Microphytobenthos are the dominant primary producers on estuarine mudflats playing a key role in the functioning of the ecosystem. Studies into microphytobenthic ecology have previously been limited by scale but the advent of fine scale analysis techniques (gm) as well as non-destructive sampling has enabled the system to be examined at a level not previously possible. This study examined the formation, structure and function of microphytobenthic biofilms using non-destructive (remote sensing by PAM fluorescence; fibreoptic light microprofiling) and destructive (cryo-freezing and Low temperature scanning electron microscopy) sampling. Many microphytobenthic organisms are motile and have evolved complex migratory strategies. Microphytobenthic migratory patterns are widely described but much remains to be elucidated about the controlling factors. The fluorescence parameter F015 (minimum fluorescence yield after 15 minutes dark adaptation) was used to monitor short-term changes in biomass at the sediment surface. Light, tidal state, endogeny and combinations thereof were all shown to control migration, demonstrating that predictable migratory rhythms cannot be assumed. Microscale sectioning showed that chlorophyll a was always concentrated in the top 400 gm (the photosynthetically active biomass). Clear migratory patterns were not detected using microscale sectioning therefore indicating that migration occurs over a scale < 400gm. Despite no changes in the chlorophyll a content in the surface layers, LTSEM analysis demonstrated diurnal taxonomic shifts providing circumstantial evidence that microphytobenthic cells sub-cycle at the sediment surface to optimise fitness. The light extinction co-efficient (k) of microphytobenthic biofilms significantly vaned with site, assemblage and also over time. 90% of the surface PPFD had always been attenuated by 400, and in many cases before 200. Traditional microphytobenthic primary productivity models do not account for changes in the spatial and temporal distribution of biomass or light attenuation and therefore their applicability to the real situation may be limited.

Much of the world's oceans lie below a depth of 200 meters, but very little is known about the creatures that inhabit these deep-sea environments. The deep-sea fish family Melamphaidae (Stephanoberyciformes) is one such example of an understudied group of fishes. Samples from the MAR-ECO (www.mar-eco.no) project represent one of the largest melamphaid collections, providing an ideal opportunity to gain information on this important, but understudied, family of fishes. The key to the family presented here is the first updated, comprehensive key since those produced by Ebeling and Weed (1963) and Keene (1987). Samples from the 2004 MAR-ECO cruise and the U.S. National Museum of Natural History provided an opportunity to review two possible new species, the Scopelogadus mizolepis subspecies, and a Poromitra crassiceps species complex. Results show that Scopeloberyx americanus and Melamphaes indicoides are new species, while the two subspecies of Scopelogadus mizolepis are most likely o nly one species and the Poromitra crassiceps complex is actually several different species of Poromitra. Data collected from the MAR-ECO cruise provided an opportunity to study the distribution, reproductive characteristics and trophic ecology of the family Melamphaidae along the Mid-Atlantic Ridge (MAR). Cluster analysis showed that there are five distinct groups of melamphaid fishes along the MAR. This analysis also supported the initial observation that the melamphaid assemblage changes between the northern and southern edges of an anti-cyclonic anomaly that could be indicative of a warm-core ring. Analysis of the reproductive characteristics of the melamphaid assemblage revealed that many of the female fishes have a high gonadosomatic index (GSI) consistent with values found for other species of deep-sea fishes during their spawning seasons. / This may indicate that melamphaids use this ridge as a spawning ground. Diets of the melamphaid fishes were composed primarily of ostracods, a mphipods, copepods and euphausiids. Scopelogadus was the only genus shown to have a high percent of gelatinous prey in their digestive system, while Melamphaes had the highest concentration of chaetognaths. This work presents data on the ecology and taxonomy of the family Melamphaidae and provides a strong base for any future work on this biomass-dominant family of fishes. / by Kyle Allen Bartow. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Thesis (Ph.D.)--Hong Kong University of Science and Technology, 2009. / Includes bibliographical references.

