Dissertations / Theses on the topic 'Marine meteorology'

Aircraft measurements are analysed from the “First Lagrangian” of the Atlantic Stratocumulus Transition Experiment (ASTEX) from south east of the Azores Islands. In this experiment, Lagrangian strategy was used and the marine air mass, that advected southward, was followed during 12 to 14 June 1992. During the experiment, the stratocumulus clouds transitioned into thin and broken stratocumulus with cumulus cloud penetrating from below. To characterise the vertical structure in the marine boundary layer the buoyancy fluxes, the variances, the turbulent kinetic energy, the momentum fluxes and humidity fluxes were examined. The buoyancy flux profiles were used to discover the decoupling of the stratocumulus and the sub-cloud layer. Turbulence analysis for all five flights shows that the cloud layer were decoupled from the underlying layer. In the cloud layer the buoyancy production due to longwave radiative cooling at cloud top, was the main source for driving the turbulence. In the sub-cloud layer, the variances indicate wind shear to be the main generator of turbulence for the first two days. Then, as sea surface temperature increases, buoyancy produced turbulence was more pronounced. The u-, v- and w-spectra and cospectra of wθ and uw give insight into the typical eddy sizes, and how the peak wavelengths vary with height. The peak wavelengths in sub-cloud and cloud layer were larger than layer depth and u- and v-spectral peak wavelengths often larger than the peak wavelength from w-spectra. While peak wavelengths in the sub-cloud layer vary with the height above the surface, they are approximately invariant with height in the cloud layer.

The vertical structure in the coastal marine atmosphere has been investigated using data from aircraft measurements performed along the Blekinge coast. The present data are from the third of October 1990. The main feature is fairly homogeneous horizontal conditions and a subceeing boundary layer which lowers from 600 meters down to about 50 meters during the day. The turbulence were found to be in a decreasing state. The turbulence parameters were normalized using normal stationary scaling, in order to compare with other results.

Thesis (M.S. in Meteorology and Oceanography)--Naval Postgraduate School, September 1990.
Thesis Advisor(s): Shaw, W.J. Second Reader: Nuss, W.A. "September 1990." Description based on title screen as viewed on December 29, 2009. DTIC Identifier(s): Marine atmospheres, marginal ice zones, geostropic wind, atmospheric boundary layer, stratus clouds, cumulus clouds, stratocumulus clouds, wind velocity, temperature inversion, air ice interactions. Author(s) subject terms: Marginal ice zone. Includes bibliographical references (p. 45-46). Also available in print.

Two days in May 1997 has been studied. During one of the days a sea breeze circulation occured, and the two days were compared in search for effects from the sea breeze on the fluxes in the marine boundary layer. Measurements were made on a tower at the small island Östergarnsholm east of the island Gotland, and by an instrumented aircraft over the sea east and west of Gotland. The direction of the geostrophic wind were about northwest during the time period, but 17 m/s during May 3 and 7 m/s during May 4. The stratification was stable over the main part of the Baltic sea because of the large temperature differences between land and sea surfaces. But as the sea breeze developed and the wind direction turned to the southeast, the stratification at Östergarnsholm changed to near neutral. Both the wind speed and the fluxes decreased with distance from the Swedish mainland and the west coast of Gotland, and the fluxes were over all very small. The momentum flux showed no big difference between the days. Because of the decrease with the distance from the coast and the wind speed it was concluded that the stratification was of greater importance than the sea breeze circulation for the momentum fluxe. But the heat flux was affected by the sea breeze. Because of the sea breeze the stratification became neutral, and thus the heat flux very small. The presence of swell in the baltic sea was also studied. The correlation coefficient gave unexpected result during May 3, with no difference for swell and no swell conditions. The angle between the swell and the wind wave was about 90° during both days, and could not be the reason for the difference. During the May 3 the stratification was mostly stable, while it on May 4 was unstable. It is suggested that this could be a reason for the behaviour of ruw.

Thesis (M.S. in Physical Oceanography and Meteorology)--Naval Postgraduate School, September 2006.
Thesis Advisor(s): Philip A. Durkee. "September 2006." Includes bibliographical references (p. 65). Also available in print.

Thesis (M.S.)--Massachusetts Institute of Technology at Woods Hole Oceanographic Institution, 2006.
"September 2006." Description based on title screen as viewed on June 8, 2010. DTIC Descriptor(s): Doppler Radar, Wind Velocity, Sound Ranging, Doppler Sonar, Buoys, Measurement, Motion, Oceanographic Equipment, Theses DTIC Identifier(s): Doppler Sodar, Sodar (Sound Detection and Ranging), ASIS Includes bibliographical references (leaf 75). Also available in print.

Thesis (M.S. in Meteorology and Physical Oceanography)--Naval Postgraduate School, September 1990.
Thesis Advisor(s): Garwood, R. W. Second Reader: Chu, P. C. "September 1990." Description based on title screen viewed on December 16, 2009. DTIC Descriptor(s): Marine meteorology, thermoclines, thickness, production, predictions, models, energy, theses, turbulence, temperature gradients, vertical orientation, heating, kinetic energy, budgets, oceans, weather stations, entrainment, north pacific ocean, shear properties, transients. DTIC Identifier(s): Mixed layer (marine) air sea interaction, entrainment shear production, mixed layer. Author(s) subject terms: air-sea interaction, entrainment shear production, mixed layer. Includes bibliographical references (p. 46-47). Also available in print.

A number of studies have investigated the distribution of higher marine fungi in temperate estuarine systems. However, little is known of the distribution of higher marine fungi along tropical and subtropical estuarine salinity gradients and how the species composition may change seasonally. The purpose of this study was to examine the distribution and seasonal occurrence of higher marine fungi along a salinity gradient in a subtropical waterway, the New River estuarine system in southern Florida. In addition, a number of physical parameters such as water temperature, salinity, dissolved oxygen and pH were measured. Five stations were established along the New River waterway. Mean salinity ranged from 2 ppt at the most freshwater station (station 1) to 32 ppt at the highest salinity station (station 5) . Physical parameters were measured every two weeks at each station. The substrates employed for fugal collection were wood panels of a hardwood, white oak (Quercus alba) and a softwood Douglas fir (Pseudotsugu menziessi). Four sets of panels were submerged at each station. One pair was removed every three months, at each station, for a period of one year. Thirteen species of fungi were identified during the course of the study. The Ascomycotina were represented by four species and the Deutermycotina were represented by nine species. Some fungal species displayed a physiological preference for higher saline waters. Trichocladium achrasporum was only isolated from station 5, with the highest salinity (32 ppt). Three known terrestrial species (Alternaria sp., Aspergillus sp. and Penicillium sp.) were isolated from the station that exhibited the lowest salinity, station 1 (2 ppt). These terrestrial species may be considered as contaminant species. Verruculina enalia, a known marine species (Kohlmeyer and Kohlmeyer 1979), was isolated from only the lower salinity regions and not the higher salinity sites. The distribution of fungal species did not appear to follow any seasonal pattern however patterns of succession were discernible. During the first period fungal diversity was at a maximum. Diversity gradually decreased with time consistent with previously observed successional patterns (Dix and Webster 1995). Compared to temperate studies of marine fungal distribution (Kirk and Brandt 1980, Kirk and Schatz 1980, Shearer 1972) species diversity was relatively low. The main theme of this study was dominance. Halosphaeria quadricornuta and Verruculina enalia were the two dominant species. The ascocarp frequency of Halosphaeria quadricornuta was inversely proportional to Verruculina enalia. This abundance pattern may suggest interference behavior.

Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 1030. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. In turn, such variations can alter the amount of carbon dioxide in the Earth's atmosphere. However, studying viral diversity presents challenges. Morphological similarities among many types of viruses make it preferable to use genetic methods of investigation, but the absence of a single gene common to all families of viruses hampers the identification of viruses in environmental samples. Nonetheless, some genes are shared within phage families, and those shared ("signature") genes can be used as markers to identify members of a family. In addition, community profiling methods can fingerprint the diversity of a viral community. Most previous studies of marine viral communities consist of a single glimpse—a representation of the community at a single time and place, or at a few depths sampled at one time. While the resources required to collect marine samples often make broader or repeated sampling impracticable, without studies conducted over greater time and spatial ranges, our knowledge of marine viral dynamics will remain limited. To gain strides in understanding spatial and temporal variability in marine viral diversity, this dissertation focused on a detailed examination of viral diversity at a single site in the Sargasso Sea. Time and depth intervals for sampling were kept as uniform as possible in order to strengthen the conclusions to be drawn from the research. The Sargasso Sea is a seasonally oligotrophic portion of the North Atlantic Ocean, characterized by deep convective winter mixing and summer stratification of the water column. A tremendous amount of oceanographic research has been conducted in the Sargasso Sea because it is home to the Bermuda Atlantic Time-series Study (BATS), one of the world's longest-running ocean time series studies. Because of the core monthly measurements made at the BATS site and the vast amount of ancillary research that uses BATS as a platform, the site is an excellent place to study viral diversity. Using a variety of techniques, this research aimed to expand our knowledge of viral dynamics by analyzing the viral community of the Sargasso Sea over a several-year period, through different seasons, and at different depths. The first chapter developed phoH as a new signature gene for assessing marine viral diversity. The phoH gene is disproportionately present in fully-sequenced marine phage, as opposed to phage isolated from non-marine environments, and is widespread in the marine environment. Diversity of the phoH gene was high, and most of the sequences recovered belonged to phylogenetic groups that did not contain any cultured representatives, indicating that cultured phage isolates do not adequately represent the diversity found in marine environments. Composition of the phoH communities at each sampled location and depth was distinguishable according to phylogenetic clustering, although most phoH clusters were recovered from multiple sites. These factors demonstrate that phoH will be useful for studying marine phage diversity worldwide. Chapter 2 analyzed the viral diversity of a depth profile at BATS by amplifying and deep sequencing the phoH gene. This comprehensive study of the gene's diversity over three different years, several seasons, and a range of depths from the surface to 1000 m revealed that the viruses at BATS contain a large pool of phoH sequences, but that most of those sequences are rare. The phoH sequences were dominated by just a few operational taxonomic units (OTUs). Rarefaction analysis showed that the sequencing was sufficient to capture the diversity of the gene at BATS, and in fact no new phylogenetic clusters were identified that were not seen in the small amount of Sanger sequencing performed for the initial phoH study in Chapter 1. Some of the more abundant phoH OTUs recurred every season and every year, in varying degrees, although similar depths and seasons clustered together. Overall, the phoH gene revealed depth-based, seasonal, and interannual differences in the diversity of the viral community at BATS. Chapter 3 continued the extensive examination of viral diversity at BATS by using several signature genes and a fingerprinting technique to assess changes between winter and summer viral communities over two depths in three different years. This chapter investigated whether the annually recurring subsurface peak in viral abundance corresponded to recurring changes in composition of the viral community in the vicinity of the peak. Clustering analysis was used to determine which samples were most similar. The results demonstrated that the viral communities at the surface and at 100 m depth were more similar to each other in winter (March), regardless of the year, than they were in summer (September), when the water column is stratified as opposed to well-mixed. These findings may stem from physical factors such as UV irradiation of viral particles during stratification, as well as seasonal and depth-related differences in host communities associated with the depth of the mixed layer. This dissertation provides substantial advances to the field of microbial ecology. First, the development of phoH as a signature gene is an important addition to the limited set of tools available for studying marine viral diversity. This research also constitutes the first deep sequencing of a signature gene for marine viruses, providing a guide for the depth of sequencing needed to capture the diversity of a marine viral community and a benchmark for the level of viral diversity to expect in an oligotrophic marine system. Finally, the dissertation expands our knowledge of the viral community at BATS by examining the community based on four different measures of composition, rather than abundance. The research presented here also suggests several avenues of future investigation, including redesigning the phoH primers to expand their scope, sampling the viral community at BATS at the precise depth of the peak in abundance, working to identify the hosts of aquatic gokushoviruses, and culturing and sequencing additional marine viruses in order to improve the reflection of natural environmental communities in genomic databases.

Atmospheric aerosols are a highly relevant component of the climate system affecting atmospheric radiative transfer and the hydrological cycle. As opposed to other key atmospheric constituents with climatic relevance, atmospheric aerosol particles are highly heterogeneous in time and space with respect to their size, concentration, chemical composition and physical properties. Many aspects of their life cycle are not understood, making them difficult to represent in climate models and hard to control as a pollutant. Aerosol-cloud interactions in particular are infamous as a major source of uncertainty in future climate predictions. Field measurements are an important source of information for the modeling community and can lead to a better understanding of chemical and microphysical processes. In this study, field data from urban, marine, and arid settings are analyzed and the impact of meteorological conditions on the evolution of aerosol particles while in the atmosphere is investigated. Particular attention is given to organic aerosols, which are a poorly understood component of atmospheric aerosols. Local wind characteristics, solar radiation, relative humidity and the presence or absence of clouds and fog are found to be crucial factors in the transport and chemical evolution of aerosol particles. Organic aerosols in particular are found to be heavily impacted by processes in the liquid phase (cloud droplets and aerosol water). The reported measurements serve to improve the process-level understanding of aerosol evolution in different environments and to inform the modeling community by providing realistic values for input parameters and validation of model calculations.

The following is a study of the regulation of production of a catabolic enzyme, beta-glucosidase, by isolated strains of marine bacteria. Catabolic enzymes transform organic matter to monosaccharides which are utilized as an energy source for growth by bacteria. The bacterial strains were isolated from the Gulf Stream off the coast of Florida, as well as from particulate matter collected from waters adjacent to the Florida coast. The first section describes the preparation of a liquid medium using sterile saltwater supplemented with inorganic nutrients and a carbohydrate component. This medium allowed growth of marine bacteria under carbohydrate-limiting conditions. A solid agar version of the media was also prepared, which allowed isolation of individual colonies of marine bacteria under carbohydrate-limiting conditions. The second section describes analyses of the regulation of beta-glucosidase production by five isolated bacterial strains using methylumbelliferyl-glucopyranoside (MUF-glu) as a model substrate. The beta-glucosidase hydrolysis of MUF-glu to glucose and a highly fluorescing product, methylumbelliferon (MUF ), allowed a measurement of enzyme activity in laboratory cultures. The experiments showed that four of the five bacterial strains isolated could regulate production of beta-glucosidase. When cellobiose, in particular, was the only carbohydrate present, the four strains showing regulatory ability produced elevated levels of enzyme activity. This elevated enzyme activity was not observed when glucose was provided as the only carbohydrate source. The fifth strain showed only low-level enzyme activity in the presence of cellobiose or glucose. This is the first evidence of the regulation of beta-glucosidase activity in particular strains of marine bacteria. Authenticity of beta-glucosidase activity was confirmed with known inhibitors of beta-glucosidase, gluconic acid, and glucose. The enzyme activities of all the isolated strains, measured by hydrolysis of MUF-glu to fluorescent MUF, showed sensitivity to both enzyme inhibitors. The sensitivity was observed as lower MUF production compared to control assay samples with no inhibitor added. The first isolated bacterial strain, from Gulf Stream waters, also showed an ability to repress the production of beta-glucosidase in the presence of glucose. This strain was tested with cylic AMP, known to neutralize glucose repression of beta-galactosidase in E.coli. Cyclic AMP, however, did not neutralize the effect· of glucose on repressing beta-glucosidase activity in the isolated marine bacterium.

Coliphages may be an alternative to bacterial indicators of sewage pollution in sea water. However, non-human sources of coliphage to the marine environment have not been investigated. A study was conducted in Southeastern Florida to determine how E. coli C (ATCC 13706) bacteriophages of non-human origin could interfere with the coliphage indicator system in the monitoring of human fecal pollution in sea water. Coliphages were detected, in variable numbers, in 12.5%, 80%, and 33.3% of human, seagull (Larus delawarensis), and pelican (Pelicanus occidentalis carolinensis) fecal samples, respectively, as well as in 100% of raw sewage samples. No coliphage was detected in feces of dolphin (Tursiops truncatus) and sea lion (Zalophus californianus). Single fecal samples of cormorant (Phalacrocorax auritus floridanus) and royal tern (Thalasseus maximus maximus) also contained coliphage. The coliphage content per gram of dry weight of raw sewage was significantly (α = 0.00007) higher than that of all the other fecal samples. Even though coliphage titers in the animal feces are lower than in raw sewage, in restricted geographical areas (i.e. marinas), non-human animal sources may still be important. Three time series analyses were performed to investigate the inconsistent detection of coliphage in human feces. Coliphage was present in only 3 out of 7 fresh human stool samples. However, coliphages appeared after several days of aging of the samples in a dilution of sterile phosphate buffered water. It is hypothesized that lysogenic bacteria in human feces release coliphage through spontaneous induction and physico-chemical conditions outside the human intestine may trigger this induction.

In this study the flux attenuation due to sensor displacement has been investigated over sea using an extensive set of data from the "Ocean Horizontal Array Turbulence Study". All previous investigations of the flux attenuation have been performed over land.

A function developed for correcting fluxes in the homogenous surface layer was compared to measured flux attenuation. This investigation revealed the possibility to find new functions describing the flux attenuation when measurements are carried out over sea. From the measured flux attenuation studied here a change in the form of correction functions was required to improve the estimated flux loss. The most significant difference found in this report compared to the previous landbased study Horst (2006) is for stable conditions, where significantly less flux loss is found over sea. Two new functions describing the attenuation due to sensor displacement over sea have been constructed.

One of these expressions has a discontinuity at z/L = 0. This is supported by measured flux attenuation. A reasonable interpretation is; however, that this discontinuity is caused by two separate turbulence regimes near neutrality on the stable and unstable side respectively. The discontinuity is thus not believed to be an effect merely of stability. A second correction function which is continuous over all stabilities has therefore also been constructed. These two functions and the correction function from Horst (2006) have been compared to measured flux loss. Based on this comparison the continuous correction function is recommended for correcting scalar fluxes measured over sea. It should be noted, however, that this expression only describes the mean attenuation and has been constructed from measurements at 5 and 5.5 m above mean sea level.

The theoretical basis used in the development of the function for flux attenuation over land allows for a direct link between a spectral shape and the attenuation expression. This link has been preserved for the new expressions presented in this report. The spectral shape corresponding to the continuous correction function has been compared to measured mean cospectra and also to the cospectra from Horst (2006) corresponding to crosswind displacements.

