 9 Sediment c luster analysis of forami niferal assemblages by station at Conch R eef, October 2008

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36 Figure 10 Bray Curtis Multidimensional Scaling (MDS) plot of similarities of foraminiferal assemblages, in sediment samples from Conch Reef, October 2008.

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37 SIMPER analysis via Bray Curtis similarity ( Appendix B ) summarized in Table 6 revealed that the sediment samples from Cluster 1 had an average similarity of 70 % with Laevipeneroplis, Asterigerina, and Quinqueloculina being the top three c ontributors to the similarity. Cluster 2 samples had an average similarity of 63 % with Laevipeneroplis, Amphistegina, and Quinque loculina being the top three contributors to the similarity. Cluster 3 samples had an average similarity of 61% with Amphistegina Laevipeneroplis, and Archaias being the top three contributors The dissimilarity between Clust ers 1 and 2 is 42% with Aste rigerina, Parasorites, and Quinqueloculina contributing most to the dissimilarity. The dissimilarity between Clusters 2 and 3 is 47% with Rosalina, Quinqueloculina, and Laevipeneroplis contributing most to the dissimilarity. The dissimilarity between Clu sters 1 and 3 is 61% with Quinqueloculina, Asterigerina and Laevipeneroplis as primary contributors An ANOSIM was run on assemblage distributions in the sediment samples with a one way analysis with the cluster number as the factor of comparison. This analysis resulted in a Global R of 0.919 and a significance level (p) of 0.1%, which indicates

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38 significant differences among the clusters ( Table 6 ) Results from the ANOSIM pairwise test between clusters reveals that the signi ficant differences are between Clusters 1 and 2, and 1 and 3, but not between 2 and 3. A two way ANOSIM was run comparing cluster and depth ranges. The test for the differences between cluster groups across all depth ranges resulted in Global R of 0.909 w ith a significance level (p) of 0.1%, a gain s how ing significant difference s between the clusters. T he test for differences between depth ranges across all sample types had a Global R of 0.107 and a significance level (p) of 4.9%, indicating a weak but sig nificant difference between the two de pth ranges (13 18m and 20 26m). Cluster analysis ( r mode) examining all genera which occurred in at least two samples revealed few significant associations ( Figure 10 ). A one way ANOSIM based on samples and FI groupi ng s, resulted in a Global R of 0.14 and s ignificance level (p) of 6.5%. An ANOSIM pairwise tes t c omparing the FI group s indicated significant differences between the occurrences of symbiont bearing taxa and stress tolerant taxa, and between stress toleran t taxa and other smaller taxa ( Table 7 ). The MDS plot with the sediment samples co mpared to the FI group ing s visually represents the physical separa tion with a stress level of 0.17 ( Figure 1 1 ).

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39 Figure 1 1 Cluster analysis of gene ra in sediment samples collected at Conch Reef, October 2008

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40 Figure 1 2 Bray Curtis MDS plot of foraminifers in the sediment samples by FI groupings. SB= Symbiont bearing, ST= Stress tolerant, and other = remaining smaller taxa.

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41 F oraminiferal a ssemblages i n rubble samples Key genera In the 21 rubble samples examined, shells of 70 foraminiferal genera were identified ( Table 4 ). F oraminiferal abundances (100 cm 2 ) per station and a summary of the foraminiferal data by station are provided ( Appendix C ). A gen us accumulation curve ( Figure 1 2 ) indicates that 90% of the genera could be found in ~ 7 samples The dominant genus was Rosalina, representing 9 % of foraminiferal shells identified followed by Quinqueloculina 8 %, Planorbulina 8 % Laevipeneroplis 7 % Mili olinella 5 % and Gav elinopsis 5 % respectfully ( Figure 1 3 ). For statistical analyses genera present in less than 5% of the samples including Bolivinellina, Trochammina, Reussella, Valvulina, Parahauerina, and Glabratella were removed from consideration ( Clark and Warwick 2001; Parker and Arnold 2002 ). Indices analysis The mean ( + SD) Taxonomic Richness [S] for the rubble samples was 49.38 + 3.9 8 The mean Shannon Diversity [H] for the rubble samples was 2.97 + 0.3 4 The mean Fisher alpha diversity for these samples was 12.91 + 1.41. The mean [D] was 0.9 4 + 0.0 1 The mean Even ness [E] for these samples was 0.55 + 0.17 The mean FORAM Index [FI] was 3 .6 0 + 0 .4 2 A summary of the data for the rubble samples i ncluding means and standard deviations for each assemblage parameter calculated is provided in Table 8 Maximum values in Table 8 were calculated for the indices based on the70 total genera identified from all rubble samples.

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42

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43 F igure 13 Randomized accumulation plot for genera of rubble samples fro m Conch Reef in October 2008 indicating that 9 0% of the genera are found in about 7 samples

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44 Figure 1 4 Twenty most abundant genera in rubble samples collected in Oc tober 2008 at Conch Reef; the 55 less c ommon

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45 Sample distribution Cluster analysis (q mode) revealed three main clusters of samples ( Figure 1 4 ). Nineteen of those samples exhibited greater than 60% similarity. The MDS plot comp aring the rubble assemblages had a stress value of 0.06 ( Figure 1 5 ) which denotes an excelle nt representation of the data set The d riving difference among the sample clusters is the quantity of stress tolerant foraminifers and the relative abundances of other smaller taxa as compared with the symbiont bearing taxa. Cluster 1 is made up of two s amples (10_3, 13_3) that had the fewest stress tolerant foraminifers; the other smaller f oraminifers were approximately three times more abundant than symbiont bearing foraminifers. Cluster 2 includes 10 samples that had approximately four times s maller foraminifers than symbiont bearing foraminifers. Subcluster 2 a included 6 samples that did no t differ significantly from each other and had four times more other smaller taxa than symbiont bearing taxa Subc luster 2b included 4 samples that did no t differ significantly from each other in which other smaller foraminifers were 1.5 t imes more abundant than symbiont bearing taxa Cluster 3 included samples in which other smaller foraminifers substantially exceed ed that o f symbiont bearing taxa. Subc luste r 3a contained one sample in which symbiont bearing taxa were the least common Subc luster 3b contained three very similar samples, which had 3.5 4.5 times more other smaller foraminifers than symbiont bearing and approximately three times more symbi ont bearing than stress tolerant taxa. S ub cluster 3c included five samples that did not differ significantly which had 3 4 times more other taxa than symbiont bearing taxa and stress tolerant taxa were more common than in

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46 other samples Rubble s amples from the same collection site cluster ed together ( e.g., 16_1, 2, and 3) or in different clusters ( e.g., 5_1, 2, 3) demonstrating that within site differences could be as great as among sites at this location.

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47 F igure 15 Cluster analysis of rubble samples, based on foraminiferal assemblages, with depth range of sampling site s indicated.

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48 F igure 16 Bray Curtis MDS plot of rubble samples based on foraminiferal assem blages at Conch Reef

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49 A n ANOSIM was run on assembla ge distribu tions in the rubble samples with a one way analysis with the cluster number as the factor of comparison This analysis resulted in a G lobal R of 0. 887 and a significance level (p) of 0.1 %, which indicates significant differences among the rubble sample cl usters SIMPER analysis via Bray Curtis similarity ( Appendix D ) summarized in Table 9 s howed that the samples from Cluster 1 had an average similarity of 75 % with Rosalina, Laevipeneroplis and Planorbulina being the top three contributors to the sim ilarity Cluster 2 samples had an average similarity of 7 3% with Laevipeneroplis, Rosalina, and Planorbulina being the top three foraminifers contributing to the similarity. Cluster 3 samples had an average similarity of 74 % with Quinqueloculina Rosalin a and Planorbulina being the top three foraminifers contributing to the similarity. The dissimilarity between Clusters 2 and 1 is 40 % with Gavelinopsis, Miliolinella and Planorbulina contributing to the dissimilarity. The dissimilarity between Clusters 2 and 3 is 4 0 % with Quinqueloculina, Rosalina and Planorbulina contributing to the dissimilarity. The dissimilarity between Clusters 1 and 3 is 61% with Quinqueloculina, Miliolinella and Rosalina contributing most to the dissimilarity. ANOSIM and SIM PER results from a pairw ise test between clusters a re shown in Table 9 indicating significant differences between each cluster pair

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50 C luster analysis (r mode) examining all genera present in at least two samples revealed f ew significant associations ( Figure 1 6 ). An MDS plot with the rubble samples compared to the FI groupings visually represented the physical separation with a stress level of 0.15 ( Figure 1 7 ). A one way ANOSIM was run with the samples and FI group ing s wh ich resulted in a Global R of 0.043 and s ignifi cance level (p) of 30 % w hich means the sample group as a whole is relatively homogeneous The p airwise test com paring the FI groups again indicated significant differences between symbiont bearing and stress tolerant taxa, and between stress tolerant taxa and other smaller taxa, but not between symbion t bearing and other smaller taxa ( Table 10 )

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51 Figure 1 7 Cluster diagram by foraminiferal genera from rubble samples collected at Conch Reef.