The discovery of deep-sea chemosynthesis-based ecosystems including hydrothermal vents and cold seeps has greatly expanded our view of life on Earth. Nevertheless, for many benthic organisms in these ecosystems, little is known about where they come from, how scattered populations are connected by larval dispersal, and how they adapt to the local environments. Mussels of Bathymodiolus platifrons (Bivalvia: Mytilidae) are one of the dominant and foundation species in deep-sea chemosynthesis-based ecosystems. They are known to have a wide geographic distribution, and are also one of the few deep-sea species capable of living in both hydrothermal vents [in Okinawa Trough (OT)] and methane seeps [in the South China Sea (SCS) and Sagami Bay (SB)]. Previous population genetics studies of B. platifrons mostly relied on one to several genes, which suffered from the lack of sensitivity required to resolve their fine-scale genetic structure, and were unable to reveal their adaptation to the local environments. With the repaid development of molecular techniques, it is now possible to address their demographic mechanisms and local adaptation from a genome-wide perspective. Therefore, in the first part of my thesis, I aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for B. platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) approach, assess the potential use of SNPs in detecting fine-scale population genetic structure and signatures of diversifying selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781 720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified from 28 B. platifrons individuals collected from a methane seep in the SCS and a hydrothermal vent in the middle OT (M-OT), with nine outlier SNPs showed significant evidence of diversifying selection. The small FST value (0.0126) estimated based on the neutral SNPs indicated high genetic connectivity between the two populations. However, the permutation test detected significant differences (P < 0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the neutral or outlier SNPs also showed that the two populations were genetically differentiated. This initial study successfully demonstrated the applicability of combining genome sequencing and 2b-RAD in population genomics studies of B. platifrons. Besides, using the survey genome of B. platifrons as a reference, a total of 10 199, 6429, and 3811 single nucleotide variants (SNVs) were detected from three bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides, and Idas sp. These results highlighted the potential of cross-species and cross-genus applications of the B. platifrons genome for SNV/SNP identification among different bathymodioline lineages, which can be further used in various evolutionary and genetic studies. To have a deeper understanding of how individuals of B. platifrons are connected among and adapt to their habitats, in the second part of my thesis, I used both mitochondrial genes and genome-wide SNPs to conduct a more comprehensive population genetics/genomics study of B. platifrons. Three mitochondrial genes (i.e. atp6, cox1, and nad4) and 6398 SNPs generated by 2b-RAD were obtained from 110 B. platifrons individuals from six representative locations along their known distribution range in the Northwestern Pacific. The small FST values based on both types of genetic markers all revealed high genetic connectivity of B. platifrons, which may have been driven by the strong ocean currents (i.e. Kuroshio Current, North Pacific Intermediate Water). However, when using SNP datasets rather than mitochondrial genes, individuals in the SCS were identified as a distinct genetic group, indicating the Luzon Strait may serve as a dispersal barrier that limits their larval exchange between the SCS and the open area in the Northwestern Pacific. Moreover, a genetic subdivision of B. platifrons in the southern OT (S-OT) from those in M-OT and SB was observed when using 125 outlier SNPs for data analyses. The outlier-associated proteins were found to be involved in various biological processes, such as DNA and protein metabolism, transcription and translation, and response to stimulus, indicating local adaptation of B. platifrons even they are confronted with extensive gene flow in the OT-SB region. Furthermore, by using SNP datasets, populations in S-OT were revealed to be the source of gene flow to those in the SCS, M-OT, and SB. Overall, these results offered novel perspectives on the potential forces that may have led to the genetic differentiation and local adaptation of B. platifrons, which can serve as an example for other deep-sea species with high dispersal potential, and contribute to the designation of marine protected areas and conservation of deep-sea chemosynthesis-based ecosystems. Molluscan shell formation is one of the most common and abundant biomineralization processes in metazoans. Although composed of less than 5 wt% of the molluscan shells, shell matrix proteins (SMPs) are known to play multiple key roles during shell formation, such as providing a gel-like micro-environment to favour mineral precipitation, promoting crystal nucleation, as well as guiding and inhibiting crystal growth. To date, all studies on SMPs have focused on molluscs in terrestrial and shallow-water ecosystems with no reports for those living in the deep ocean. Herein, the third part of my thesis was to study the shell proteomes of B. platifrons and its shallow-water relative Modiolus philippinarum with the aim to bridge such knowledge gaps in biomineralization studies. A total of 94 and 55 SMPs were identified from the shell matrices of B. platifrons and M. philippinarum, respectively, with 31 SMPs shared between two species. These SMPs can be assigned into six broad categories, comprising calcium binding, polysaccharide interaction, enzyme, extracellular matrix-related proteins, immunity-related proteins, and those with uncharacterized functions. Many of them, such as tyrosinases, carbonic anhydrases, collagens, chitin-related proteins, peroxidases, as well as proteinase and proteinase inhibitor domain-containing proteins, have been widely found in molluscan shell matrices and other metazoan calcified tissues (e.g. exoskeletons of corals, tubes of tubeworms), whereas some others, such as cystatins, were found for the first time in molluscan shell matrices, and ferric-chelate reductase-like proteins and heme-binding proteins were to be detected for the first time in metazoan calcified tissues. This is the first report of the shell proteome of deep-sea molluscs, which will support various follow-up studies to better understand the functions of these SMPs, especially in relation to environmental adaptation. Overall, my population genetics/genomics studies have improved our understanding of the population dynamics, genetic connectivity, fine-scale genetic structure, and local adaptation of B. platifrons in the Northwestern Pacific, and my proteomics study has shed light on the biomineralization processes of molluscs in the deep ocean.

