Academic literature on the topic 'Biological oceanography'

Abstract Platt, T., Sathyendranath, S., and Fuentes-Yaco, C., 2007. Biological oceanography and fisheries management: perspective after 10 years. – ICES Journal of Marine Science, 64: 863–869. Despite 100 years of research into the relationship between oceanographic factors and fish recruitment, it has proved very difficult to demonstrate causal connections between properties of the marine ecosystem and the success of fisheries. Some authors have been led to conclude that such causal connections, therefore, do not exist: a corollary would be that biological oceanography is of limited relevance to fisheries issues. However, it would be premature to dismiss biological oceanography as a tool in fisheries management. If we have not been able to implicate ecosystem factors as a significant source of variance in fish recruitment, it may be because the search has been conducted at an inappropriate scale, a consequence of the limitations of ships as oceanographic platforms. The advent of remotely sensed data from satellites greatly extends the scales of time and space at which synoptic oceanography can be carried out. Access to such data allows a wider range of hypotheses to be tested, than is possible with ships alone, on the relationship between ecosystem factors and recruitment. Applications in both the Atlantic and Pacific have demonstrated strong fluctuations between years in the timing and the intensity of phytoplankton dynamics, with implications for recruitment and growth of exploited populations of fish and invertebrates. The results provide essential intelligence for those charged with stewardship of the marine environment.

Of all the classical oceanographic disciplines, we are probably least well equipped to further the understanding of biological oceanography through the data that will be provided by an Integrated Sustained Ocean Observing System (IOOS). What's more, some of the same federal agencies that would normally be approached to invest in the development of new sensor systems for IOOS biological applications are now faced with more pressing priorities—homeland security among them—all competing for the same limited resources. This paper introduces some technologies and applications that are capable of conducting sustained biological oceanographic observations and how these technologies may be used for ocean biological resource assessment while simultaneously helping to secure our nation's borders. Particular emphasis is given to passive acoustic systems that may be employed both to monitor biota as well as anthropogenic activity. Also discussed are potential dual use applications in both oceanography and USCG mission execution, including High Frequency Surface Wave Radar (HFSWR). Finally, a number of existing and emerging telemetry techniques and systems are described that may provide the extensive data connectivity for the offshore sensors required of the IOOS, as well as improve coastal security.

In the last quarter of the twentieth century, an innovative three-dimensional graphical technique was introduced into biological oceanography and ecology, where it spread rapidly. Used to improve scientists' understanding of the importance of scale within oceanic ecosystems, this influential diagram addressed biological scales from phytoplankton to fish, physical scales from diurnal tides to ocean currents, and temporal scales from hours to ice ages. Yet the Stommel Diagram (named for physical oceanographer Henry Stommel, who created it in 1963) had not been devised to aid ecological investigations. Rather, Stommel intended it to help plan large-scale research programs in physical oceanography, particularly as Cold War research funding enabled a dramatic expansion of physical oceanography in the 1960s. Marine ecologists utilized the Stommel Diagram to enhance research on biological production in ocean environments, a key concern by the 1970s amid growing alarm about overfishing and ocean pollution. Before the end of the twentieth century, the diagram had become a significant tool within the discipline of ecology. Tracing the path that Stommel's graphical techniques traveled from the physical to the biological environmental sciences reveals a great deal about practices in these distinct research communities and their relative professional and institutional standings in the Cold War era. Crucial to appreciating the course of that path is an understanding of the divergent intellectual and social contexts of the physical versus the biological environmental sciences.