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52 Figure 1 8 Bray Curtis (r mode) MDS plot of rubble samples by FI groupings. SB= Symbiont bearing, ST= Stress tolerant, and other = rem aining smaller taxa.

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53 Comparison of foraminiferal assemblages in sediment and rubble sample s Key genera In all sediment and rubble samples collected from Conch Reef in October 2008, 72 foraminiferal genera in total were identified ( Table 4 ). Those genera found in sediment samples but not in rubble were Reophax and Cibicoides; both were rare. Genera that were observed in the rubble but not in the sediment were Bolivinellina, Cassidulina, Floresina, Glabratella, Haynesina, Parahauerina, Reussella, Sigmavirgulina, Trochammina, and Valvulina. Again, none of these was particularly common in the samples. Indices analysis A ssemblage indices show ed that there were more genera per sample in the rubble than in the sediment. The FI wa s lower in t he rubble samples, while the Fishers [ ] wa s slightly higher both reflecting the greater abundance and div ersity of other smaller foraminifers in the rubble samples. The Shannon Diversity [H] Index [D] and mean Evenness [E] were very similar between sediment and rubble samples. Species richness by order as an indicator of biodiversity ca n be seen in Figure 1 8 Most species belong to the order Miliolida with 57, followed by Rotalida with 34, and Bulminida with 15. In total there were 117 species representing 72 genera, 37 families, and 8 o rders ( Appendix E ).

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54 F igure 1 9 Spe cies richness by foraminiferal order of samples collected at Conch Reef, October 2008

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55 Sample distribution The no rmalized data for the sediment and rubble samples were analyzed in PRIMER as with the other da ta. After combining the sediment and rubble samples genera present in less than 5% of the samples were not in cluded in statistical analyses ( Clark and Warwick 2 001; Parker and Arnold 2002) Those genera were Bolivinellina, Cibicoides, Glabratella, Parahauerina, Reophax Reussella, Trochammina, and Valvulina Cluster analysis (q mode) comparing the sediment and rub ble samples by sample type showed three major clu sters ( Figure 1 9 ). The MDS plot of the same data had a stress value of 0.11 indicating a good representation of the data ( Figure 20 ). ANOSIM and SIMPER analyses via Bray Curtis similarity ( Appendix F ) were run u sing a one way analysis using comparison of s ediment to rubble samples, with clusters u tilized as the factor of comparison ( Table 1 1 ) The ANOSIM analysis resulted in a Global R of 0.909 and a confidence (p) value of 0.1%, which, along with the pairwise comparison statistics confirms that differences betw een clusters are significant.

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56 Cluster 1 consisted of all 21 rubble samples with Rosalina, Quinqueloculina and Planorbulina as the top three contributors to the average similarity of 76% Cluster 1 con tained 3 outliers, one of which was station 11_2 with the highest foraminifers/gram and the lowest FI of the rubble sampl es. The other two outliers had the fewest foraminifers per gram, the highest FI, the fewest stress tolerant specimens, and contained more Archaias than any o ther rubble samples. Cluster 1 contained 9 s ymbiont bearing 3 s tress tolerant, 1 agglutinated taxon and numerous other smaller taxa found more consistently in rubble samples. Cluster 2 co nsisted of 12 sediment samples with Laevipeneroplis, Quinquelocu lina, and Asterigerina being the top three contributors to the average similarity of 71% Cluster 2 includes two outliers; both of which contain more taxa abundant in rubble samples (examples Rosalina, Discorbis rosea and Milionella) than other sediment samples; all samples have more other smaller foraminifers than symbiont bearing taxa. Cluster 2 included 8 s ymbiont bearing 1 s tress tolerant 2 agglutinated genera, and numerous other smaller taxa. Cluster 3 consisted of the remaining 5 sediment sample s with Amphistegina Laevipeneroplis and Archaias being the top three foraminifers contributing to the average similarity of 63% Cluster 3 contained more symbiont bearing foraminifers than other smaller taxa, as well as four of which contain the lowest density sediment samples. Cluster 3 included 6 s ymbiont bearing genera no s tress tolerant 1 agglutinated and the rest other smaller taxa. The dissimilarity between Clusters 1 and 2 is 36 % with Planorbulina, Bolivina and Asterigerina contributing most to the dissimilarity. The dissimilarity between clusters 1 and 3 is 54 % with Miliolinella, Rosalina and Cyclorbiculina contributing

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57 most to the dissimilarity. The dissimilarity between clusters 3 and 2 is 41% with Rosalina, Miliolinella and Textulari a contributing the most to the dissimilarity ( Table 1 1 ). ANOSIM analysis was made on the combined data set with the factor of comparison changed to sample type R esults produced a Global R of 0.732 with a significance level of 0.1%. This indicates a signifi cant difference between the sample types. SIMPER analysis via Bray Curtis similarity ( Appendix G ) comparison of sediment and rubble samples revealed that sediment samples grouped at 65% similarity with Laevipeneroplis, Amphistegina Quinqueloculina and A sterigerina as the top four foraminifers contributing to the similarity. Rubble samples group together at 76% similarity with Rosalina, Quinqueloculina Planorbulina and Laevipeneroplis a s the top four contributors to the similarity. Sediment and rubble samples were 41% dissimilar with Planorbulina, Bolivina Asterigerina and Rosalina contributing most to the dissimilarity ( Table 1 2 )

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58 Figure 20 Cluster analysis of the combined data set (sediment and rubble samples) noting sample types at Conch Reef October 20 08

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59 Figure 2 1. Bray Curtis MDS plot of all samples, based on relative abundances of foraminifers.

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60 Cluster an al ysis (r mode) ( Figure 21 ) based on foraminiferal genera in the comb ined data set exhibited a n MDS stress value of 0.15 which is a good representation of the data A one way ANOSIM assessed FI group ing s which resulted in a Global R: 0.119 and s ignificance level (p) of 7.8% indicating that the assemblage is relatively h omogeneous as a whole comparing sediment and rubble samples H owever the pair wise test comparing the FI groups revealed significant difference s b etween symbiont bearing and s tress tolerant taxa and between s tress tolerant and other foraminifers ( Table 1 3 ) as in previous anlayses.

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61 Figure 2 2 Cluster analysis of foraminiferal genera using the combined (sediment and rubble) data set.

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62 C oncentration ratio A concentration ratio was calculated by comparing the relative abundances of 20 genera that were most common in both sample sets ( Table 1 4 ). The sediment abundances (S) w ere divided by the rubble abundances (R) to establish a ratio (S/R) The fi ve symbiont bearing taxa, along with one agglutinated textularid ( Textularia ) and one agglutinated miliolid ( ** Siphonaptera ) were 2.5 5.5 times more abundant in sediments than in the rubble samples. In contrast, the smaller more fragile taxa w ere under represented by at least half in most cases ( Figure 2 2 ).

