Analyses of foraminiferal assemblages involve time consuming microscopic assessment of sediment samples. Image recognition software, which systematically matches features within sample images against an image library, is widely used in contexts ranging from law enforcement to medical research. At present, scientific applications such as identification of specimens in plankton samples utilize flow through systems in which samples are suspended in liquid and pass through a beam of light where the images are captured using transmitted light. Identification of foraminifers generally utilizes reflected light, because most shells are relatively opaque. My goal was to design and test a protocol to directly image foraminiferal specimens using reflected light and then apply recognition software to those images. A library of high quality digital images was established by photographing foraminifers identified conventionally from sediment samples from the west Florida shelf. Recognition software, VisualSpreadsheet™ by Fluid Imaging Technologies, Inc., was then trained to improve automated assemblage counts and those results were compared to results from direct visual assessment. The auto classification feature produced composite accuracies of foraminiferal groups in the range of 60–70% compared to traditional visual identification by a researcher using a stereo microscope. Site SC34, the source of images for the original image library, had an initial accuracy of 75% that was improved slightly through an alteration to one of the software classes, but composite accuracy plateaued at 60% with the updated filters. Thus, image acquisition advancements and further development of image recognition software will be required to improve automated or semi automated foraminiferal classifications. However, other potential applications were noted. For example, an advantage of acquiring digital images of entire samples or subsamples is the ability to collect quantitative data such as diameter and length, allowing size-frequency assessments of foraminiferal populations while possibly automating grain size analyses without requiring separate processing. In addition, data files of library and sample specimens can be readily shared with other researchers.

A goal of the U.S. Environmental Protection Agency is to develop protocols applicable to coral reefs to distinguish between the effects of local water quality and those associated with regional to global environmental change. One test case is the current-dominated southeast coast of Florida where the Delray Outfall delivers 30 million gallons per day (114,000 cubic meters per day) of secondary-treated sewage into the ocean. Five study sites were established at depths between 15 and 18 m, and at distances between 1 and 18 km distance from the outfall, where the Stony Coral Rapid Bioassessment Protocol (RBP) was conducted to determine coral cover and selected other parameters. During sampling, 29 surface sediment samples were collected that I analyzed with respect to sediment texture, foraminiferal assemblages, and sediment constituents. Most samples were characterized by fine sands with <2% mud. A total of 77 genera of foraminifers were identified, averaging 28 genera per sample. Abundances of foraminiferal shells varied among samples by more than an order of magnitude (83 to 1010 shells per g sediment). The Foraminifera in Reef Assessment and Monitoring (FORAM) Index was calculated from the foraminiferal data, yielding values of 3 or more for all sites, with 26 of the 29 test sites yielding values >4, indicating that water quality should support coral growth. Sediment constituent analyses revealed that the sediments were overwhelmingly dominated by unidentifiable fragments (60%), with molluscan debris second (20%), and calcareous algae third (4.5%); larger foraminiferal shells and coral fragments together made up < 5.5%. The resulting sediment constituent (SEDCON) Index was consistently <2, indicating that erosional processes dominate over sediment production along the sampled shelf area. Results provided by the FORAM and SEDCON indices are consistent with results for stony coral based on the RBP. Stony coral cover was low at all sites, <2%, indicating that coral occurs in the area but neither dominates the benthos nor builds reefs. No relationship was observed between any parameter and distance from the Delray Outfall. However, both the RBP and FORAM Index indicated poorest conditions at the Horseshoe site, suggesting unidentified stressors in that vicinity.