At a height of 10 m and a sensor displacement of 0.2 m the mean flux attenuation is about 1.3-4% in the stability interval −1 < z/L < 1.5 when using the new correction functions presented in this report.

Coral reefs in Broward County are increasingly threatened by coastal and marine construction activities. Infrastructure installation (cables, pipelines, and sewer outfalls), beach renourishment, and dredge and fill operations have both anticipated and inadvertent impacts which may result in reef damage. Mitigation practices consisting of impact avoidance and minimization are necessary to prevent and offset reef damage. Coral transplantation is a commonly utilized impact minimization tool which aims to protect corals threatened by impending construction projects. Coral colonies are removed from their natural habitats and relocated to analogous unthreatened sites prior to construction. This study focuses on coral transplantation that occurred as impact minimization for two recently completed coastal and marine construction projects in Broward County. The first project involved relocation of colonies to natural reef away from potential damage by a natural gas pipeline geotechnical survey. The second project involved relocation of colonies to an artificial reef in relation to a beach renourishment project. Colonies from both projects were monitored and analyzed in regards to survival and growth to determine transplantation success. A combined 1100 colonies were transplanted for these projects, with approximately 25% of these chosen for 18-24 months of monitoring. The projects had high attachment rates between 92-100% and survival rates between 87-99%. A majority of colonies exhibited positive growth at an average rate of 0.03%-0.04% of initial tissue area per day. There were no apparent detrimental effects of transplantation such as reduced initial growth rates, disease, bleaching, or increased partial mortality. These results indicate that coral transplantation was highly successful from a biological standpoint. This study also demonstrates that coral transplantation is a valid and effective component of impact minimization whereby colonies that may otherwise be destroyed, can be successfully preserved. For this study, coral transplantation proved to be an economically worthwhile method of conserving an ecologically and economically valuable reef resource. However, coral transplantation is only one facet of impact minimization and mitigation. Ideally, future mitigation projects should also aim to reduce habitat loss and preserve biota in addition to stony corals.

Batch cultures of the cyanobacteria Synechococcus spp. (strains 48 Syn and 2346) and Porphyridium cruentum (Rhodophyta) were grown in nitrogen-limited (N:P=4:l) and phosphorus-limited (N:P=50:l) seawater media. Optical properties, including particle size (forward angle light scatter), particle granularity (right angle light scatter) and relative mean channel red (> 600 nm) and green (510-550 nm) fluorescence were measured for 10 days using a flow cytometer. Dissolved nitrogen (nitrate), phosphorus (phosphate), cell abundance and chlorophyll concentrations were also measured. Results indicated that phosphorus-limited cultures yield higher chlorophyll concentration, fluorescence and granularity (right angle scatter) values than did nitrogen-limited cultures. Comparison of these samples with a preliminary investigation shows nutrient-rich cultures (N:P=4:l, N:P=50:l) have larger particle size and higher fluorescence values than relatively nutrient-poor cells cultured in f/20 media. Secondary (R2) populations have been determined for all samples, either by light scatter or fluorescence anomalies. Particularly notable was Synechococcus 2346 (phosphorus-limited) which exhibited a secondary population characteristic for more than half of the experiment. Highly fluorescent particles are suggested as either formative daughter cells, cellular “clumping" or a cellular optical response to batch culture turbidity; these particles have a profound influence on the relative refractive index of the culture with time. Flow cytometric analysis can be an effective tool in the determination of not only differences in the optical properties and fluorescent signatures of various cyanobacterial strains, but also of population variation within a single strain.

The current study examines salinity tolerance in naked amoebae. A biodiversity study was conducted in the Salton Sea, an inland lake in southern California, with an average salinity of 44 ‰. Amoebae were also collected from hypersaline ponds around the perimeter of the Sea where salinities averaged 160 ‰. A total of 45 species of amoebae were isolated, about one third of which were new to science. One Salton Sea species, Platyamoeba pseudovannellida n.sp. was found to survived over the range 0 - 150 ‰. A first estimate of abundances of amoebae in the Sea showed that densities could reach 237,120 cells L-1. Many of the isolates were observed to consume cyanobacteria and algae suggesting that amoebae are important regulators of blooms in the Sea, although this was not tested experimentally. Samples from the intertidal zone of a beach, a habitat also subject to salinity fluctuations, provided the first abundances of naked amoebae in sand. Densities ranged between 181 and 8473 amoebae cm-3, again suggesting that amoebae are important micrograzers in this challenging environment. From the aforementioned studies, 6 clones of amoebae were isolated for salinity tolerance experiments (2 marine beach isolates, 2 Salton Sea isolates, and 2 hypersaline pond isolates). A seventh clone, Acanthamoeba polyphaga, a common freshwater/soil amoeba was obtained from the Culture Collection of Algae and Protozoa (CCAP). The experiments compared the effects of gradual versus no acclimatization and used growth rate and culture yield as indices of effect. Generally, amoebae were tolerant over a wide range of salinity conditions and were not markedly influenced by pre-conditioning to salinity regimes. Acanthamoeba grew in 0 -12 ‰, marine clones 2 and 3 in 0 - 110 ‰, Salton Sea clones 4 and 5 in 0 - 150 ‰, and the hypersaline clones 6 and 7 in 0 - 270 ‰ salt. The results suggest that most amoebae are essentially unaffected in terms of growth and yield by moderate and severe salinity changes. The survival and activity of large populations of amoebae in sites subject to salinity challenges suggest that they should be considered in future studies designed to understand their as yet undefined ecological role.

Thesis (M.S. in Meteorology and Physical Oceanography)--Naval Postgraduate School, September 2005.
Thesis Advisor(s): D. Benjamin Reeder, John A. Colosi. Includes bibliographical references (p. 95-97). Also available online.

A study of air mass origin’s effect on marine stratus and stratocumulus clouds has been performed on clouds north of Scandinavia between 2000 and 2004. The aerosol number size distribution of the air masses has been obtained from measurements in northern Finland. A trajectory model has been used to calculate trajectories to and from the measurement stations. The back trajectories were calculated using the measurement site as receptor to make sure the air masses had the right origin, and forward trajectories were calculated from receptor stations to assure adequate flow conditions. Satellite data of microphysical parameters of clouds from the Moderate Resolution Imaging Spectrometer (MODIS) has been downloaded where the trajectories indicated that clouds could be studied, and where the satellite images displayed low-level clouds. The 25 % days with the highest number of aerosol with a diameter over 80 nm (N₈₀) and the 35% with the lowest N₈₀ have been used to represent polluted and clean conditions respectively. After screening trajectories and satellite imagery, 22 cases of clouds with northerly trajectories that had low N₈₀ values (i.e. clean) and 25 southerly cases with high N₈₀ values (i.e. polluted) where identified for further analysis.

   The average cloud optical thickness (τ) for all polluted pixels was more than twice that of the clean pixels. This can most likely be related to the differences in aerosol concentrations in accordance with the indirect effect, yet some difference in τ caused by different meteorological situations cannot be ruled out. The mean cloud droplet effective radius (a_ef) was for the polluted pixels 11.2 µm and for the clean pixels 15.5 µm, which results in a difference of 4.3 µm and clearly demonstrates the effect that increased aerosol numbers has on clouds. A non-linear relationship between a_ef and N₈₀ has been obtained which indicates that changes in lower values of aerosol numbers affect a_ef more than changes in larger aerosol loads. The results from this study also indicate that there is a larger difference in the microphysical cloud parameters between the polluted and clean cases in spring and autumn than in summer.

Marine sponges were examined from shallow waters of southeast Florida and the Florida Keys to determine species composition and distribution of commensal amphipod crustaceans from shallow reef, mangrove, and seagrass habitats. Twenty sponge species were investigated during this study, sixteen of which housed amphipods in the families Colomastigidae and/or Leucothoidae. Six species of commensal amphipods were identified. Leucothoe spinicarpa (Abildgaard) species "complex" was the most dominant amphipod commensal, representing 63% of the total amphipods collected. The L. spinicarpa "complex" contains four local morphotypes, which are diagnosed and briefly described. Common sponge hosts included Callyspongia vaginalis, Mycale sp., and Myriastra kallitetilla.