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63 Figure 2 3 Concentration ratio of the 20 most c ommon genera, calculated by dividing the average relative abundance of each genus in the sediment by its average relative abundance in the rubble

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64 Comparison of live v ersus dead foraminiferal assemblages A lthough samples were not stained, the specimens of some species collected live can be distinguished when the protoplasm has distinctive color, as previously noted for those taxa that host algal endosymbionts (Hallock et al. 1986b ; Goldstein and Corliss 1994; Bernhard 2000 ). In the sedim ent, ten genera were readily distinguishable as being alive or dead at the time of collection. Four of the genera were symbiont bearing foraminifers, Amphistegina Asterigerina, Laevipeneroplis and Peneroplis; the remaining were other smaller rotalida taxa In the rubble, 28 genera were readily distinguishable as alive or dead at the time of collection Nine of the genera were symbiont bearing foraminifers, Amphistegina Archaias Asterigerina, Cyclorbiculina, Heterostegina, Laevipeneroplis, Parasorites, Peneroplis and Sor ites 4 were stre ss tolerant, 4 small other taxa and the remaining 11 were smaller Rotalida tax a ( Table 1 5 ). Discorbis rosea was the only taxon for which the proportion of specimens collected live in se diments exceeded that of the rubb le sample s Langer Morphotype The Langer (1993) Morphotype categories ( Figure 3 ) were incorporated in to the comparison of live to dead foraminifers ( Table 1 5 ) and in comparing the relative abundances of foraminifers in sediment and rubble samples (Table 16 17 ). The rela ti ve abundances of foraminifers in each samp le type were distinguished by the Langer Morphotype are shown in Table 17 The total a bundances of each Morphotype were div i ded by the total abundance for that sample type to calculate the abundance of foraminifer s for each Morphotype. The calculations of the foraminiferal abundances by

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65 Langer Morphotype ( Table 16 ) show that the sediment and rubble were essentially the same Only three genera from my samples were included in that category ( Heterostegina, Cribroel phidium, and Elphidium ), which were more abundant in the sediments. Table 15 Percentage of live foraminifers found in sediment and rubble with Langer Morphotype and colored a ccording to functional categories

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66 Table 16. Langer Morphotype comparison of foraminiferal relative abundances in sediment and rubble samples from Conch Reef, October 2008. Morphotyp es Sediment Abundance # Genera in Sediment Rubble Abundance # Genera in Rubble A Attached 1.84 2 1.57 2 B Temporarily motile 35.74 21 36.12 23 C Motile (filter feeders) 2.11 2 1.28 3 D Permanently motile 60.32 39 61.03 42

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67

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68

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69 D ISCUSSION History of previous studies C lassic systematic paleontolog ical studies of Caribbean ben thic foraminiferal assemblages include those of (1839), Cushman ( 1922 19 30 ), and Bock ( 1971). The modern foraminiferal assemblages of the Florida reef tract are well known (e.g, Bock 1971 ; Culver and Buzas 1982 ; Martin 1986 ; Cockey et al. 1996 ). The primary difference s in the assemblages between t he species list presented in this study and previous studies are in the more recent generic dist inctions ( Loeblich and Tappan 198 7 ). This list includes for example Abditodentrix, Triloculinella and Pseudotriloculina, which were previously classified as Triloculina or Quinqueloculina. Lidz and Rose (1989) reported approximately 50 foraminiferal spec ies common in Florida reef sediments representing 32 genera and 20 families Wright and Hay ( 1971 ) found 117 species representing 60 genera from the Florida reef tract. Both of those data sets included a great er range of environments than this data set fro m a single shelf margin reef. Nevertheless, the results of this study document that the taxonomy of the benthic foraminiferal assemblages on the Florida reef tract is well known and are well represented at any reef location.

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70 Sample homogeneity and distr ibution My samples overall are very homogenous Hydrodynamics, and sediment movement and transport, especially of shells of smaller foraminifers, may account for the relatively homogeneity of the suites of samples within a sampled area Sixty genera were identified from the sediment samples and 70 genera in the rubble samples. The primary differences between sample types are in the relative abundances of smaller foraminifers. In both, more than 70% of the genera occur at 1% abundance or less. The 12 ge nera not found in both sample types were uncommon, typically occurring in only one or two samples overall. Thus, the sediment assemblages, which were mostly dead shells, well represent ed taxa living primarily on solid and phytal substrates in the area. Despite the taxonomic similarity between rubble and sediment samples, t he relative abundances of the most common taxa found in the sediment samples differed from those found on the rubble Sonication of the rubble material may have contributed to the pres ence of the specimens attached to substrates like algal mats, where the foraminifera were living. Taphonomic destruction and sediment sorting reduced the relative abundances of smaller taxa ( Table 1 7 ). Nevertheless, about 70% of the sediment samples clust ered with the rubble samples at greater than 60% similarity Comparing the relative abundances of the 20 most common taxa between the two sample sets ( Table 1 4 ) indicates that the smaller taxa are under represented in the sediments compared to genera with larger or more robust shells. In sediment samples, six of the top 20 taxa are symbiont bearing genera, three of which are the most abundant

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71 overall. In the rubble samples, the three most abundant genera are other smaller foraminifers, and only three sym biont bearing genera are among the top 20. The distributions of Asterigerina carinata (only one species of this genus occurs in Florida) were notable in my study, as in previous studies. These foraminifers have intermediate sized shells, are thick walled and biconvex in shape, and host algal symbionts. The s hells and even living specimens of this species are commonly found abundantly in both sediment and rubble samples. Previous studies have noted the abundance of this species in higher energy environmen ts (Crevison et al. 2006 ; Ramirez 2008 ; Baker et al. 2009 ). Similarly, the robust asymbiotic Discorbis rosea was also very common, both as dead shel ls and specimens collected live in sediments, consistent with those previous studies. The abundance of Di scorbis rosea indicate s moderate to high energy environments (Triffleman et al. 1991; Peebles et al. 1997). Robust shelled foraminifers are resistant to breakage and, depending upon shape less susceptible to transport Individual foraminiferal species fro m high energy environments with coarse sediment substrates have stronger shells than similar sized individuals from low energy habitats (Wetmore 1987). Concentration ratio The concentration ratios ( Figure 2 2 ) revealed the tendency for the larger and more robust taxa to be concentrated in the sediments compared to smaller and more delicate taxa. Amphistegina, Archaias, Asterigerina, Borelis, and Laevipeneroplis all exhibited concentrations ratios between approximately 1.5 and 3. Cyclorbiculina had the

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72 hig hest concentration ratio of the symbiont bearing taxa. This might be an artifact of its larger, wing shaped structure, which may enhance transport of the she lls from shallower environments ( H ohenegger et al. 1999 ) Archaias a symbiont bearing Miliolida has robust shells that are thick and reinforced by pillars, which form the chamberlets for algal symbionts. This test shape and thickness enables Archaias shells to be resistant to abrasion and win nowing and therefore to accumulate in carbonate sediments (Martin 1986). In addition to Discorbis two other smaller genera were found more than twice as commonly in sediment as on rubble ( Figure 2 2 ). Siphonaptera an agglutinated miliolid, was approximately five times more common, while Textularia which belon gs to the agglutinate Order Textularida, was about 2.5 times more common in sediment. Whether that difference indicates that these taxa live in sediments or are simply more re sistant to destruction is not known but one can speculate on both possibilities In the first possibility, sediment particles with which to build an agglutinated shell are more readily available to foraminifers living in the sediments. Moreove r, living in sediments likely necessitates a stronger shell. Siphonatera was previously r eported ( Hallock et al. 2003 ; Carna han et al. 2009 ) as clustering wit h symbiont bearing foraminifers. Two other smaller m iliolid genera, Articulina and Quinqueloculina, were found equally commonly in sediment and rubble samples ( Figure 2 2 ). Both genera ar e relatively diverse and some species in both genera have intermediate sized and relatively thick shells. Again, members of these genera may be living in the sediment as commonly

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73 as on rubble, and those with relatively thick shells would have higher prese rvation potential. Wetmore (1987) reported that test strength increases with size and with increasing physical energy in the environment. Species living in coarse sediments have stronger shells relative to their size than species living in fine sediments or on algae. Overall shape, chamber size and arrangement, wall thickness, test composition, and strength of connections between chambers would all be expected to affect the test strength ( Boltovskoy and Wright 1976 ; Wetmore 1987) S ample assemblages reve aled no relationship to sediment texture, which varied little across the study area ( Table 2 ). The sediment samples with the fewest shells per gram that differed most from the other sediment samples, and from the rubble samples, were either from shallower depths or from the immediate vicinity of the underwater habitat, either of which could have resulted in disturbance that resulted in additional removal of smaller shells. Martin (1986) did not report Planorbulina and Rosalina in his sediment samples from near Mosquito Bank in the Florida Keys. While these two species are either permanently attached ( Planorbulina ) or temporarily attached ( Rosalina ), they were both fou nd alive in low percentages in sediment samples. Langer (1993) states that while Rosali n a and other species with similar tes t shapes are primarily attached, they do have the capability to detach themselves in response to unfavorable environmental conditions or competition for space No significant depth trends were found, which is not surp rising given the limited range of depths sample d (13 26m) However, there were a few subtle differences in