Heavy-metal pollution is an issue of concern in estuaries such as Biscayne Bay that are heavily influenced by agricultural, urban, and harbor activities. The goals of this study were to provide a state of the bay assessment that can be used to interpret changes that have occurred over the past 60 years in Biscayne Bay, to provide a baseline to compare changes in the ecosystems during and after execution of the Comprehensive Everglades Restorations Plan (CERP), and to determine if benthic foraminiferal assemblages in Biscayne Bay reflect heavy-metal contamination in sediments. Surficial samples were collected at 147 sites throughout the bay. Analyses included geochemical assessment of the mud fraction for 32 chemical parameters, grain-size analysis, and assessment of foraminiferal assemblages at the genus level. Geochemical analyses revealed elevated concentrations of a suite of heavy metals in the sediments of the northern bay, between Miami and Key Biscayne, and the periphery of the southern bay from Black Creek Canal south to Turkey Point. Cluster analysis, multi-dimensional scaling, and multivariate-correlation analyses revealed three distinct foraminiferal assemblages. One assemblage, characteristic of the northern bay, was defined by stress-tolerant taxa including Ammonia, Cribroelphidium, Nonion, and Haynesina, which were present in low abundances. Distribution of this assemblage correlated with the most elevated concentrations of heavy metals. The assemblage that defined the southwestern margin of the bay was dominated by Ammonia and Quinqueloculina. This assemblage is characterized by the lowest diversities and highest abundances, and is likely influenced by both reduced salinity and elevated organic-carbon concentrations.

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.

Submitted by Biblioteca de Pós-Graduação em Geoquímica BGQ (bgq@ndc.uff.br) on 2016-05-03T16:41:23Z No. of bitstreams: 1 GASPAR_2014_TeseUFF.pdf: 5686020 bytes, checksum: 1a09a81a8e3faf6aa6834f79b7c46c47 (MD5) / Made available in DSpace on 2016-05-03T16:41:23Z (GMT). No. of bitstreams: 1 GASPAR_2014_TeseUFF.pdf: 5686020 bytes, checksum: 1a09a81a8e3faf6aa6834f79b7c46c47 (MD5) / Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geociências-Geoquímica. Niterói, RJ / Este estudo teve como objetivo principal avaliar a saúde do ecossistema recifal do Atol das Rocas utilizando como indicadores as associações de foraminíferos bentônicos, Índice FORAM e saúde e cobertura de corais. Além disso, descrever a razão Mg/Ca em testas recentes de Nonion commune para identificar mais uma possível espécie para estudos paleoclimáticos. Um total de 276 transeções de ponto e faixa (20x1m) foram realizadas em 6 expedições (out/07, mar e dez/10, mai/11, mai e nov/12) e revelaram coberturas de corais variando entre ~3 e 50%, de acordo com o padrão de circulação de água nas piscinas. Relações entre branqueamento/doenças em corais e anomalias de temperatura foram registradas para 2010. O que pode ter causado uma redução significativa na cobertura de corais em 4 piscinas abertas, após março e dezembro de 2010. A prevalência de doenças, que lesionam e causam mortalidade parcial ou total dos corais, foi alta nessas piscinas. As doenças atingiram maiores porcentagens e persistem por mais tempo que o branqueamento. Em 2012, sem registro de temperatura muito elevadas, a cobertura para de apresentar sinais de declínio, embora ainda existam colônias doentes. Fatores como altos níveis de radiação solar, alta transparência da água, pouca profundidade, intenso fluxo de água, baixa diversidade de corais, dominância do gênero Siderastrea e o contato direto dos corais com muitas algas podem ter contribuído para os altos percentuais de doenças. Além disso, um total de 105 amostras de sedimento superficial foi coletado em dezembro de 2010 e maio de 2011 nas mesmas piscinas. Foram identificados 108 gêneros de foraminíferos bentônicos, porém a maioria com abundância inferior a 1%. Os gêneros Archaias, Quinqueloculina, Sorites, Amphistegina e Borelis dominaram nos dois períodos de amostragem, e juntos representam mais de 60% da abundância relativa em todas as piscinas. Uma relação positiva e significativa foi encontrada entre a granulometria e a densidade de foraminíferos. As menores densidades foram encontradas nas piscinas abertas com intenso fluxo de água. A alta transparência da água, pouca profundidade, intenso fluxo de água, abundância de algas e ambiente carbonático favorecem o domínio de Archaias angulatus nas associações de foraminíferos. A proporção dos foraminíferos que possuem endossimbiontes é superior a 40% em todas as piscinas, resultando em valores médios de Índice FORAM (IF) entre 5,76 e 9,15, com uma média geral