Fish larvae in Australian waters have been studied progressively in the last 2-3 decades including the distribution and abundance of taxa, growth and age, their prey and predators. However, the effect of nutrient limitation on ichthyoplankton is unstudied, particularly in the oligotrophic Australian waters. My study was aimed to examine the effect of natural or anthropogenic nutrients on the abundance, distribution, growth and condition of fish larvae along-shore of the NSW coast (latitude 30-34S), where the East Australian Current departs the NSW coast and generates local upwelling of cool nutrient-rich water. This study shows no significant difference in the total abundance or diversity of either larval fishes amongst the 112 taxa (111 families and 1 order), among regions within or upstream of the upwelling. However in both months, there were distinctive ichthyoplankton assemblages at the family level. The Carangidae, Labridae, Lutjanidae, Microcanthidae, Myctophidae and Scombridae were more abundant in the EAC or oceanic water masses, while the Callionymidae, Clupeidae, Platycephalidae, Sillaginidae and Terapontidae were mostly found in the surface or deep upwelled/uplifted water masses. This pattern is observed in other ichthyoplankton studies and may be a general and useful method to determine mixing of water masses. Larvae of silver trevally (Pseudocaranx dentex) and yellowtail scad (Trachurus novaezelandiae) were generally larger and less abundant in the topographically induced upwelling region, than north of the region in pre-upwelled conditions of the East Australian Current. Both species were mostly at the preflexion stage (less than 4.3 mm in body length and less than 10 days old) in the pre-upwelled conditions, particularly during November, and proportionally more larger and older larvae in the upwelled waters (mostly post-flexion, greater than 4.3 mm in body length and greater than 10 days old). Ages from sagittal otoliths ranged from 2-25 increments (~days) and exhibited linear growth for both species and months over the size range (3-15 mm standard length). The otolith radius-length relationship and the growth rates were similar between species and months, despite the 3-4C difference between months. Overall growth rates of the younger larvae were uniform throughout the entire sampling area (0.5-0.6 mm.d-1), while older larvae grew significantly faster in the upwelled water (0.41 mm.d-1) compared to the non-upwelled conditions (0.34 mm.d-1). Both species tended to be depleted in 13C in the upwelling region (from ???18.5 to ???19.0), consistent with expected ratios from deeper water, whereas the 15N composition tended to increase in Pseudocaranx, but decrease in Trachurus indicating different diets and possibly trophic level. The early life history of both species indicates spawning in pre-upwelled waters, but larval transport into upwelled waters is necessary for faster growth in the post-flexion stage. The assemblage of larval fishes did differ between the upwelled region and a region south of Sydney???s deepwater outfalls, but the difference was ascribed to a latitudinal effect and the EAC. Both larval carangids were enriched in 15N, possibly due to the enriched dissolved organic matter of primary treated sewage. In summary, this study found that the larval fish community can provide a biological means to trace water masses, and estimate their degree of mixing. Remarkably there was no significant effect of upwelling or sewage addition to the abundance or diversity of larval fish, in the nutrient poor waters of the East Australian Current. Larval carangids and pilchards were abundant in late spring off northern NSW, and their early life histories were inferred. Both larval carangid species seem to be spawned in the EAC waters, but as post-flexion larvae grew faster in the upwelled zone. Pre-flexion (less than 10 day old) larval carangids of both genera indicated spawning in the EAC, and the rarer post-flexion (greater than 10 days old) carangids grew faster in the upwelled waters. Here, both genera had stable isotope signatures characteristic of upwelled waters for carbon, but had different nitrogen signatures, indicative of different diets and trophic level status. Larval pilchards actually grew more slowly in the upwelling region, as observed in coastal waters off Japan, and their nursery grounds may be further offshore in the Tasman Front, analogous to their early life history in the Kuroshio Extension.

The work in this dissertation represents an attempt to investigate multiple temporal and spatial scales of inquiry relating to the variability of marine resources throughout the Gulf of Mexico large marine ecosystem (Gulf LME). This effort was undertaken over two spatial extents within the greater Gulf LME using two different time-series of fisheries monitoring data. Case studies demonstrating simple frameworks and best practices are presented with the aim of aiding researchers seeking to reduce errors and biases in scientific decision making. Two of the studies focused on three years of groundfish survey data collected across the West Florida Shelf (WFS), an ecosystem that occupies the eastern portion of the Gulf LME and which spans the entire latitudinal extent of the state of Florida. A third study was related to the entire area covered by the Gulf LME, and explored a 30-year dataset containing over 100 long-term monitoring time-series of indicators representing (1) fisheries resource status and structure, (2) human use patterns and resource extractions, and (3) large- and small-scale environmental and climatological characteristics. Finally, a fourth project involved testing the reliability of a popular new clustering algorithm in ecology using data simulation techniques.