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74 individual genera and average abundances of foraminifers related to depth. In both the sediment and rubble samples, the deeper stations had higher absolute abundances of foraminifers. Baker et al. ( 2009) reported that live larger foraminifers at Conch Reef in creased in abundance with depth over approximately the same depth range. In the sediment samples Quinqueloculina Laevipeneroplis, and Asterig erina were more abundant at the deeper depths. In the rubble samples, Quinqueloculina, Amphistegina, and Asterigerina were more abundant in the deeper samples. Faunal assemblages Faunal assemblages rather than individual species of foraminifers tend to b e diagnostic as environmental indicators ( Lidz and Rose 1989). The composition of benthic foraminiferal assemblages is influenced by test production, taphonomic destruction, vertical mixing, and horizontal transport ( Loubere et al. 1993 ; Walker and Goldst ein 1999). The most important taphonomic processes affecting the assemblage of benthic foraminifers are transport and destruction of shells Interpretation of the data from this study shows the sediment assemblages are dominated by foraminifers that are more robust Previous studies found that shells of calcareous species ( Cibicides lobatulus ) remained intact longer than shells of an agglutinated species ( Reophax atlantica ), and the relative survival time of the shells of those two species appeared to co rrespond to the increased energy of the microhabitat in which they live d ( Miller and Ellison 1982; Wetmore 1987)

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75 Crevison et al. (2006) analyzed cores taken along the Florida reef track and found strong evidence for vertical mixing, as individual cores w ere very homogeneous and did not stratigraphically reveal the decadal changes found in surf ace sediments reported by Cockey et al. (1996) and Lidz and Hallock (2000). Crevison et al. ( 2006) also noted strong differences in sorting and taphonomic destructi on between cor es from the middle keys region which were well sorted and exhibited a more even distribution of functional groups tha n cores from the upper and lower keys, which contained a more diverse assemblage of shells of smaller taxa. Total assembla ge controversy Basing analyses on total assemblages in sediment samples is controversial among some foraminiferal researchers. Shefflett ( 1961 ) Murray and Alve ( 1999a b ) Patterson et al. ( 1999 ), Murray and Pudsey ( 2004) and others contended that t his me thod miss es many specimens due to taphonomic loss. Particularly i n higher latitudes, hyposaline (estuarine) and deep sea enviro n ments dissolution often prec l udes preservation of calcareous shells ( Aller 1982; Murray and Alve 1999a b; Patterson et al. 199 9 ; Murray and Pudsey 2004). In environments with significant t errigenous input, t he taphonomic loss can be attributed to shells breaking against much hard er quartz sands However, in tropical estuaries and coastal regions where salinity is near normal t he maj ority of the taxa live on phyta l or hard sub strates (Cockey et al. 1996; Peebles et al. 1997) live individual s are lost due to sorting and not to dissolution, and breakage can occur but is less frequent when sediment have similar hardness W hen worki ng in areas where

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76 taphonomic loss or environmental changes have occurred in the area sampled within the last few years, the total assemblages should be interpreted cautiously (Martinez Colon et al. 2009) When analyzing the data from this study, it shows that the total foraminiferal assemblage in the sediments is a good representation of what taxa had been living in the area of study. Comparison of live v ersus dead foraminiferal assemblages Previous studies on live v ersus dead assemblages in the Baltic Sea by A lve ( 1999 ) reported that living foraminifers typically were not abundant in sediment samples. The dead assemblage observed had a much higher diversity L iving populations in the North Atlantic have been observed in both percentages and total numbers, t o fluctuate greatly while corresponding total populations fluctuate only in total numbers (Scott and Medioli 1980). According to Murray and Alve ( 1999 a ), the dead assemblages represent the time averaged contribution of empty shells from the production of successive living assemblages and subsequent modification due to postmortem processes. Buzas et al (2002) reported that dead assemblages depicted modern environments, while the live assemblage in any given sample is a represent at ion of When the dead assemblage and the live assemblage differ substantially it could be representative of a loca l bloom. Murray and Alve ( 2000) took replicate samples adjacent to each other and found substantial spatial variation m ay occur within a centimet er. Studies that compared live and dead assemblages in reef sediment samples ( e.g., Cockey et al. 1996 ; Peebles et al. 1997 ) reported that foraminifers collected alive

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77 typically made up less than 10 % of the foraminiferal shells identified and therefore, d ifferences between dead and total assemblages were insufficient to justify the greater expenditure of effort to distinguish between them. Comparing live v ersus dead assemblages was not a primary goal of this study; hence, the samples evaluated were not prese rved and stained. Nevertheless, the protoplasm color is read ily preserved in som e genera, so specimens collected live are easily distinguished from dead shells. In t he sediment samples 10 genera were identified that included live specimens In t he rubb le samples 28 genera were identified t hat included specimens collected alive ( Table 14 ). O f the genera for which individuals collected live were identifiable, about 15% of the specimens in the sediments and about 85% of those in the rubble were collected alive. Thus, future studies in this area should consider doing a live vs. dead comparison including all available substrates. Abundances o f larger foraminifers collected live from Conch Reef and other Florida reef tract sites by Baker et al. ( 2009 ) sho w numbers that varied with season and depth Over a five year period, Buzas et al. (2002) observed no overall increase or decrease in densities of foraminifers in his study. However, individual species densities often exhibited maximum densities at parti cular times of the year. Substrate, currents, wave intensity, and wave direction affect local distributions of foraminiferal assemblages but do not alter regional patterns ( Lidz and Rose 1989) In s ome areas of the Indian River, there was a seasonal cycl e, while other areas and species exhibited patchiness, even between sites within a few meters of each other ( Buzas 1968 1970 ). The

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78 distribution of live benthic foraminifers can change substantially in a short distance, even in areas that have the similar physical and chemical characteristics (Peebles et al. 1997 ). Most reef dwelling taxa tend to live on phytal or hard substrates rather than directly on the sediments. Martin (1986) found that, in the northern Florida Keys, Archaias lived primarily on vege tation. He found virtually no living Archaias in the sediment samples. Similarly, I found neither live Archaias nor Cyclorbiculina in the sediment, though many dead shells. Archaias in Florida Bay near Long Key are abundant on epiphytes or macroalgae (F ujita and Hallock 1999). Because these taxa have relatively large shells that are resistant to destruction, their dead shells are widespread in the shelf sediments of the tropical western Atlantic and Caribbean (Martin 1986; Triffleman et al. 1991; Peebles et al. 1997 ). Within sample versus within site variability Samples in this study were evaluated to see if there was a difference in the total assemblage s between samples and sample type. Four sediment samples (5, 6, 15, and 16) were evaluated with two s ubsamples each to determine within sample variability Sediment sub samples 5 and 5b were not significant ly different from each other nor from sample 13 which cluster ed together ( Figure 8 ). These samples ha d the least amount of total foraminifers yet t he highest FI values of 6.3 7.4 as well as the most abundant symbiont bearing taxa compared to o ther foraminiferal taxa. Sediment subs amples 6 and 6b were significant ly different The sub samples were nearly identical with respect to symbiont bearing taxa ; the differences between the two

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79 sub samples were more abundant other smaller taxa Between the two sub samples, there was a d ifference of 10 genera as well. Both differences could be accounted for by one subsample containing finer material. Intra site variabil ity was also evaluated for the r ubble samples. Three samples each were examined from stations 5, 6, 15 and 16 Again samples from the same site could be very similar (16_1, 2, 3) or as different as between sites ( e.g., 5_1 versus 5_2 and 5_3). Indices The Foram Index was developed to relate the response of the calcifying benthic community to the status and suitability of the environment for future reef growth (Hallock et al. 2003 ). T he mean FI of the sediment samples w as 5.6 + 0. 8, indicating that the water quality at Conch Reef is suitable for reef growth The F I was developed using sediment samples because their collection adds minimal time or effort to a field sampling effort. Moreover, collection of sediment samples for analysis of total assemblages does not require transport of preservatives, minimizing costs of collection and transport to the laboratory ( Hallock et al. 2003 ). Although the FI design was to be applied to sediment samples, some researchers have applied it to live assembla ges ( P. Hallo ck, personal communication 03/2011 ). My study provided the o pportunity to compare the FI values from rubble substrate, which predominantly represented the live assemblage, and from the total assemblage from sediments. The mean FI for the liv e assemblages was lower, 3.6 + 0.4 ; but still indicates