Thesis (M. S.)--Earth and Atmospheric Sciences, Georgia Institute of Technology, 2010.
Committee Chair: Di Lorenzo, Emanuele; Committee Member: Bracco, Annalisa; Committee Member: Lynch-Stieglitz, Jean. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Escherichia coli, the preferred bacterial indicator for fecal pollution in fresh waters, does not conform to the concept of an indicator microorganism because it is rapidly killed or inactivated by seawater. This series of papers investigated the value of coliphage, a virus which infects E. coli, as an indicator of pollution in saline waters. In order to be an accurate indicator an organism must (1) be ubiquitous in wastewater, (2) survive and be detectable at least as long as the harmful organisms, and (3) be easy to isolate and identify. A review of the literature determined that coliphage were more resistant than the common bacterial indicators to physico-chemical factors such as inorganic ions, temperature, heavy metals, nutrients, and antibiotics. Coliphage correlation with their bacterial hosts and similarities in behavior to the pathogenic viruses make them both bacterial and viral indicators. Various culture media and host culture strains were investigated for maximum plaque forming unit (pfu) production. Two way analysis of variance showed that selection of a suitable host was of paramount importance. While selection of the culture medium was significant, it was of lesser importance. Host strain ATCC 13706 and tryptic soy agar gave the highest recovery of pfu's. One ml log phase E.coli host culture, five ml of water sample or dilution, and five ml of culture media (maintained at 44.5 C) were combined in a sterile screw cap tube, mixed, poured into a sterile 100 X 15 mm petri dish, and incubated at 35 C. Plaque forming units were counted after 24 hrs. and expressed per 100 ml of sample. The method proved repeatable; the titer of frozen phage aliquots declined slightly over 77 days but, the slope of the trend was not significantly different from zero at the 0.10 level (r = 0.55). These repeated analyses were done with different batches of media and hosts and represent a test of total method repeatability. Bench studies utilizing a decimal dilution series of sewage contaminated freshwater and uncontaminated seawater showed that both coliform and coliphage closely follow a theoretical dilution curve immediately after dilution with seawater. However, coliform bacteria die off at a higher rate than coliphage at higher salinities over time. Field validation studies in fresh and brackish water (<10 >ppt) compared coliphage with total and fecal coliforms (n = 53) and gave correlation coefficients of 0.98 and 0.91 respectively. The regression equation for these samples was: log coliphage = 0.983 (log total coliform) -1.001 The combined total coliform/coliphage relationship at 68 saltwater (>10 ppt) stations yielded a correlation coefficient of 0. 45. Coliphage are a logical choice for a fecal indicator in marine waters since their titers are closely related to total and fecal coliform in freshwater, survive much better than coliforms in seawater, and they can be enumerated by a simple method which is not subject to salinity artifacts. The constant relation of coliphage and coliforms in freshwater indicate a possible link to current water quality standards based on total or fecal coliforms. Since coliphage pfu are a rather constant 8 - 10 % of total coliform cfu in low salinity waters where coliform inactivation is less severe, a coliphage titer of 80 – 100 pfu per 100 ml in seawater may indicate water quality equivalent to that indicated by a coliform count of 1000 cfu per 100 mI. This could aid in the interpretation of coliphage data relative to current coliform-based water quality codes. Monitoring of sanitary water quality in Bell Channel Bay, Bahamas, during repair of a sewer plant showed that following chlorination and diversion of the effluent to a deep well, total coliform declined rapidly below detection limits. Coliphage remained easily detectable ten days later. Two canals and two marinas on Biscayne Bay were assayed for coliphage to compare sanitary water quality related to point and non-point source pollution. The Biscayne Canal was impacted by periodic upstream sewage spills, while the Little River displayed chronic contamination along its length by liveaboard boats or sewer leaks. Coliphage were shown to persist six days longer than coliform after a sewage spil l was tracked in the Canal. The liveaboard Dinner Key marina displayed low-level, spotty contamination with no seasonal pattern. King's Bay marina was free of detectable fecal contamination during the study. The use of coliphage allowed the assessment and monitoring of fecal contamination in marine waters where coliform bacteria were not suitable.

Time series and spectral analyses are applied to meteorological data (wind velocity, air temperature, barometric pressure) and sea level measurements from a total of 13 monitoring stations along the Turkish Coast. Analyses of four-year time series identify main time scales of transport and motion while establishing seasonal characteristics, i.e. distinguishing, for instance, between winter storms and summer sea-breeze system. Marine flow data acquired by acoustic doppler current profilers (ADCP) is also analyzed to better understand the response of the Turkish Strait System dynamics to short-term climatic variability. The cumulative results obtained from these analyses determine temporal and spatial scales of coastal atmospheric and marine fluxes as affected by the regional climate system

Diseases in marine animals are emerging at an increasing rate. Disease forecasting enabled by virus surveillance presents a proactive solution for managing emerging diseases. Broad viral surveys aid in disease forecasting by providing baseline data on viral diversity associated with various hosts, including many that are not associated with disease. However, these viruses can become pathogens due to expansion in host or geographic range, as well as when changing conditions shift the balance between commensal viruses and the host immune system. Therefore, it is extremely valuable to identify and characterize viruses present in many different hosts in a variety of environments, regardless of whether the hosts are symptomatic or not. The lack of a universal gene shared by all viruses makes virus surveillance difficult, because no single assay exists that can detect the enormous diversity of viruses. Viral metagenomics circumvents this issue by purifying viral particles directly from host tissues and sequencing the nucleic acids, allowing for virus identification. However, virus identification is only the first step, which should ideally be followed by complete sequencing of the viral genome to identify genes of interest and develop assays to reveal viral prevalence, tropism, ecology, and pathogenicity. This dissertation focuses on the discovery of novel viruses in marine animals, characterization of complete viral genomes, and the development of subsequent diagnostic assays for further analysis of virus ecology. First, viral metagenomics was used to explore the viruses present in the healthy Weddell seal (Leptonychotes weddellii) population in Antarctica, which led to the discovery of highly prevalent small, circular single-stranded DNA (ssDNA) viruses. The lack of knowledge regarding the viruses of Antarctic wildlife warrants this study to determine baseline viral communities in healthy animals that can be used to survey changes over time. From the healthy Weddell seals, viral metagenomics led to the discovery of 152 novel anellovirus genomes, encompassing two anellovirus species. Characterizing these viruses is important for understanding the prevalence and diversity of ssDNA viruses, which have only recently been described in marine animals. Furthermore, since emerging diseases can be caused by changing conditions affecting host susceptibility to a virus that was previously not related to disease (opportunistic pathogen), having baseline data allows for quick identification of the pathogen. In addition to determining baseline data, viral metagenomics can explore the role of viruses in disease. A novel virus, Asterias forbesi-associated circular virus (AfaCV), was discovered in the Atlantic sea star Asterias forbesi displaying symptoms of sea star wasting disease (SSWD). AfaCV was the first circular replicase-encoding ssDNA (CRESS-DNA) virus discovered in echinoderms, but it was only present in 10% of SSWD sea stars indicating it is not involved in the development of the disease. This dissertation also focuses on elucidating the role of two previously characterized viruses, chelonid fibropapillomatosis-associated herpesvirus (CHHV5; Chelonid herpesvirus 5, ChHV5) and Zalophus californianus anellovirus (ZcAV), in animal health. PCR amplicon sequencing was used to obtain large portions of the 132 kb genome of ChHV5, the putative etiological agent of the neoplastic sea turtle disease, fibropapillomatosis. Obtaining the genome of ChHV5 from Florida green, Kemp’s ridley, and loggerhead sea turtles provides data for phylogenetic analysis across geographic locations and sea turtle species, as well as a reference for designing downstream molecular assays to examine viral latency. ZcAV was first described from the lungs of captive sea lions involved in a mortality event. PCR could not detect ZcAV in the blood of infected animals, and since sea lions are a protected species, it is not possible to obtain lung biopsies from live sea lions to determine ZcAV prevalence or its role in sea lion health. To answer these important questions, an enzyme-linked immunosorbent assay (ELISA) was developed to detect antibodies to ZcAV in serum from wild sea lion populations. This newly developed ELISA showed that sea lions mount an immune response to ZcAV, and was used to determine the prevalence of ZcAV among wild sea lion populations. This dissertation makes an important contribution to marine science through discovery and characterization of viruses present in healthy and diseased marine animals. Several different methods were used for virus whole-genome sequencing including viral metagenomics, PCR amplicon sequencing, and target enrichment. These findings were expanded upon by developing and using PCR assays and a serological assay to screen for virus prevalence. These methods have implications for viral surveillance and understanding the role of novel viruses in animal health.