The work in Chapter Two, focused on the WFS, describes a quantitatively defensible technique to define daytime and nighttime groundfish assemblages, based on the nautical twilight starting and ending times at a sampling station. It also describes the differences between these two unique diel communities, the indicator species that comprise them, and environmental drivers that organize them at daily and inter-annual time scales. Finally, the differential responses in the diel, and inter-annual communities were used to provide evidence for a large-scale event that began to show an environmental signal in 2010 and subsided in 2011 and beyond. The event was manifested in the organization of the benthic fishes beginning weakly in 2010, peaking in 2011, and fully dissipating by 2012. The biotic effects of the event appeared to disproportionately affect the nighttime assemblage of fishes sampled on the WFS.

Chapter Three explores the same WFS ecosystem, using the same fisheries-independent dataset, but also includes explicit modeling of the spatial variability captured by the sampling program undertaking the annual monitoring effort. The results also provided evidence of a disturbance that largely affected the nighttime fish community, and which was operating at spatial scales of variability that were larger than the extent of the shelf system itself. Like the previous study, the timing of this event is coincident with the 2010 Deepwater Horizon oil spill, the subsequent sub-marine dispersal of pollutants, and the cessation of spillage. Furthermore, the spatial models uncovered the influence of known spatial-abiotic gradients within the Gulf LME related to (1) depth, (2) temperature, and (3) salinity on the organization of daytime groundfish communities. Finally, the models developed also described which non-spatially structured abiotic variables were important to the observed beta-diversity. The ultimate results were the decomposition of the biotic response, within years and divided by diel classification, into the (1) pure-spatial, (2) pure-abiotic, (3) spatial-abiotic, and (4) unexplained fractions of variation.

Chapter Five employs a clustering technique to identify regime states that relies on hypothesis testing and the use of resemblance profiles as decision criteria. This clustering method avoids some of the arbitrary nature of common clustering solutions seen in ecology, however, it had never been rigorously subjected to numerical data simulation studies. Therefore, a formal investigation of the functional limits of the clustering method was undertaken prior to its use on real fisheries monitoring data, and is presented in Chapter Four. The results of this study are a set of recommendations for researchers seeking to utilize the new method, and the advice is applied in a case study in Chapter Five.

Chapter Five presents the ecosystem-level fisheries indicator selection heuristic (EL-FISH) framework for examining long-term time-series data based on ecological monitoring for resources management. The focus of this study is the Gulf LME, encompassing the period of 1980-2011, and it specifically sought to determine to what extent the natural and anthropogenic induced environmental variability, including fishing extractions, affected the structure, function, and status of marine fisheries resources. The methods encompassed by EL-FISH, and the resulting ecosystem model that accounted for ~73% of the variability in biotic resources, allowed for (1) the identification and description of three fisheries resource regime state phase shifts in time, (2) the determination of the effects of fishing and environmental pressures on resources, and (3) providing context and evidence for trade-offs to be considered by managers and stakeholders when addressing fisheries management concerns. The EL-FISH method is fully transferrable and readily adapts to any set of continuous monitoring data. (Abstract shortened by ProQuest.)

Recruitment of marine fishes is largely determined by biological and oceanographic factors acting on early life stages. Coastal upwelling has long been recognized as a critical factor influencing the survival of larvae and recruitment to adult populations. Dynamics in regional upwelling influence the magnitude and timing of primary productivity, affecting the availability of critical food sources for larval fish. In addition, upwelling-relaxation cycles affect the dispersal of marine larvae and their onshore delivery prior to settlement. Challenges with tracking larvae, however, have limited our understanding of how oceanography influences the early life stages of fishes. The objective of this dissertation is to evaluate the biological and oceanographic drivers of larval growth, settlement, and recruitment, using rockfishes ( Sebastes spp.) as model organisms.