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80 a significant contribution b y symbiont bearing foraminifers, there by supporting the asse ss ment that water quality at Conch Reef is suitable for calcifying symbioses. There were no significant differe nces seen in the means of the other indices calculated between sediment and rubble samples other than FI and the number of genera found in the samp les. Although Hayek and Buzas ( 2010 ) recommend the use of the se indices for assessing biodiversity those indices did not reveal any significant differences in my samples Rese archers have used these indices, because t he absolute number of taxa identified is to some degree a function of the number of individuals found in a sampl e. F oraminiferal genera were more abundant in the rubble samples (49) than in the sediment samples (34). However when standardized for the number of individuals counted per samples the Fishers diversity index indicates there is no significant difference in diversities between the sample type. Thus the FI in this case was the only index that showed a difference in the sample sets. The sediment reveals what taxa have been living in that ar ea in the past or that are present at the time of sampling. The underlying observation for the FI is that sediments on healthy reefs have a larger proportion of shells of symbiont bearing foraminifers compared to other smaller foraminifers and stress tole rant foraminifers ( Hallock 1988; Hallock et al. 2003 ). Foraminifers found in the sediments are represented primarily by empty shells while live specimens can be found living on a variety of substrate s A ccording to Engle (2000 p. 3 1 tor of the response of benthic organisms to perturbations in the environment would not only quantify their present

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81 condition in the eco s y stems but would also integrate the effects of anthropogenic and natural stressors on the organisms over time ( Boesch a nd Rosenberg 1981; Messer et al. 1991). This information is precisely what foraminiferal shells in the sediments can provide ( Hallock et al. 2003 ).

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82 C ONCLUSIONS Overall, the foraminiferal assemblage at Conch Reef was extremely homogenous taxonomically. In October 2008 117 foraminiferal species, representing 72 genera, 37 families, and 8 o rders were identified in 1 7 sediment samp les and 21 rubble samples collected from a depth range of 13 to 26 m Foraminiferal assemblages in the sediment samples were more variable than in the rubble samples. Sixty two genera in total were found in the sediment samples, while 70 genera in total were found in the rubble samples. Tw o rare genera occurred only in sediment samples, while 10 genera were found only in the rubble The sonication of rubble material is important to describe the species living on the rubble. Without sonication, those foraminifera living in the substrate on the rubble ( e.g., algal mats) could have be en missed. Overall, the differences between the foraminiferal assemblages found in the rubble and sediment were primarily the differences in relative abundances of the taxa. Depth and sediment texture were not significant factors influencing, the foraminiferal assemblage s over the depth range sampl ed Sediment samples included 12 s ymbiont bearing foraminiferal genera representing 41% of the total assemblage, 10 s tress tolerant genera representing 3%, p lanktic taxa represent ing 2% of the assemblage and 40 other smaller f oraminiferal

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83 genera represent ing 54% of the total. Ten s amples were sufficient to encounter 90% of t he genera found Sediments reflect the taphonomic assemblage in the area In the rubble samples 12 s ymbiont bearing f oraminiferal genera represented 20% of the total assemblage, 12 s tress tolerant g enera represented 6%, p lanktic foraminifers represented 1% and 46 other smaller f oraminiferal genera represented 73 % of the total foraminiferal assemblage Seven samples were sufficient to encounter 90% of the genera found on reef rubbl e. A concentration ratio comparing relative abundances in r ubble vs. s ediment revealed that smaller taxa were more abundant in the rubble, while shells of larger, symbiont bearing taxa were about 2.5 5.5 times more concentrated in the sediment, indicatin g winnowing of sm aller taxa Shells of Siphonatera an agglutinated miliolid, and Textularia an agglutinated textularid, were more abundant in sediments as compared to rubble, indicating their high preservation potential The concentration ratio provide s a loss index that reflects the size and durability of foraminiferal taxa. F diversities were slightly lower in assemblages from sediments ( 11.4 + 2.3 ) compared to rubble samples ( 12.9 + 1.4 ). This alpha index measures the diversity with in an area or community. In this set of samples, the diversity in the rubble is slightl y higher than those in the sediment, due to foraminifers living on the rubble rather than in the sediment. M ean Shannon Diversity [H] [D] and Evenness [E] were similar between sample types. In contrast, the FORAM Index was hig her in assemblages from sediment samples ( 5.6 + 0.8 ) compared with rubble samples (3.6 + 0.4 ). The mean FORAM Index [FI] for the sediment samples (5.6 + 0.8) indicates

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84 that water quality at Conch Reef is suitable for calcifying symbioses. The most abunda nt symbiont bearing genera were Amphistegina, Laevipeneroplis, Asterigerina and Archaias. There are inter site differences in the foraminiferal assemblages on both reef rubble and sediment samples from Conch Reef. The driving difference among the rubbl e stations was the quantity of stress tolerant foraminifers and the relative abundance of other smaller taxa. The rubble samples exhibited > 70 % similarity among the stations. Sediment samples differed among the stations, with the difference being the site s that contained an assemblage that was similar to a rubble sample with greater abundances of stress tolerant foraminifers and of other smaller taxa. The other major differences in the sediment samples were in the shells/gram and the presence of symbi ont bearing foraminifers. One set of replicate rubble s amples from the same station clustered together H owever another set of rubble samples replicates did not cluster together, demonstrating the intra site differences could be as great as inter site. Th e foraminiferal assemblages from rubble samples differ ed from the assemblage s in the sediment sample, primarily in relative abundances. The taxonomic differences were in minimal and were mainly in occurrences of rare taxa. Thus, s ediment samples appear t o adequately represent the local populations for foraminiferal assemblages in a reef ecosystem.

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85 REFERENCES Aller, R.C., 1982 Carbonate Dissolution in Nearshore Terrigenous Muds: the Role of Ph ysical and Biological Reworking : Journal of Geology v. 90 p 79 95. Alve, E., 1999, Colonization of New Habitats by Benthic Foraminifera: a Review: Earth Science Reviews v. 46, p 167 185. Baker, R.D., Hallock, P., Moses, E.F., Williams, D.E., and Ramirez, A., 2009 Larger Foraminifers of the Florida Reef Tra ct, USA: Distribution P atterns on Reef Rubble Habitats: Journal of Foraminiferal Research v 39, p. 267 277. Bernhard, J. M., 2000, Distin guishing Live f rom Dead Foraminifera: Methods Review and Proper Applications: Micropaleontology v.46, p. 37 46. Bla tt, H., Middlet on, G. V., and Murray, R. C. 1972 Origin of sedimentary rocks : Prentice Hall, N.J 782 pp. Bo ck, W.D. 1971 A Handbook of Benth ic Foraminifera of Florida Bay and Adjacent W aters In: Jones, J.I., and Bock W.D., (E ds ), A Symposium of Recent South Florida Foraminifera : Miami Geol ogical Soc iety Mem oir v 1, p 1 72. Boesc h, D.F. and Rosenberg, R., 1981, Response to Stres s in Marine Benthic Communities, In : Barrett, W.G. and Rosenberg, R ( E ds ), Stress effects on Natural Ecosystems Wi ley Interscience, New York, pp. 179 200 Boltovskoy, E., and Wright R., 1976 Recent Foraminifera: Junk, The Hague, 515 pp. Buzas, M.A., 1968, On the Spatial Distribution of Foraminiferal: Contributions from the Cushman Foundation for Foraminiferal R esearch v.19, p. 1 11.