Chapter 1 Producing thematic coral reef benthic habitat maps from single-beam acoustic backscatter has been hindered by uncertainties in interpreting the acoustic energy parameters E1 (~roughness) and E2 (~hardness), typically limiting such maps to sediment classification schemes. In this study acoustic interpretation was guided by high-resolution LIDAR (Light Detection And Ranging) bathymetry. Each acoustic record, acquired from a BioSonics DT-X echosounder and multiplexed 38 and 418 kHz transducers, was paired with a spatially-coincident value of a LIDAR-derived proxy for topographic complexity (Reef-Volume) and its membership to one of eight LIDAR-delineated benthic habitat classes. The discriminatory capabilities of the 38 and 418 kHz signals were generally similar. Individually, the E1 and E2 parameters of both frequencies differentiated between levels of LIDAR Reef-Volume and most benthic habitat classes, but could not unambiguously delineate benthic habitats. Plotted in E1:E2 Cartesian space, both frequencies formed two main groupings: uncolonized sand habitats and colonized reefal habitats. E1 and E2 were significantly correlated at both frequencies; positively over the sand habitats and negatively over the reefal habitats, where the scattering influence of epibenthic biota strengthened the E1:E2 interdependence. However, sufficient independence existed between E1 and E2 to clearly delineate habitats using the multi-echo E1/E2 Bottom Ratio method. The point-by-point calibration provided by the LIDAR data was essential for resolving the uncertainties surrounding the factors informing the acoustic parameters in a large, survey-scale dataset. The findings of this study indicate that properly interpreted single-beam acoustic data can be used to thematically categorize coral reef benthic habitats. Chapter 2 A large-scale acoustic survey was conducted in Apr-May 2008, with the objective of quantifying the abundance and distribution of seasonal drift macroalgae (DMA) in the Indian River Lagoon. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart. The river edges were surveyed to a minimum depth of approximately 1.3 m. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 418 kHz. The 38 and 418 kHz hydroacoustic data were processed with BioSonics Visual Bottom Typer (VBT) seabed classification software to obtain values of E1’ (time integral of the squared amplitude of the 1st part of the 1st echo waveform), E1 (2nd part of 1st echo), E2 (complete 2nd echo), and FD (fractal dimension characterizing the shape of the 1st echo). Following quality analysis, a training dataset was compiled from 131 hydroacoustic + video samples collected across the extent of the study area. The 38 and 418 kHz E1’, E1, E2, and FD datasets were merged and submitted to a series of three discriminant analyses (DA) to refine the training samples into three pure end-member categories; bare substrate, short SAV (typically Caluerpa prolifera, ~10cm or less), and DMA. The Fisher’s linear discriminant functions from the third and final descriptive DA were used to classify each of the 480,000+ hydroacoustic survey records as either bare, short SAV, or DMA. The classified survey records were then used to calculate the biomass of DMA as the product of average DMA cover for a block of ten records times the wet weight of DMA. The DMA biomass was found to be 69,859 metric tons (wet weight) within the 293.1 km2 study area. The acoustically-predicted mean percent cover of DMA was (i) significantly greater within the navigation channels (18.3%) than outside (12.2%), and (ii) significantly greater in the Indian River (12.9%) than in the Banana River (9.3%). The overall predictive accuracy of total SAV (i.e. short SAV plus DMA) was 78.9% (n=246) at three levels of cover (0-33, 33-66, and 66-100%). The Tau coefficient, a measure of the improvement of the classification scheme over random assignment, was 0.683 ± 0.076 (95% CI), i.e. the rate of misclassifications was 68.3% less than would be expected from random assignment of hydroacoustic records to total SAV cover. The incorporation of multi-plexed digital transducers in conjunction with new post-processing techniques realized the goal of establishing an accurate, efficient, and temporally consistent method for acoustically mapping DMA biomass. Chapter 3 This chapter presents the results of a large-scale hydroacoustic survey conducted in April-May 2008. The objective of this study was to map the distribution and vertical extent of muck in the Indian River Lagoon, utilizing the data collected during a seasonal drift macroalgae survey. Indian River was surveyed from the Sebastian Inlet to its northernmost extent in the Titusville area. Banana River was surveyed from its convergence with the Indian River northward to the Federal Manatee Zone near Cape Canaveral. The survey vessel was navigated along pre-planned lines running east-west and spaced 200 m apart, except for when muck was indicated by the oscilloscope display, at which point a meandering path was adopted to demarcate the horizontal extent of muck. Hydroacoustic data were collected with a BioSonics DT-X echosounder and two multi-plexed digital transducers operating at 38 and 420 kHz. The vertical extent of muck was derived from the 38 kHz hydroacoustic signal, which was processed with Visual Analyzer, a fish-finding software package produced by BioSonics Inc. The software was adapted to integrate echo energy below the water-sediment interface, and a set of post-processing algorithms were developed to translate the sub-bottom echo energy profile into continuous scale estimates of muck thickness. In this manner 500,000+ 38 kHz pings were translated into 88,927 geo-located estimates of muck layer thickness, down to a minimum bottom depth of 1 m. Ground-truthing was conducted in July 2008 at twenty sites within the Indian River. The predictions of muck layer thickness were found to be accurate over the ground-truthed range of 0-3m (r2 = 0.882, SE=0.52m). The vertical distribution of acoustically-predicted muck demonstrated the tendency for muck to accumulate in deeper areas of the lagoon. For the case of Indian River (excluding navigation channels), muck was not detected in depths shallower than 1.4m and rare in the range of 1.4-2.2 m (only 3.6% of records had a predicted muck thickness greater than 0.5 m). The frequency of muck plateaued between 2.2-3.4 m (9.6%) before making a sharp rise to 82% in the range of 4-5 m. As expected, the mean muck layer thickness was significantly greater within the navigation channels (0.56 m) than outside of them (0.08 m). A significant latitudinal trend of muck thickness was detected within the Indian River navigation channels. The mean muck thickness decreased from 1.38 m at its northernmost origins to 0.83 m in the Titusville area before plateauing at approximately 0.4 m for the remainder of segments. Outside of the main ICW channels, 23 individual muck deposits were identified; 22 in the Indian River and 1 in the Banana River. Factors in descending order of co-occurrence were proximity to causeways or jetties, riverbed depressions, and proximity to shore and drainage channels. In conclusion, this study establishes that a single-beam acoustic survey is a cost-effective and accurate alternative for mapping the distribution and vertical extent of muck deposits in the shallow-water environment of the Indian River Lagoon. Moreover, the temporal consistency afforded by a digital transducer allows for direct and meaningful comparisons between successive surveys. Chapter 4 A thematic map of benthic habitat was produced for a coral reef in the Republic of Palau, utilizing hydroacoustic data acquired with a BioSonics DT-X echosounder and a single-beam 418 kHz digital transducer. This paper describes and assesses a supervised classification scheme that used a series of three discriminant analyses (DA) to refine training samples into end-member structural and biological elements, utilizing E1′ (leading edge of 1st echo), E1 (trailing edge of 1st echo), E2 (complete 2nd echo), fractal dimension (1st echo shape), and depth as predictor variables. Hydroacoustic training samples were assigned to one of six predefined groups based on the plurality of benthic elements (sand, sparse SAV, rubble, pavement, rugose hardbottom, branching coral), visually estimated from spatially co-located ground-truthing videos. Records that classified incorrectly or failed to exceed a minimum probability of group membership were removed from the training dataset until only ‘pure’ end-member records remained. This refinement of ‘mixed’ training samples circumvented the dilemma typically imposed by the benthic heterogeneity of coral reefs, i.e. to either train the acoustic ground discrimination system (AGDS) on homogeneous benthos and leave the heterogeneous benthos un-classified, or attempt to capture the many ‘mixed’ classes and overwhelm the discriminatory capability of the AGDS. This was made possible by a conjunction of narrow beamwidth (6.4o) and shallow depth (1.2 to 17.5 m), which produced a sonar footprint small enough to resolve most of the microscale features used to define benthic groups. Survey data classified from the 3rd-Pass training DA were found to (i) conform to visually-apparent contours of satellite imagery, (ii) agree with the structural and biological delineations of a benthic habitat map created from visual interpretation of 2004 IKONOS imagery, and (iii) yield values of benthic cover that agreed closely with independent, contemporaneous video transects. The methodology was proven on a coral reef environment for which high quality satellite imagery existed, as an example of the potential for single-beam systems to thematically map coral reefs in deep or turbid settings where optical methods are unsatisfactory. Chapter 5 Beginning In the winter of 2003-2004, several episodes of red drift macroalgae blooms resulted in massive amounts of macroalgae washing ashore the beaches of Sanibel Island, Bonita Springs, and Ft Meyer Florida. A study conducted after the first event supported a link to increasing land-based nutrient enrichment. A large-scale program was initiated in May 2008, with the primary goal of further defining the possible roles and sources of nutrient enrichment with respect to nuisance macroalgae blooms. This study reports the results of the hydroacoustic mapping component of this program. The goal of this study was to identify areas of substrate suitable for supporting a macroalgae bloom. Areas within San Carlos Bay and offshore Sanibel Island, FL were hydroacoustically surveyed from nearshore to about 11 km offshore during the periods of October 6-10, 2008 and May 10-22, 2009. The hydroacoustic data was acquired with a BioSonics DT-X echosounder and a multiplexed single-beam digital transducers operating at 38 and 418 kHz. Eleven acoustic parameters derived from the 38 and 418 kHz signals were utilized to classify the survey data into 5 ascending categories of visually-apparent seabed roughness. Classes 1 and 2 were both primarily constituted of unconsolidated silt and sand-sized sediments, unsuitable for a bloom. Class 3 is a marginal substrate for a bloom, consisting of packed sand and large intact shell debris. Classes 4 and 5 offer the best attachment sites for a bloom, consisting of consolidated shell hash, live hardbottom, and submerged aquatic vegetation. The majority (~ 80%) of acoustic classifications were of soft bottom sediments (classes 1-2), but there were two significant expanses of rough seabed suitable for macroalgae attachment. These two areas covered a total of 19 km2, within which ~ 56% of the hydroacoustic records classified as “rough” (classes 3-5). The first was a large area of seagrass beds and live hardbottom in the mouth of San Carlos Bay, where large amounts of macroalgae were variably present during the April-May 2009 surveys. The second was offshore Lighthouse Point, near the mouth of San Carlos Bay, situated near a large sand spit that extended from the beach to approximately 6 km offshore. Along the west side of the sand spit there were substantial areas of moderate to high bottom roughness, mostly in the form of consolidated shell hash. The average depths of these two acoustically-rough areas were only 5.0 and 4.0 m, so sufficient irradiance to initiate a bloom could be assumed. These textured and shallow areas on or near the mouth of San Carlos Bay are presumably potential sources for macroalgae attachment and growth, which could easily be transported onto the beaches under some storm conditions given the close proximity to the shoreline. In contrast, the areas in open Gulf of Mexico waters were classified predominantly as soft sediments with low bottom roughness. The site offshore Redfish Pass had a moderate (~22%) proportion of “rough” classifications out to 5km offshore, but from 5-10km offshore the bottom classified as >95% soft sediments. The other two Gulf of Mexico sites classified as >95% soft sediments from nearshore to 11 km offshore. Independent, concurrent video transects indicated there were small areas with large amounts of shell and live hard bottom that occurred sporadically greater than 10km offshore, but all things considered the open Gulf waters around Sanibel Island may not be a major source of drift macroalgae. Chapter 6 This study presents the results of methods developed for acoustic remote sensing of Acropora cervicornis, a threatened species of scleractinian sporadically occurring on the nearshore hardbottom of Southeast Florida. The objective was to develop techniques for mapping isolated Acropora patches on a scale larger than what is feasible using on-the-ground methods. A time-series of A. cervicornis cover could inform resource managers about the fate of such patches, e.g. do they appear and vanish, creep by extension from a central point, or leap by colony fragmentation. The main challenge to acoustically mapping A. cervicornis was distinguishing it from gorgonians occupying the same habitat. Hydroacoustic surveys were conducted in October 2009 at two nearshore sites in Broward County, FL utilizing a BioSonics DT-X echosounder and multiplexed single-beam digital transducers operating at frequencies of 38 and 418 kHz. NCRI scientists have monitored the spatial extent and percent cover of A. cervicornis within these sites, providing an ideal background against which to calibrate the hydroacoustic predictions. Two approaches were evaluated. The first approach utilized BioSonics EcoSAV post-processing software, designed to predict areal cover and canopy height of submerged aquatic vegetation using a series of heuristic pattern-recognition algorithms. Anchored over A. cervicornis, the 38 and 418 kHz signals performed similarly well. Anchored over gorgonians, the 38 kHz signal detected the canopy roughly half as frequently as the 418 kHz signal. Undifferentiated 418 kHz EcoSAV cover was allocated to either A. cervicornis or gorgonians exploiting this frequency-dependent detection. The second approach utilized the acoustic energy (E0, E1′, E1, and E2) and shape (fractal dimension) parameters obtained from BioSonics Visual Bottom Typer software. A dual-frequency training dataset was used to classify records as sand, bare pavement, gorgonians, or A. cervicornis. Both approaches yielded promising results, based on a number of metrics, unambiguously demonstrating that single-beam AGDS are capable of reliably detecting A. cervicornis and gorgonians under controlled conditions.