The role of Serrivomer beanii in bathypelagic food webs is poorly known, but abundance and biomass estimates from the 2004 G.O. Sars MAR-ECO Expedition suggest it to have a high level of importance. MAR-ECO, a Census of Marine Life field project, has allowed us to increase our knowledge of S. beanii through spatial analysis, including the congeneric species Serrivomer lanceolatoides, and trophic analysis. Serrivomer beanii abundance and biomass exhibited a decreasing trend along the northern Mid-Atlantic Ridge from north to south. In terms of size, S. beanii was found to increase as distance from the ridge decreased, suggesting a topographic aggregation strategy. The diet of S. beanii consisted of crustaceans, cephalopods, and teleosts. The trophic results of this study reveal a likely "alternative" trophic pathway in the deep mid-North Atlantic, and perhaps other, bathypelagic ecosystems: higher trophic-level predators are supported by micronektonic invertebrates as primary prey. / by Megan E. Geidner. / Thesis (M.S.)--Florida Atlantic University, 2008. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2008. Mode of access: World Wide Web.

Crude oil causes both lethal and sublethal effects on marine organisms, but the impact upon sensory function remains unexplored. Elasmobranchs rely upon the effective functioning of their sensory systems for use in feeding, mating, and predator avoidance. The objective of this study was to test the effect of crude oil upon the olfactory and electroreceptive sensitivity of the Atlantic stingray, Dasyatis sabina. The magnitudes of the electro-olfactogram (EOG) responses were significantly depressed by 26% (Glutamic Acid) to 157% (Cysteine) for all amino acids when stingrays were exposed to crude oil. The shapes of the EOG responses when exposed to oil were also significantly different, exhibiting a more protracted response compared to un-exposed stingrays. Oil exposed stingrays exhibited a significant decrease in orientation distance to prey-simulating electric fields. This study is the first to quantify the effects of crude oil on olfactory and electrosensory sensitivity of marine predators. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2016. / FAU Electronic Theses and Dissertations Collection

This project used a variety of genetic markers to investigate the evolution and population genetics of hydrothermal vent fauna that were recovered from the Scotia Sea, in the Atlantic sector of the Southern Ocean. The origins of one of these species, an undescribed species of Kiwa sp. found on the East Scotia Ridge (ESR) and its constituent family Kiwaidae, a group of vent and seep-associated decapod squat lobsters (infraorder Anomura) was investigated using a concatenated nine-gene dataset and key divergences were dated using fossil calibrations. These results confirm earlier research showing Kiwaidae reside in the superfamily Chirostyloidea, but form a monophyletic clade with the non-chemosynthetic family Chirostylidae and not Eumunididae. Chirostyloid families diverged in the Cretaceous, although extant Kiwaidae radiated in the Eocene, consistent with many other chemosynthetic taxa that appear recently derived. The basal tree position of Pacific species (and the Alaska location of a likely stem-lineage kiwaid fossil) suggests kiwaids originated in the East Pacific. Within a Southern Hemisphere clade, the divergence between the southeastern Pacific K. hirsuta and a non-Pacific lineage (Kiwa sp. ESR and Southwest Indian Ridge kiwaids) is no earlier than 25.9 Ma, consistent with a spread from the Pacific into the Scotia Sea and beyond via now-extinct active ridge connections or mediated by a Miocene onset of the Antarctic Circumpolar Current (ACC) through a newly-opened Drake Passage. This project also investigated the population genetics of three undescribed species found at two vent fields ~ 440 km apart at either end of the ESR: Kiwa sp., a peltospirid gastropod and Lepetodrilus sp. limpets. Lepetodrilus sp. was also found at the Kemp Caldera, a submerged part of the South Sandwich Islands (SSI). Analyses of cytochrome c oxidase subunit 1 (COI) as well as microsatellite loci developed from Roche 454 sequence libraries revealed no