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89 Hallock, P. and Talge, H.K., 1993 Benthic Foraminifer Amphistegina gibbosa in the Florida Keys in 1991 92 : Proceedings of the Colloq uium on Global Aspects of Coral Reefs: Health, Hazards, and History Miami, Florida, June 10 11, p. 94 100. Hallock, P. and Talge, H.K. 1994, A Predatory Foraminifer Flore sina a mphiphaga n. sp., fr om the Florida Keys: Journal of Foraminiferal Research v.24, p. 210 213 Hallock, P., Cottey, T.L., Forward, L.B., and Halas, J., 1986 Population Biology and Sediment Production of Archaias angulatus (Foraminiferida) in Largo Sound, Florida : Journal of Foraminiferal Research v. 16 p. 1 8. Hallock, P., Lid z, B.H., Cockey Burkhard, E.M., and Donnelly, K.B., 2003 Foraminifera as Bioindicators in Coral Reef Assessment and Monitoring: The FORAM Index : Environmental Monitoring and Assessment v.81, p. 221 238. Hallock P Talge H K Cockey E M and Muller R G ., 1995, A New Disease in Reef D welling Foraminifera; I mplications for C oastal S edimentation : Journal of Foraminiferal Research v. 25 p. 280 286 Hallock, P., Williams, D.E., Fisher, E.M., and Toler, S.K. 2006a Bleaching in Foraminifera with Algal Symbionts: Implications for Reef Monitoring and Risk Assessment : Anuario de Instituto de Geociencias UFRJ v.29, p. 108 128. Hallock, P., Williams, D.E., Toler, S.K., Fisher, E.M., and Talge, H.K. 2006b Bleaching in Reef Dwelling Foraminifers: Implica tions for Reef D ecline : Proceedings of the 10 th International Coral Reef Symposium Okinawa, Japan, June 2004 p. 729 737. Hayek, L. C., and Buzas, M. A., 1997 Surveying Natural Populations : Columbia University Press, New York, 563 pp. Hayek, L. C., and Buzas, M. A., 2010, Surveying Natural Populations: Qu antitative T ools for Assessing B iodiversity : Columbia University Press, New York, 61 6 pp.

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90 Hohenegger, J., Yordanova, E., Nakano, Y., and Tatazreiter, F., 1999 Habitats of Larger Foraminifera on the Up per Reef Slope of Sesoko Island, Okinawa Japan : Mar ine Micropaleontology v. 36, p. 109 168 Hottinger, L., Halicz, E., and Reiss, Z. 1993, Recent Foraminifera from the Gulf of Aqaba, Red Sea : Slovenska Akaademija Znanosti in Umetnosti, Ljubljana, Slovaki a, 230 pp Jones, R. W. 1994 The Challenger Foraminifera : Oxford University Press London, England, 300pp. Langer, M.R., 1993 Ep iphytic F oraminifera : Marine Micropaleontology v.20, p. 235 265. Lee, J.J., and Anderson, O.R., 1991, Symbiosis in For aminifera, In: J.J. Lee and O.R. Anderson (Eds), Biology of Foraminifera Academic Press, London, pp.157 220. Lee, J.J Muller, W.A. Stone, R.J., McEnery, M. W., and Zucker, W., 1969 Standing Crop of Foraminifera in Sublittoral Epiphytic Communities o f a Long Island Salt Marsh : Marine Biology v 4, p.44 61 Lidz, B.H., and Hallock, P., 2000, Sedimentary Petrology of a Declining Reef Ecosystem, Florida Reef Tract (U.S.A): Journal of Coastal Research v.16, p.675 697. Lidz, B. H., and Rose, P. R. 19 89 Diagnostic Foraminiferal Assemblages o f Florida Bay and Adjacent Shallow Waters: A Comparison : Bulletin of Marine Sc ience v 44 p. 399 418 Loeblich, A.R. Jr. and Tappan, H., 1987 Foraminiferal Genera and their Classification : Van Nost rand Reinhold, New York, 970 pp.

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91 Loubere, P., Gary, A., and Lagoe, M. 1993 Generation of the Benthic Foraminiferal Assemblage: T heory and Preliminary Data : Mar ine Micropaleontology v. 20, p. 165 181 Lynts, G.W., 1966 Variation of Foraminiferal Standing Crop over Short Distances in Buttonwood Sound, Florida Bay : Limnology and Oceanography v.11, p. 562 566. Martin, R.E., 1986, H abitat and Distribution of the Foraminifer Archaias Angulatus (Fitchel and Moll) (Miliolida, S oritidae) Northern Florida Keys: J ournal of Foraminiferal Research, v.16, p. 201 206 Martin, R.E. and Wright, R.C., 1988 Information Loss in the Transition fr om Life to Death Assemblages of Foraminifera in Back Reef Environments, Key Largo, Florida : Journal of Paleontology v. 62 p. 399 410. Martinez Colon, M., Hallock, P., and Green Ruiz, C., 2009 Strategies for Using Shallow Water Benthic Foraminifers as Bi oindicators of Potenti ally Toxic Elements: A Review: Journal of Foraminiferal Research v 39 p. 278 299. McManus, J.W., and Polsenberg, J.F. 2004 Coral A lg al P hase S hifts on C oral R eefs: Ecological and Environmental A spects : Progress i n Oceanography v 60 p. 263 279 Mes ser, J.J., Linthurst, R.A., and Overton, W.S., 1991 An EPA P rogram for M onitoring E cological S tatus and Trends: Environmental Monitoring and Assessment v. 17, p. 67 78 Miller, D.S., and Ellison, R.L. 1982 The Relationship of Foram inifera and Submarine Topography on New Jersey Delaware Continental Shelf: Bulletin of the Geological Society of America v.93, p. 239 245 Murray J. W., 1983, Population D ynamics of B enthic Foraminifera: Results from the Exe Estuary, England: Journal of Foraminiferal Research v.13, p. 1 12.

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94 Schafer, C. T. 2000 Monitoring Nearshore Marine Environmen ts Using Benthic Foraminifera: Some Protocols and P itfalls: Mi cropaleontology v.46, p. 161 169 Sen Gupta, B., (Ed ) 1999 Modern Foraminifera : Kluwer Academic Publisher, Dordrecht 371 pp. Severin, K.P. 1983 Test Morphology of Benthic Foraminifera as a Discriminator of Biofaces : Marine Micropaleontology v.8 p. 65 76 Shifflett, E. 1961 Living Dead and Total Foraminiferal Fau nas, Heald Bank, Gulf of Mexico: Micropaleontology v.7, p. 45 54 Triffleman, N.J., Hallock, P., Hine, A.C. and Peebles, M., 1991, Distribution of Foraminiferal Tests in Sediments of Serranilla Bank S ite Nicaraguan Rise, Southwestern Caribbean: Journal of Foraminiferal Research v.21, p.39 47. Walker, S.E., and Goldstein, S.T. 1999 Taphonomic Tiering: E xperimental F ield T aphonomy of M ollusks and F oraminifera A bove and B elow the S ediment W ater I nterface : Palaeogeography, Palaeoclimatology, Palaeoecology v.149, p. 227 244 Wentworth, C. K ., 1922 A S cale of G rade and C la ss T erms for C lastic S ediments : Journal of Geology v.30, p. 377 392. Wetmore, K.L. 1987, Correlations b etween Test Strength, Morphology, and Habitat in Some Benthic Foraminifera from the Coast of Washington : Journal of Foraminiferal Research v. 17 p 1 13 Wooldridge, S.A. 2009 A New C onceptual M odel for the Warm W ater B reakdown of the Coral Algae Endosymbios is: Marine and Freshwater Research v.60, p.483 496

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95 Wright, R.C., and Hay, W.W., 1971, The Abundance and Distribution of Foraminifers in a Back Reef Environment Molasses Reef, Florida In: Jones J.I., and Bock W.D., ( E ds.), A Symposium of Recent Sout h Florida Foraminifera: Miami Geological Society Memoir v. 1, p. 121 174 Zeiss, C., 2002, AxioVison v4.4, Digital Imagine Processing Software, Carl Zeiss Microimaging, Germany. www.uncw.edu/aquarius www.floridakeys.noaa.gov.com

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96 APPENDICES

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97 Appendix A Raw data from sediment samples

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98 Appendix A (Continued)

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99 Appendix A (Continued)

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100 Appendix A (Continued)

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101 Appendix B. Raw SIMPER results from sediment samples

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106 A ppendix B (Continued)

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107 Appendix C: Raw data from rubble samples