Oceans cover about 70% of the earth’s surface. They are the largest source of the atmospheric water vapour and act as enormous heat reservoirs. Thus in order to predict the future weather and climate it is of great importance to understand the processes governing the exchange of water vapour and heat between the ocean and atmosphere. This exchange is to a large extent mediated by turbulent eddies. Current numerical climate and weather forecast models are unable to resolve the turbulence, which means that the turbulent exchange needs to be simplified by using parameterizations.

Tower based measurements at the Östergarnsholm Island in the Baltic Sea have been used to study the air-sea turbulent exchange of latent and sensible heat and the heat flux parameterizations. Although the measurements are made at an island, data obtained at this site is shown to represent open ocean conditions during most situations for winds coming from the east-south sector. It is found that during conditions with small air-sea temperature differences and wind speeds above 10 m s^-1, the structure of the turbulence is re-organized. Drier and colder air from aloft is transported to the surface by detached eddies, which considerably enhance the turbulent heat fluxes. The fluxes where observed to be much larger than predicted by current state-of-the-art parameterizations. The turbulence regime during these conditions is termed the Unstable Very Close to Neutral Regime, the UVCN-regime.

The global increase of the latent and sensible heat fluxes due to the UVCN-regime is calculated to 2.4 W m^-2 and 0.8 W m^-2 respectively. This is comparable to the current increase of the radiative forcing due to anthropogenic emissions of greenhouse gases, reported in Intergovernmental Panel on Climate Change fourth assessment report (IPCC AR4). Thus the UVCN-effect could have a significant influence when predicting the future weather and climate.

Anthropogenic nutrient enrichment and coastal eutrophication are a primary threat to the biological integrity of coral reef ecosystems. Macroalgal blooms are one symptom of eutrophication and provide useful 'bioindicators' of the nutrient dynamics associated with the eutrophication process. This study used marine macroalgae to monitor physiological processes associated with eutrophication by comparing the degree of phosphorus (P) limitation in reef and nearshore environments of the highly developed Florida Keys with the relatively pristine Bahamas by measuring enzymatic alkaline phosphatase activity (APA), tissue composition, and water column nutrient concentrations [total nitrogen (TN) and total phosphorus (TP)]. Experimental nutrient enrichment studies were also performed to help interpret the field data from the Florida Keys and the Bahamas. Despite their large spatial scale and habitat heterogeneity between the Florida Keys and the Bahamas, and the inherent biological variability among the numerous taxa assayed, highly significant and distinct differences in macroalgae between the two study areas were evident. The analysis showed macroalgal APA was 2.5-fold higher in reef environments and 1.5-fold higher in nearshore environments in the Florida Keys than the Bahamas, indicating higher P-limitation in the Florida Keys. This was related to the significantly higher water column TN concentrations within the Florida Keys. Additionally, a significant and positively correlated relationship was detected between macro algal APA and tissue N:P ratios, indicating that elevated water column N causes the N:P ratio of macro algae to increase, leading to the observed increase in P-limitation. These findings showed that marine macroalgae are a useful means to monitor and gauge the degree and type of nutrient limitation and that N inputs as well as P inputs need to be considered for the protection of water quality in carbonate-rich, coral reef regions.

The diet and feeding habits of the southern stingray, Dasyatis americana, were investigated through aerial surveys, land-based observations, and quantitative analysis of stomach contents. The field research was conducted in the Exuma Cays Land and Sea Park, central Bahamas. Systematic aerial surveys and the land-based observations were made to determine population density and feeding periodicity in terms of time or tidal phase. In August, 1989, systematic surveys were flown over two cays in the Park; a 12 km2 area around Waderick Wells Cay and a 21km2 area around Shroud Cay. Both survey areas were flown three times over different times of the day. Over the large area covered by the aerial surveys the population varied over time of day. A significantly higher density occurred in the morning for both grids and was lowest in the afternoon for both grids suggesting that the stingrays prefer to feed early in the day in the summer. The peak density was 2.07 stingrays per km2 for the Waderick Wells survey area and 1.87 per km2 for the Shroud survey area. A total of 117 hours of land-based observations were made over 4 months; with 28 to 31 hours of observations in April and May 1990 and January and July, 1991. The land-based observations indicated that the stingrays were actively feeding throughout the day, but showed some increase in feeding activity during the high tidal phase. The habitat utilization was recorded during the land-based observations and showed that the stingrays spent most of their time feeding in the soft sediment habitats, thus taking advantage of the soft sediment algal turf and sandy shoal habitats that dominate the shallow marine environments within the Park. Eighteen stingrays were collected in January, 1991 for stomach content analysis. Decapod crustaceans were the most important prey category, but the large number of prey types found in all of the stomachs indicates that the southern stingray is a generalist feeder. There were no empty stomachs and 77% of the stomachs had more than 20 prey items. Stomach fullness measures did not indicate any feeding periodicity. The southern stingray is a generalist feeder taking advantage of a broad range of prey types and opportunistic in its feeding habits, showing no strong feeding periodicity.

More than 500 species of higher marine fungi in over 300 genera have been described. Many marine fungi are highly specialized for marine environments relative to their terrestrial counterparts, having appendaged ascospores and conidia to aid in buoyancy, entrapment, and adherence to substrates. They have been reported to inhabit a wide variety of substrates including decaying wood, leaves, calcareous and chitinous substrates, seaweeds, and seagrasses. Most early studies on marine fungi were carried out in temperate regions. Investigations have now shifted to tropical locations in order to better evaluate the abundance and diversity of marine fungi on a global basis. Many surveys have focused on mangrove habitats in the Pacific and Atlantic Oceans, resulting in the discovery of many new taxa. The purpose of this study was to examine the distribution and seasonal occurrence of higher marine fungi along a salinity gradient in a marine estuary, Henderson Creek in Rookery Bay Reserve Naples, Florida. Parameters including temperature and salinity were measured. Three stations were established along Henderson Creek. Mean salinity ranged from 5 ppt at the low salinity station Visitor Center to 36ppt at the high salinity station Field Station. Substrates used for fungal collections were wood panels of a hardwood Oak (Quercus sp.) and a softwood Pine (Pinus sp.). Four panels were submerged at each station and removed in 3 month increments over the course of one year. One-hundred-and-sixteen species of filamentous higher marine fungi were identified over the course of this study, including seventy-one Ascomycetes, three Basidiomycetes, and forty-one Deuteromycetes. There was no clear pattern of seasonality in the species composition. Total species diversity and richness decreased in each 3month period following the first 3 month period. Changes in salinity appeared to alter the ratio of Ascomycetes to Fungi Imperfecti observed at each station. Marine fungi in this collection were compared with previous reports on the east coast of Florida (Adams, 2003a; Kukich, 2005; Vogel, Schatz, Laubach, & Rogerson, 2008). A higher total species number as well as greater diversity was observed in this study when compared with reports from mangroves in southeast Florida. Marine fungi are active decomposers in mangrove environments and contribute to total dissolved organic matter in estuarine and near shore ecosystems. While most studies focused on the taxonomy of marine fungi, few have looked at their ecology. Further studies will have to be conducted to better determine the role of filamentous marine fungi in near shore and estuarine environments.