Overlap of larval production and favorable feeding conditions may drive recruitment for many temperate marine fishes, as small changes in larval growth can result in order-of-magnitude differences in year-class-strength. In Chapter 1, I assess the influence of regional productivity, temperature, and larval condition in explaining growth in rockfishes. I employ a combination of otolith microstructure and satellite imagery to measure initial larval growth and estimate the productivity and temperature experienced by individuals to determine their relative importance in subsequent growth at metamorphosis. I compare model performance using indexed environmental conditions scaled over three different regions. In both years of study, net primary productivity explained the most variation in pre-metamorphic growth relative to temperature and initial growth. This relationship was consistent across spatial regions. Recent settlement, juvenile recruitment, and individual growth were significantly higher in a year when productivity bloomed earlier and individual larvae experienced higher levels of productivity. These results support the hypothesis that large-scale oceanographic processes that stimulate upwelling and secondary production are primary drivers of larval growth and subsequent year-class strength in rockfishes.

Characterizing the behavior of larvae prior to settlement is integral to understanding population dynamics because coastal oceanography may facilitate or limit settlement. Otolith microchemistry can be used to determine patterns of fish movement, although there is a limited understanding of how this tool can be applied in coastal marine systems. My goal in Chapter 2 is to evaluate the application of otolith microchemistry to characterize water mass associations of settlement-stage marine fish in a coastal upwelling region using a three-step approach. First, I characterize seawater chemistry of coastal water masses across multiple years, finding significant differences in the chemical signatures of strong upwelling, weak upwelling, and relaxation. Second, I experimentally determine the effect of temperature on the partitioning of trace elements in otoliths for two rockfishes to find that the effect of temperature on otolith partition coefficients was element- and species-specific. Finally, I compare the synchrony in seawater and otolith chemistry of settlement-stage rockfishes that were exposed to naturally variable conditions over an upwelling-relaxation cycle. I subsequently evaluate whether laser ablation inductively coupled plasma mass spectrometry effectively measures otolith chemistry over ecologically relevant time scales. I discovered that elemental concentrations in otoliths respond rapidly to changes in seawater chemistry and reflect equivalent proportional changes. This study provides evidence that elemental signatures are valuable tools for reconstructing larval histories of marine fish.

In Chapter 3, I use otolith chemistry to examine water mass associations of two juvenile rockfishes during onshore transport and settlement in an upwelling region. I develop a chemical proxy for upwelling and relaxation by characterizing Sr/Ca and Ba/Ca signatures of otoliths collected during these oceanographic conditions. Otolith chemistry differed between rockfishes collected during upwelling and relaxation, with signatures unique to each year. I subsequently compare otolith signatures of rockfishes collected during high and low settlement periods to determine whether specific water masses affect settlement. I provide evidence that copper rockfish associate with upwelling currents during periods of high settlement, suggesting that upwelling may facilitate settlement for these species. Conversely, I found evidence that the closely related gopher rockfish associate with relaxation events during peak settlement periods. This research takes an important first step at in evaluating the utility of trace element signatures to characterize larval fish movement during onshore delivery and settlement in marine systems. Together, these studies improve our understanding of how coastal upwelling impacts larval growth, settlement, and recruitment, which provides important information for understanding population dynamics in marine ecosystems.

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A research survey was conducted, consisting of six transects between 38°- 46°S and 38 - 41°45'E, during the austral autumn of 2007. The aim of the survey was to investigate the physical, chemical and biological dynamics of the Subtropical Convergence (STC), in the SW Indian sector of the Southern Ocean. Satellite data was obtained and in-situ data were collected. Mixed layer depth (MLD), geostrophic velocities, density and Brunt Vaisala frequencies were calculated. The STC meandered across the survey area between 41 ° - 42°15'S. The total integrated Chl-a ranged from 12.8 to 40.1 mg Chl-a/m2. The most significant correlation between biological and physical data was that of Chl-a and MLD (r=-0.374, n=45, p=0.013) over the entire survey region. Phosphate and nitrate (r=0.8779, n=45, p=0.001) measured over the survey region were strongly correlated, as expected. The surface currents showed cyclonic motion between 38° - 39°E and 38 - 42°S, with the exception of an eddy-like feature between 39.5°and 40.5"S and generally anti-cyclonic motion to the east of 39°E.