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111 Appendix D: Raw SIMPER results from rubble samples

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12 0 Appendix E: Foraminiferal Species list for Conch Reef, Florida Table E1 Foraminiferal species identified in samples collected at Conch Reef in October 2008. Order Genus Species Species Author Reference with Ill ustrations Buliminida Abditodentrix rhoimboidalis (Millett) Cimerman and La n ger, 1991 Plate 61 Figures 4 6 Buliminida Bolivina lowmani Phleger and Parker Bock 1971 Plate 16 Figure 14 Buliminida Bolivina pulchella Cushman Bock 1971 Plate 17 Figure 1 B uliminida Bolivina striatula Cushman Bock 1971 Plate 17 Figure 2 Buliminida Bolivinellina lanceolata (Parker) Bock 1971 Plate 16 Figure 13 Buliminida Brizalina goesit Cushman Bock 1971 Plate 16 Figure 11 Buliminida Brizalina mexicana Cushman Galloway and Hemingway, 1971 Plate 17 Figure 3 Buliminida Rectobolivina advena (Cushman) Bock 1971 Plate17 Figure 5 Buliminida Cassidulina laevigata d'Orbigny Phleger and Parker, 1951 Plate 14 Figures 6a 6b Buliminida Cassidulina subglobosa Brady Bock 1971 Pl ate 23 Figure 12 Buliminida Floresina amphiphaga Hallock and Talge Hallock and Talge, 1994 Plate 1 Figures 1 4 Buliminida Fursenkoina compressa (Bailey) Bock 1971 Plate 23 Figure 7 Buliminida Reussella atlantica Cushman Loeblich and Tappan, 1987 Plate 575 Figures 9 12 Buliminida Sigmavirgulina tortuosa (Brady) Loeblich and Tappan, 1987 Plate 579 Figures 1 5 Buliminida Trifarina bella (Phleger and Parker) Bock 1971 Plate 17 Figure 13 Globigerinida Globigerinella siphonifera (d'Orbigny) Bock 1971 Pl ate 25 Figures 1 2 Globigerinida Globigerinoides ruber d'Orbigny Loeblich and Tappan, 1987 Plate 536 Figures 1 6 Globigerinida Globorotalia tumida (d'Orbigny) Loeblich and Tappan, 1987 Plate 515 Figures 4 6 Lituolida Reophax difflugiformis Brady Bock 1 971 Plate 1 Figure 8 Lituolida Valvulina oviedoiana d'Orbigny Bock 1971 Plate 2 Figure 11 Miliolida Androsina lucasi Levy Loeblich and Tappan, 1987 Plate 410 Figures 6 10 Miliolida Archaias angulatus (Fichtel and Moll) Bock 1971 Plate 14 Figures 1 3

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121 Appendix E (Continued) Table E1 Continued Order Genus Species Species Author Reference with Illustrations Miliolida Borelis pulchra (d'Orbigny) Bock 1971 Plate 14 Figure 7 Miliolida Cyclorbiculina compressa (d'Orbigny) Loeblich and Tappan, 1987 Pla te 412 Figures 1 6 Miliolida Laevipeneroplis bradyi Cushman Bock 1971 Plate 2 Figure 8 Miliolida Laevipeneroplis carinatus d'Orbigny Bock 1971 Plate 13 Figure 9 Miliolida Laevipeneroplis proteus d'Orbigny Bock 1971 Plate 13 Figure 11 Miliolida Monal ysidium politum Chapman Bock 1971 Plate 13 Figure 12 Miliolida Parasorites orbitolitoides (Hofker) Bock 1971 Plate 13 Figure 15 Miliolida Peneroplis pertusus (Forskal) Bock 1971 Plate 13 Figure 10 Miliolida Sorites dominicensis Ehrenberg Richardson, 2006 Figures 1 2 Miliolida Adelosina fitterei Acosta Bock 1971 Plate 10 Figures 5 7 Miliolida Affinetrina bermudzi (Acosta) Bock 1971 Plate 9 Figures 9 11 Miliolida Affinetrina oblonga (Montague) Bock 1971 Plate 11 Figures 2 4 Miliolida Articulina a ntillarum Cushman Bock 1971 Plate 12 Figure 13 Miliolida Articulina mexicana Cushman Bock 1971 Plate 13 Figure 3 Miliolida Articulina mucronata (d'Orbigny) Bock 1971 Plate 13 Figure 4 Miliolida Articulina sagra Brady Bock 1971 Plate 13 Figure 7 Mil iolida Cornuspiroides foliacea (Phillipi) Bock 1971 Plate 3 Figure 4 Miliolida Cycloforina subpoeyana (Cushman) Bock 1971 Plate 7 Figures 10 12 Miliolida Cylcoforina arenata (Cushman) Bock 1971 Plate 3 Figure 8 Miliolida Hauerina bradyi Cushman Bock 1971 Plate 12 Figure 9 Miliolida Lachlanella bicarinata (d'Orbigny) Bock 1971 Plate 9 Figures 12 13 Miliolida Lachlanella polygona (d'Orbigny) Bock 1971 Plate 7 Figures 1 3 Miliolida Miliolinella circularis (Bornemann) Bock 1971 Plate 12 Figure 5

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122 A ppendix E (Continued) Table E1 Continued Order Genus Species Species Author Reference with Illustrations Miliolida Miliolinella fichteliana (d'Orbigny) Bock 1971 Plate 12 Figure 6 Miliolida Miliolinella labiosa (d'Orbigny) Bock 1971 Plate 12 Figur e 7 Miliolida Pseudohauerina speciosa (Karrer) Bock 1971 Plate 12 Figures 10 11 Miliolida Pseudoschlumbergerina ovata (Sidebottom) Hottinger, et al. 1993 Plate 46 Figures 1 6 Miliolida Pseudoschlumbergerina spp. Loeblich and Tappan, 1987 Miliolida Pse udotriloculina bosciana (d'Orbigny) Bock 1971 Plate 5 Figures 3 5 Miliolida Pseudotriloculina laevigata d'Orbigny Bock 1971 Plate 6 Figures 4 6 Miliolida Pyrgo denticulata (Brady) Bock 1971 Plate 8 Figure 11 Miliolida Pyrgo elongata (d'Orbigny) Bock 1971 Plate 8 Figure 12 Miliolida Pyrgo fornasinii Chapman and Parr. Bock 1971 Plate 8 Figure 13 Miliolida Quinqueloculina bicostata d'Orbigny Bock 1971 Plate 4 Figures 9 11 Miliolida Quinqueloculina bicarinata d'Orbigny Bock 1971 Plate 4 Figures 6 8 Miliolida Quinqueloculina candeina d'Orbigny Poag, 1981 Plate 55 and 56 Figures 4 4a Miliolida Quinqueloculina collumnosa Cushman Bock 1971 Plate 5 Figures 9 11 Miliolida Quinqueloculina lamarckiana d'Orbigny Bock 1971 Plate 6 Figures 7 9 Miliolida Quinqueloculina parkeri Cushman Bock 1971 Plate 6 Figures 10 12 Miliolida Quinqueloculina seminulum (Linnaeus) Bock 1971 Plate 7 Figures 7 9 Miliolida Quinqueloculina tricarinata d'Orbigny Bock 1971 Plate 8 Figures 1 2 Miliolida Schlumbergerina alveo liniformis Cushman Bock 1971 Plate 12 Figure 12 Miliolida Siphonaptera agglutinans (d'Orbigny) Bock 1971 Plate 4 Figures 3 5 Miliolida Siphonaptera bidentata d'Orbigny Bock 1971 Plate 5 Figures 1 2 Miliolida Siphonaptera horrida (Cushman) Bock 1971 Plate 6 Figures 1 3