Bacterial growth rates and bacterivore grazing rates were compared to concentrations of dissolved polysaccharide and monosaccharide over diel periods in subtropical marine coastal waters by incubating large volumes of natural water in situ. Growth and grazing rates were detennined by the dilution method with 4 hour incubations. Carbohydrates were measured with the 3-Methyl-2-benzothiazolinone hydrozone hydrochloride hydrate (MBTH) colorimetric assay. Diel studies were conducted in April, August, and September 1997. Bacterial growth rates and bacterivore grazing rates as well as dissolved polysaccharide and monosaccharide concentrations varied significantly over the diel period of each study. There was inverse variation between bacterial growth rates and monosaccharide concentrations in two of the three studies, when daily average monosaccharide concentrations were 80 μgC/l or less. In the third study, monosaccharide concentrations were higher and the inverse relation with bacterial growth rates was less apparent. The diel pattern of bacterivore grazing rates followed that of bacterial growth rates in each study and were significantly correlated in two of three studies. Daily average bacterial growth rates were never significantly different than daily average bacterivore grazing rates. Bacterivore grazing rates were never directly related to dissolved carbohydrates, but were negatively correlated with total dissolved carbohydrates and monosaccharides in one study.

Batch cultures of Fayella panamenis were pulse fed Heterocapsa triquetra at concentrations ranging from 200 to 3,000 cells/ml. The digestion process was followed using both bright field and epifluoresence microscopy for live and fixed ciliates. Ingestion rates, vacuole passage times, and the time required for complete digestion of vacuolar contents were determined during pulse feeding experiments. Findings indicate the following. 1) The digestion rate of Favella panamenis begins to saturate at 2,000-2,500 Heterocapsa/ml. The ingestion rate increases over the range of Heterocapsa/ml studied (200 to 3,000 cells/ml). 2) Each ciliate could fully digest ≤ 3 Heterocapsa simultaneously. If the cell ingested ≥ 4 Heterocapsa at one feeding, the food items were excreted partially digested. Ingestion of ≥ 3 Heterocapsa per ciliate began at an initial food concentration of 2,500 Heterocapsa/ml. The results suggests that the rate of digestive enzyme production may limit the transfer of energy through microbial food webs under food saturating or bloom conditions. This may ultimately decrease growth efficiencies at high feeding rates, which then must be considered in energy and carbon flow calculations.

The Florida manatee (Trichechus manatus latirostris) inhabits a unique aquatic niche. Adaptations to this niche include obligate herbivory, low metabolic rate, large body size, and supernumerary teeth. Consequences of these adaptations are, cold intolerance, low population rate of increase, and range restrictions. Manatee life history traits also have influenced brain evolution. In the past, examination of only gross anatomical brain structures in manatee brains have led to the fallacy that manatee brains are poorly developed. In order to answer questions about the internal structure of the Florida manatee brain, cerebral isocortex, caudal to the lateral fissure, of the manatee brain was examined and its cytoarchitecture documented. It was found that the manatee brain is surprisingly complex. Cell counts and cortical thickness were measured in the manatee and other aquatic mammals in order to better understand the manatee’s place in brain evolution. Although manatees possess a small brain size relative to body size and a lissencephalic but unusually thick cerebral cortex, there is a high percentage of cerebral cortex to brain volume, and a highly organized cytoarchitecture which is differentiated into numerous cortical areas. Manatee brain characteristics appear to be on the same evolutionary adaptive level as dolphin brain characteristics. Functions for cortical areas defined in this study and in previous studies are suggested. However, due to the lack of electrophysiological data on manatees and a detailed examination of the manatee thalamus, functional assignments should be considered as preliminary contingent upon further study.

The purpose of this study was to compare the fish communities in mitigated and natural mangrove areas in the Port Everglades estuary. This study of fish recolonization of recently (ca. 5 years) planted mangrove forests, tested the null hypothesis that the species composition, size distribution and abundance of fish collected in natural, established and mitigated mangrove environments were the same. Two natural mangrove areas and two mitigated mangrove areas were used as study sites in John U. Lloyd Park. Two natural mangrove areas and two mitigated mangrove areas were used as study sites in West Lake Park. A variety of sampling gear types were utilized in the collection of fishes. Sampling was only done at low tide for all areas. Differences (chi square) in the abundances of fishes occurred between the natural mangrove sites in John U. Lloyd and West Lake Parks. These differences are thought to be due largely to differences in the hydrodynamic environment (i.e. tidal flushing, discharge rates of waterflow) and seasonality (i.e. month). However, differences between the fish communities in the mitigated areas of both parks were not significant at the 0.05 level of probability. Small fishes, the forage base for the larger piscivores, were equally represented in the mitigated sites throughout the study, and always dominated their respective communities numerically. Differences between natural and mitigated mangrove areas occurred in the distributions of transient species. In general, these transient fishes occurred only in the natural sites: the larval stage of one transient species, however, was found only in the mitigated sites. Likewise, within a species, smaller fishes were generally found in the mitigated sites and larger fishes were found in the natural sites. Thus, differences in the distributions of fishes between the mitigated and natural mangrove sites may be due to food availability as well as structural differences (i.e. spacing of plants) in each habitat. This study shows that mitigated mangrove forests are suitable habitats for small, forage species and presently there are differences in the fish populations in the natural and mitigated mangrove environments, the largest mangrove ecosystem remaining in Broward County.

Orcas, Orcinus orca, also known as "killer whales," are a species that have been the subject of long-term research. The aim of this study was to quantify percussive behaviors of a population of orcas, identify which individuals in a pod were displaying such behaviors, determine the context in which these behaviors occurred, and offer suggestions to the purpose, if any, that percussive activity may serve in this community. The study was conducted in Johnstone Strait, British Columbia, Canada during the summer months of 1992-1993. Observations were made during daylight hours. Whales were encountered either opportunistically, or by reports from other whale-watchers and researchers. A total of 542 hours of observational data were collected from 86 individual whales. Behavioral categories were defined as feeding, socializing, traveling, and resting. The most often observed percussive behaviors were tailslaps; they were therefore analyzed in the greatest detail. The number of tail slaps produced during feeding, socializing, aggregation, directional changes, and in the presence of boats were statistically compared. It has been suggested that calves and juveniles engage in percussive activity as a form of play during socializing, and that percussive behavior may aid in building physical strength and motor training. Adolescents and adults may engage in percussive actions to convey information about a direction change to other animals, strengthen social ties, express sociosexual behavior, and assist in social development, all of which could establish and strengthen social skills and social bonds among other individuals in the community. Other hypotheses for percussive behavior in this community include: forms of aggression; a type of warning signal; incidental occurrences due to elevated activity levels; a form of greeting among individuals; an expression of courtship behavior; a way to establish or re-establish dominant-subordinate relationships; an aid in the capture of prey during feeding; and a type of energy release either before or after resting behavior. It appears that each age class may have its own agenda for displaying percussive activity, depending on the context in which it was performed. The reason why each individual engages in percussive actions may be multifaceted for various situations, and each reason may not be bound to a particular context. The high level of occurrence of percussive behaviors implies that they are relevant to the daily activities of the northern resident community of orcas that inhabit the region of Johnstone Strait, British Columbia, Canada.

Time series of zooplankton concentrations and current velocities were collected with a bottom mounted (190 m) 307.2 kHz acoustic Doppler current profiler (ADCP) at the shelf break off Fort Lauderdale, Florida. Simultaneously, time series of temperature and salinity were collected with a moored CTD in the Port Everglades estuary approximately 4 km inshore of the ADCP mooring. Software was developed to extract acoustic volume scattering strength data (Vs) from the ADCP data stream. Vs is a relative measure of zooplankton concentration. In addition, eastward velocity and northward velocity data were collected from the ADCP. Data were recorded in two minute averages, with additional processing yielding hourly averages. Acoustic volume scattering strength and current velocity records from 176, 136, 95, and 56 m deep were isolated during post-processing for spectral analysis. The acoustic estimate of zooplankton concentration was found to be coherent with current velocity (both north and east components) at frequencies corresponding to the scales of Gulf Stream meanders (2-10 days per cycle) and diurnal and semi-diurnal tidal variability (24 and 12 hours per cycle, respectively). Estuarine salinity variations were also coherent with variability in circulation at the shelf break at the energetic periods of 24, 12, 8 and 6 hours per cycle. Estuarine salinity varied inversely with the distance of the Gulf Stream front from shore (0.5 - 6 week observation interval). Apparently, low frequency variability in the salinity of estuarine water is also associated with variability in the position of the Gulf Stream. It would appear that variability of Gulf Stream position and flow influences the cross-shelf transport of planktonic organisms, such as fish larvae, at a variety of temporal scales and thereby links offshore and estuarine ecosystems off southeast Florida.