para o Atol igual a 7,0. Portanto, o IF indica que a qualidade da água é favorável ao crescimento e/ou recuperação recifal, mas não apresentou correlação com cobertura de coral ou algas, assim como em outras regiões recifais do Brasil. Recomenda-se que o monitoramento da cobertura e saúde recifal e dos foraminíferos sejam complementares e não independentes. Para as análises de geoquímica elementar nas testas de foraminíferos recentes, com o método de ablação a laser (LA-ICP-MS) foram utilizados 50 exemplares de Nonion commune que estavam vivos no momento da coleta, com tamanhos entre 200-354 μm. As médias das razões de Mg/Ca registradas nesse trabalho - 6,12 a 7,85 mmol/mol - estão de acordo com a faixa de variação encontradas para foraminíferos bentônicos sem endossimbiontes e para águas rasas e quentes. A relação entre os valores de Mg/Ca e o tamanho da carapaça, sugerem que futuras análises considerem apenas testas maiores que 250 μm e, preferencialmente, com variações de apenas 50 μm no tamanho das mesmas. É possível sugerir que essa espécie possa ser usada em futuros estudos baseados em Mg/Ca com finalidade de reconstrução de paleotemperaturas, pois parecem ter relação com a temperatura de calcificação, embora um estudo mais detalhado em um ambiente com variações sazonais de TSM mais acentuadas, seja necessário para confirmar essa relação. A continuidade do monitoramento é essencial para compreender como esse ambiente tão importante irá se recuperar e/ou responder aos futuros eventos de anomalias térmicas / This study aimed to assess Rocas Atoll coral reef health by monitoring corals cover and health, as well the benthic foraminifera assemblages and the FORAM Index (FI) in 15 tide pools. Furthermore, the Mg/Ca ratios for recent (stained) foraminifera Nonion commune from Rocas Atoll were also described. A total of 276 point intercept transects and belt transects (20x1m) were surveyed during 6 expeditions (Oct/07, Mar and Dec/10, May/11, May and Nov/12) and revealed coral cover ranging between ~3 and 50% inside tide pools. Bleached and diseased corals were positive related to SST anomalies recorded for 2010, and might be the main reason of a significant coral cover decline in 4 open tide pools. Coral diseases reached higher percentages and persist longer than bleaching. In 2012 no high temperature was recorded and coral cover showing no signs of decline. High radiation levels, clear water, shallow depth, high water flow, low coral diversity, high abundance of one species (Siderastrea stellata) and direct algal contact might be influenced the high percentages of coral diseases. A total of 105 surface sediment samples were collected between December 2010 and May 2011 at the same tide pools. A total of 108 genera of benthic foraminifera were identified, however most of them showed abundance lower than 1%. The genera Archaias, Quinqueloculina, Sorites, Amphistegina and Borelis were dominant in the two sampling periods, and together represent more than 60% relative abundance in all tide pools. A significant and positive relation was found between the grain size and benthic foraminifera density. Lowest densities were founded in open tide pools with high water flow. Clear water, shallow depth, high water flow, high algae abundance and carbonate environment resulted in Archaias angulatus associations. Symbiont-bearing foraminifera proportion is above 40% in all tide pools, resulting FORAM Index (FI) values between 5.76 and 9.15, with mean value 7.0 for Rocas Atoll. Therefore, the FI indicates that the water quality is favorable to growth and/or reef recovery, but showed no correlation with coral cover and algae. It is recommended that monitoring coral cover and health and foraminifera to be complementary and not independent. Trace element composition analyses of recent foraminifera, using the laser ablation (LA-ICP-MS), were conducted in 50 tests of Nonion commune (alive at sampling time), tests sizes ranged from 200-354 μm. The mean Mg/Ca ratios recorded were - 6.12 to 7.85 mmol/mol - consistent with the range of variation found for smaller benthic foraminifera and to shallow and warm waters. The relation between Mg/Ca rations and test size, suggest that future analysis considers only tests greater than 250 μm, and varying only 50 μm. It is possible to suggest that this species may be used in future paleotemperatures research Mg/Cabased, since they appear to be related to the seawater calcification temperature, although a more detailed study in an environment with a higher seasonal SST variations is necessary to confirm this relation. Continuing monitoring is essential to understand how Rocas Atoll will recover and/or respond to future events of thermal stress anomalies