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123 Appendix E (Continued) Table E1 Continued Order Genus Species Species Author Reference with Illustrations Miliolida Spirolina arietinus (Batsch) Bock 1971 Plate 13 Figure 14 Miliolida Spiroloculina antillarum d'Orbigny Bock 19 71 Plate 3 Figure 7 Miliolida Spiroloculina communis Cushman Bock 1971 Plate 3 Figure 10 Miliolida Triloculina linneiana Bandy Bock 1971 Plate 10 Figures 11 12 Miliolida Triloculina triangularis (d'Orbigny) Bock 1971 Plate 8 Figures 6 7 Miliolida Tr iloculina tricarinata d'Orbigny Bock 1971 Plate 12 Figures 1 2 Miliolida Triloculina trigonula (Lamarck) Bock 1971 Plate 12 Figures 3 4 Miliolida Triloculinella spp. Cimerman and La n ger, 1991 Plate 44 Figure 5 Miliolida Wiesnerella auriculata (Egger) Loeblich and Tappan, 1987 Plate 330 Figures 11 13 Rotalida Amphistegina gibbosa d'Orbigny Hallock and others, 1995 Plate 1 Rotalida Asterigerina carinata d'Orbigny Bock 1971 Plate 19 Figure 12 Rotalida Heterostegina depressa d'Orbigny Bock 1971 Plate 21 Figure 3 Rotalida Ammonia parkinsoniana (d'Orbigny) Bock 1971 Plate 20 Figures 5 6 Rotalida Cribroelphidium poeyanum Cushman and Bronnimann Bock 1971 Plate 21 Figures 1 2 Rotalida Elphidium advenum (Cushman) Bock 1971 Plate 20 Figures 7 8 Rotali da Elphidium discoidale (d'Orbigny) Bock 1971 Plate 20 Figures 9 10 Rotalida Elphidium sagrum (d'Orbigny) Bock 1971 Plate 20 Figures 11 12 Rotalida Haynesina despresula (Kornfeld) Bock 1971 Plate 23 Figure 14 Rotalida Nonionella spp. Loeblich and Ta ppan, 1987 Rotalida Nonionoides grateloupi (d'Orbigny) Bock 1971 Plate 23 Figure 15 Rotalida Cancris sagra (d'Orbigny) Bock 1971 Plate 19 Figures 6 7 Rotalida Cibicides robustus (Flint) Bock 1971 Plate 22 Figures 5 6

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124 Appendix E (Continu ed) Table E 1 Continued Order Genus Species Species Author Reference with Illustrations Rotalida Cibicoides spp. Loeblich and Tappan, 1987 Rotalida Cymballoporetta squammosa (d'Orbigny) Bock 1971 Plate 23 Figures 1 2 Rotalida Discogypsina vesicularis Silvestri Loeblich and Tappan, 1987 Plate 661 Figures 11 13 Rotalida Discorbinella bertheloti (d'Orbigny) Loeblich and Tappan, 1987 Plate 630 Figures 1 4 Rotalida Discorbis rosea (d'Orbigny) Bock 1971 Plate 17 Figures 15 16 Rotalida Eponides antillarum d'Orbign y Bock 1971 Plate 21 Figures 4 5 Rotalida Eponides repandus (Fichtel and Moll) Bock 1971 Plate 21 Figures 6 7 Rotalida Gavelinopsis praegeri (Heron Allen and Earland) Loeblich and Tappan, 1987 Plate 608 Figures 6 12 Rotalida Glabratella pulvinata (Bra dy) Jones et al. 1994 Plate 88 Figure 10 Rotalida Lobatula lobatula (Walker and Jacob) Loeblich and Tappan, 1987 Plate 637 Figures 10 13 Rotalida Neoconorbina orbicularis (Terquem) Bock 1971 Plate 18 Figures 7 8 Rotalida Neoeponides mira (Cushman) Bock 1971 Plate 18 Figures 3 4 Rotalida Planorbulina acervalis Brady Bock 1971 Plate 22 Figures 9 10 Rotalida Planorbulina mediterranasis d'Orbigny Bock 1971 Plate 22 Figures 11 12 Rotalida Rosalina bahameaensis Todd and Low Poag, 1981 Plate 41 42 Figure 3 Rotalida Rosalina bradyi Cushman Cimerman and Langer 1991 Plate 71 Figures 1 5 Rotalida Rosalina concinna (Brady) Poag, 1981 Plate 41 42 Figure 4 Rotalida Rosalina floridana (Cushman) Bock 1971 Plate 18 Figures 9 10 Rotalida Rosalina floridensis (Cushman) Poag, 1981 Plate 41 42 Figure 2 Rotalida Rosalina subaraucana (Cushman) Poag, 1981 Plate 41 42 Figure 1 Rotalida Siphonina pulchra Cushman Bock 1971 Plate 19 Figures 10 11 Spirillinida Spirillina vivipara Ehrenberg Bock 1971 Plate 20 Figure 4

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125 Appendix E (Continued) Table E1 Continued Order Genus Species Species Author Reference with Illustrations Textularida Bigenerina nosdosaria d'Orbigny Bock 1971 Plate 2 Figure 6 Textularida Clavulina tricarinata d'Orbigny Bock 1971 Plate 2 Figu re 14 Textularida Textularia agglutinans d'Orbigny Bock 1971 Plate 2 Figure 1 Textularida Textularia conica d'Orbigny Bock 1971 Plate 2 Figure 3 Trochamminida Trochammina japonica Ishiwada Bock 1971 Plate 2 Figures 8 9

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126 Appendix F: Raw SIMPER results on the combined data set by Clusters

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127 Appendix F (Continued)

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128 Appendix F (Continued)

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129 Appendix F (Continued)

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130 Appendix F (Continued)

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131 Appendix F (Continued)

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132 Appendix F (Continued)

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133 Appendix F (Continued)

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134 Appendix G: Raw SIMPER results on the combined data set to sample type

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135 Appendix G (Continued)

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136 Appendix G (Continued)

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137 Appendix G (Continued)


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Stephenson, Christy Michelle.
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Foraminiferal assemblages on sediment and reef rubble at conch reef, florida usa
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ABSTRACT: ABSTRACT Foraminiferal Assemblages on Sediments and Reef Rubble at Conch Reef, Florida USA Christy Stephenson Benthic foraminiferal assemblages are widely used to interpret responses of the benthic communities to environmental stresses. This study compares epibiotic foraminiferal assemblages, collected from reef rubble, with those from reef sediments. The study site, Conch Reef, is the site of the Aquarius Underwater Habitat research facility and includes protected areas used only for scientific studies. Although a number of studies have enumerated foraminiferal taxa from the Florida reef tract, no projects have focused on the assemblages that occur at Conch Reef. Sediment and reef rubbles samples were collected via SCUBA from a depth range of 13 to 26 m during October 2008. Foraminiferal assemblages were assessed and compared between the two sample types. A total of 117 foraminiferal species, representing 72 genera, 37 families, and 8 orders were identified in 13 sediment samples and 21 rubble samples. In the rubble samples, 70 genera were identified, including 12 symbiont-bearing genera representing 20% of the total assemblage, 12 stress-tolerant genera representing 6%, planktic foraminifers representing 1%, and 46 other smaller foraminiferal genera representing 73% of the total foraminiferal assemblage. The rubble samples were quite homogenous. The mean (+SD) Fisher alpha α diversity of genera in these samples was 12.9 + 1.4. Sediment samples included 60 of the same genera. The 12 symbiont-bearing genera represented 41% of the total assemblage, 10 stress-tolerant genera represented 3%, planktic taxa represented 2%, and 40 other smaller foraminiferal genera represented 54% of the total assemblage. Overall, the taxonomic assemblages were very similar between the sample types, with sediment assemblages clearly representing the local and regional reef foraminiferal assemblage. The mean (+SD) Fisher alpha α for sediment samples was 11.4 + 2.3, which is not significantly different from that found for the rubble samples. A concentration ratio comparing relative abundances in sediment vs. rubble samples revealed that shells of larger, symbiont-bearing taxa were about 2.5-5.5 times more concentrated in the sediment, indicating winnowing of smaller taxa. Shells of Siphonatera, an agglutinated miliolid, and Textularia, an agglutinated textularid, were more abundant in sediments than in rubble, indicating high preservation potential. The concentration ratio provides a new taphonomic index that reflects the size and durability of foraminiferal taxa. The mean FORAM Index (FI) for the sediment samples (5.57 + 0.83) indicates that water quality at Conch Reef is suitable for calcifying symbioses. The most abundant symbiont-bearing genera were Amphistegina, Laevipeneroplis, Asterigerina, and Archaias.
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Advisor:
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Benthic Communities
Concentration Ratio
Coral Reef
Environmental Indicators
Foram Index
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Dissertations, Academic
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