differentiation along the ESR for all three species consistent with panmixia, or the dominance of non-equilibrium processes between vent field colonies within a metapopulation, possibly enhanced further by cold-induced arrested larval development. Despite apparent connectivity along the ESR, both COI and microsatellites revealed differentiation between ESR limpets and Kemp Caldera limpets ~ 95 km to the east, possibly owing to the hydrographic isolation of the caldera. Both COI and microsatellite diversity patterns were consistent with recent (< 1 Ma) demographic expansions for all three species (although the influence of selection sweeps on COI cannot be discounted); a pattern observed worldwide at vent communities and may reflect demographic instability over time as a consequence of the stochastic birth and death of vent colonies within a metapopulation. Different COI bottleneck ages between the three species (excluding the influence of possible selection) as well as the absence of kiwaids and peltospirids at Kemp, have been attributed to differences in life history, in particular larval morphology and presumed dispersal strategy. These results highlight the role of larval dispersal of vent fauna along active spreading ridges, both in maintaining vent metapopulations across vent colonies prone to stochastic birth and extinction in the short term, but also in the spread of taxa globally and the formation of biogeographic provinces. The likelihood that the three species presented here exist at vents east of the ESR and SSI, prompts further exploration along ridges in the South Atlantic, in order to investigate the effect of the ACC in enhancing gene flow and delineating biogeographic provinces.

Natural cycles of environmental variability and long-term deoxygenation in the ocean impose oxygen deficiency (hypoxia) on marine communities. My research exploits a naturally occurring hypoxia cycle in Saanich Inlet, British Columbia, Canada where I combined spatial surveys with remotely operated vehicles, ecological time-series from the subsea cabled observatory VENUS, and lab-based respirometry experiments to examine the influence of seasonally variable oxygen conditions on epibenthic communities. In situ oxygen thresholds established for dozens of fish and invertebrate species in this system show they naturally occur in lower oxygen levels than what general lethal and sublethal thresholds would predict. Expansion of hypoxic waters induced a loss of community structure which was previously characterized by disjunct distributions among species. Communities in variable hypoxia also have scale-dependent structure across a range of time scales but are primarily synchronized to a seasonal oscillation between two phases. Time-series revealed timing of diurnal movement in the slender sole Lyopsetta exilis and reproductive behavior of squat lobster Munida quadrispina in the hypoxia cycle. Hypoxia-induced mortality of sessile species slowed the rate of community recovery after deoxygenation. The 10-year oxygen time-series from VENUS, revealed a significant increase in the annual low-oxygen period in Saanich Inlet and that deoxygenation has occurred in this system since 2006. Differences in the critical oxygen thresholds (O2crit) and standard metabolic rates of key species (spot prawn Pandalus platyceros, slender sole, and squat lobster) determined the lowest in situ oxygen at which populations occurred and explained disproportionate shifts in distributions and community respiration. Finally, a meta-analysis on global O2crit reported for crustaceans showed that hypoxia tolerance differs among major ocean basins. Long-term trends of deoxygenation suggest a future regime shift may occur when the duration at which a system remains below critical oxygen levels exceeds the time needed for communities to recover. Species-specific traits will determine the critical threshold and the nature of the community response in systems influenced by variable states of oxygen deficiency. However, oceanographic and evolutionary history provides context when determining the regional response of benthic communities influenced by rapidly changing environments. / Graduate / 0329 / 0416 / 0433 / jwfchu@gmail.com