Concentrations of methanesulfonate (MSA), nitrate (NO3-) and non-sea-salt sulfate (nssSO4-) were compared for five different air mass categories encountered during a 1993 NOAA cruise in the North Atlantic. NO3- and nssSO4- concentrations were highest during air masses originating from Europe and the United States. MSA concentrations increased with increasing latitude. Dry deposition fluxes for the three analytes were compared with respect to particle size and air mass category. MSA had a mixed distribution with particle size, nssSO4- was found primarily on smaller particles (<1.1 μm radius), and NO3- was found primarily on larger particles (≥ 1. 1 μm radius). With respect to air mass category, the highest dry deposition flux for the three analytes was found during sampled air with European continental influence. Total dry deposition fluxes (all particle sizes) were compared with previous studies in the North Atlantic with respect to air mass category. The NO3- and nssSO4- fluxes in this study are lower than those reported in the mid 1980's in both clean marine air and air masses originating from the United States. These differences are probably due to interannual variation. Atmospheric nitrogen deposition from air masses originating in the U.S., found during this study, was considerably lower than the minimum nitrogen requirement for new primary production expressed in previous studies.

Cyclic variations in skeletal structure of long-lived reef corals produce annual density bands evident by X-radiography and X-ray computed tomography. The chemical composition of the calcium carbonate (CaCO3) skeleton and the chronological reliability of these high-density (HD) and low-density (LD) bands can provide accurate records for reconstruction of long-term climatic and ecological conditions. Due to variability across coral taxa, the architectural variations responsible for density banding are not completely understood. The western Atlantic/Caribbean reef coral, Diploria strigosa, is the first meandroid (brain) coral analyzed for skeletal variations relative to density band formation. Skeletal architecture analyses consisted of X-radiography, densitometry, X-ray computed tomography, and computer image analysis techniques. High-density bands correlated with thickened septa and tightly organized and thickened columella. Dissepiment spacing and colline thickness remained relatively constant between high and low-density bands. Results suggest that relationships between skeletal architecture and density banding for D. strigosa differ slightly from previously reported results for Montastraea and Porites. Skeletal structural analyses provide insights relative to density band formation and suggest D. strigosa is a good candidate for isotopic/trace element analyses and a recorder of long-term growth histories.

Tissue samples from twenty bottlenose dolphins from a stable, residential community of coastal dolphins in the western Gulf of Mexico were analyzed for toxic PCB congeners and chlorinated pesticides. The tissues analyzed (blubber and melon) were from known individuals in a long-term (27+ y) study that stranded and were recovered for necropsy. Substantial demographic data were available on these individuals and utilized in the analysis of maternal transfer of organochlorines to young. The male dolphins in this study were shown to accumulate organochlorine contaminants with age. In female dolphins the organochlorine levels were found to decline with age. These results are in agreement with previous studies, with gestational and lactational transfer accounting for the decline seen in the females. A lengthening in interreproductive interval by increasing organochlorine levels after approximately age 30 y is noted in the females. For the first time, this study quantified the organochlorine levels of the first calf of a female, testing the hypothesis that the first-born of a female receives a substantially greater organochlorine load than subsequent calves. The first-born calf (age 5.3 mo) had the highest blubber ΣPCB, total DDT, HCB, and total pesticide levels of all animals in this study. The organochlorine levels in this calf were 2-5 fold higher than in a similarly aged, fourth-born calf. All animals in this study had appreciable EPCBlevels (range 0.07 - 26.9 ug/g wet weight; 2.6 - 203.2 ug/g lipid weight), and EDDT (range 0.06 - 10.3 wet weight; 0.9 - 88.1 ug/g lipid weight). These values are in a moderate range compared to other studies, but not far below levels at which western Gulf of Mexico bottlenose dolphins evidenced mortality events in 1990 and 1992. Further monitoring of this population is warranted.

Blue tilapia, Oreochromis aureus were cultured from fingerling through maturation, in outdoor tanks, at varying salinities, for a period of nine months, from September 19, 1997 to June 19, 1998. Twelve tanks were used for testing four different salinities, with three replicates each. Each tank had a surface area of 0.8 m2, a water depth of 48cm, and held a volume of 350 liters. Each tank was stocked with ten O. aureus, with a total mean weight of 100 grams, and fed 5% to 10% body weight per day depending on size throughout the study. Salinity was the only induced variable throughout the experiment. Three tanks were the freshwater control group and salinity was held at 0 ppt. Salinities in three tanks were maintained at 10 ± 2ppt. Salinities in three tanks were maintained at 20 ± 2ppt and the salinities for the remaining three tanks were maintained at 30 ± 2ppt. Complete water changes were done each month, and the fish were individually weighed and an estimate of uneaten food was done. Any morphological or behavioral changes were noted for each fish, and each was regularly checked for eggs. During the ninth month, reproduction resulted in viable eggs occurring in the freshwater control group and two tanks with salinities of 10 ppt. Light orange colored eggs were found in the mouths of females in tanks with salinities of 20 ppt, but the eggs were not viable. The fish in one tank suffered a mass mortality in month seven, so it was removed from reproduction computations. Reproduction also occurred during the ninth month in the freshwater control groups. Light orange colored eggs were found in the mouths of females in tanks with salinities of 20 ppt, but the eggs were not viable. Eggs with a grayish tint were found in the mouths of females in tanks with salinities of 30 ppt, but the eggs were also not viable. One high salinity tank was removed after nine months due to disease, but females were holding eggs with a gray color and eggs were examined and found not to be viable. No reproduction occurred in tanks with salinities of 20 ppt or higher during the experiment. Weight gain was shown to be positive and linear with salinity. The control group had the least weight gain with a final mean weight gain of 565 grams per tank. In tanks with salinities of 10 ppt, final mean weight gain of the fish was 697 grams; and in tanks with water salinities of 20 ppt, a final mean weight gain of the fish was 815 grams at the close of the experiment. Fish within tanks with salinities of 30 ppt, showed the most gain, with a mean weight gain of 927 grams these differences were shown to be statistically significant (P< .004). Morphological changes and the occurrence of disease were evident between the fish in the control tanks and the fish in all other tanks. Tank 3, with 20 ppt salinity developed bacterial septicemia, caused by Streptococcus sp .. This disease produced some lesions, enlarged heads and sunken bellies as well as a dark green cast to the dorsal area. During the eighth month, the fish in a tank with salinity of 30 ppt developed a toxic algae bloom and the fish contracted a disease, which manifested itself by producing epithelial erosion, highly suggestive of the dinoflagellate pathogen Pfiesteria piscicida. Within a week, nine of the ten fish suffered severe epithelial loss and were close to death. Other changes accompanying increased salinity were brighter red flashing on the dorsal and pectoral fins and tail. Thus the results are consistent with a hypothesis that higher salinity severely restricts reproduction and increases growth rates, but it was also appears that increased disease accompanies increased salinity. Thus the use of saltwater does not appear to be advantageous for the culture of this species.

The response of diel extracellular α and β-glucosidase activity to in situ dissolved carbohydrates was explored in coastal marine waters. The hypothesis being tested was to determine whether natural substrate could regulate enzyme activity. Relative enzyme activity was determined using artificial 4-methylumbelliferone (MUF) substrate derivatives at low substrate concentrations (300 nM). Disssolved carbohydrate concentrations were measured using the 3-methyl-2-benzothlazolinone hydrazone hydrochloride (MBTH) method: a spectrophotometric determination of monosaccharide concentrations. Six studies were conducted and p-glucosidase activity (BOA) was found to be positively correlated with dissolved polysaccharide concentrations (PCHO) in two studies which suggests that PCHO can potentially regulate BOA. A significant inverse correlation (Spearman) between dissolved monosaccharides (MCHO) and β-glucosidase activity was found in one study suggesting that MCHO was capable of repressing and/or inhibiting the activity of β-glucosidase under some conditions. Three significant positive relationships were found between α-glucosidase (AOA) and BOA suggesting that there was a tight coupling between substrate release and hydrolysis. No obvious relationships were found between hydrolytic enzymes and dissolved carbohydrates in three diel studies. This may have been due to uncontrollable factors such as nutrient limitation, grazing and the inability to distinguish between α- and β-glucans. Combined data for PCHO and BOA showed an inverse relationship suggesting that high levels of naturally occurring PCHO may compete with MUF-β-glucans for β-glucosidase active sites causing a lower rate of MUF-β-glucan hydrolysis.

The distribution and abundance of ghost crab (Ocypode quadrata) burrows on Hillsboro Beach, Florida, and their relationship to, and effect on sea turtle nests were documented at three control sites and three experimental sites from April 1994 through October 1994. The three experimental sites were located immediately to the east of three open beach sea turtle hatcheries and the control sites were established on nearby open beaches. The purpose of this work was 1) to determine if a larger population of O. quadrata occurred near sea turtle hatcheries than elsewhere along Hillsboro Beach and 2) to assess possible impacts of O. quadrata infestation on turtle hatchling emergence success. O. quadrata abundance was not significantly different at the experimental and control areas. Within the hatcheries, ghost crabs did invade sea turtle nests both before and after hatching. The emergence success of nests invaded prior to hatching was significantly lower than for non-invaded nests. Ghost crab predation appeared to significantly increase the percentages of unhatched eggs, but did not significantly change the percentages of pipped eggs or dead-in-nest hatchlings, relative to uninvaded nests.