Burial is an important life history strategy employed by benthic fishes that has not been fully explored in its diversity by the biomechanical literature. This thesis explores the mechanism by which the Pacific sandfish buries as well as the physical limitations of the behavior. We first investigate the role of the ventilatory pump in the burial behavior of sandfish by using high-speed videography, dye, and digital particle image velocimetry (DPIV). We determined that sandfish employ a modification of the ventilatory pump, which is used repeatedly to fluidize the substrate ventral to the head. This modification of the ventilatory pump should reduce the energetic costs associated with burial as it decreases the cost of transport typically associated with ‘shoveling’ substrate. Second, we investigate the physical limitations that are caused by the reliance on the ventilatory pump to fluidize substrate. We used sand beds of varying grain sizes, and therefore varied the minimum velocities of fluidization, to determine how sandfish respond variation in substrata. We determined that sandfish can bury in grains smaller than 1.00mm in diameter but were unable to bury in any substrate larger than 1.00mm. We also determined that there was an increase in the time it took sandfish to bury in those substrates smaller than 1.00mm as grain size increased. There was no change in the frequency of the behavior, however, suggesting that sandfish have very little ability to bury in larger substrates. We also determined that it is probably not the absolute velocity produced by the opercular jet that determines burial success, but the ability burying behavior to maintain the sand’s momentum during the expansive phase that occurs between bouts of opercular jetting.

Shallow subtidal epibenthic communities worldwide are under threat from exploitation, pollution, eutrophication, acidification, climate change, and invasive species, with implications for ecosystem diversity, productivity, function, and services. Subtidal ecosystems in the Gulf of Maine are particularly impacted, making it crucial to understand these habitats so that our impacts can be predicted and mitigated. I investigated the basic ecological forces that structure shallow subtidal epibenthic communities in this region, and how invasive species integrate themselves into these communities. I used community phylogenetic and functional trait analyses to investigate if invertebrate communities in the rocky subtidal are assembled via deterministic or random forces, experimental manipulations to quantify how macroalgae might influence sessile invertebrates on subtidal surfaces, and measurements of life history traits of Botrylloides violaceus, an invasive colonial ascidian, to estimate whether growth of this species differs among man-made versus natural habitats. Based on community phylogenetic analyses, rocky subtidal invertebrate communities appear to be structured by deterministic forces, with evidence for both competitive exclusion and environmental filtering operating at different spatial scales. These findings support existing studies that show that competition structures communities at local scales, and also expand our knowledge of the processes that act regionally, i.e. environmental filtering. On shallow sunlit experimental surfaces suspended from floating docks, macroalgae had little effect on invertebrate abundance or diversity, contrary to findings from experiments in the rocky subtidal. Macroalgae did influence composition as well as enhance invertebrate colonization in the early stages of community assembly. Different factors appear to influence the balance between heterotrophs and autotrophs in floating dock and rocky subtidal systems with implications for community structure, function and productivity. In different habitats, colonies of the invasive ascidian B. violaceus exhibited differences in life history traits. It grew faster and attained larger sizes in man-made floating dock versus natural rocky subtidal and eelgrass bed habitats. Again, differences among habitats appear to influence invasion success. In conclusion, competitive exclusion, facilitation, and environmental filtering play key roles in controlling the structure, composition, and function of shallow subtidal communities. Invasive species have the potential to disrupt these forces as they integrate themselves into man-made and subsequently natural habitats.

An unparalleled data catalog of well-documented, interoperable oceanographic data and information, openly accessible to all end-users through an intuitive web-based interface for the purposes of advancing marine research, education, and policy. Conference Website: https://web.whoi.edu/ocb-workshop/

“Praktikum auf See” is a cruise planned for master students of the biological oceanography at GEOMAR-Kiel. The main purpose of the expedition is to engage students in the real ocean science and exposing them to the “research-life on the sea”. We are going to sample for different fauna and flora of the central and easterly Baltic to be able to track biodiversity changes along the salinity gradient. This year’s cruise is combined with the sampling for the Horizon 2020 Project “GoJelly” in which samples for ecological studies of gelatinous zooplankton will be taken (www.gojelly.eu).

This technical manual guides the user through the process of creating a data table for the submission of taxonomic and morphological information for plankton and other particles from images to a repository. Guidance is provided to produce documentation that should accompany the submission of plankton and other particle data to a repository, describes data collection and processing techniques, and outlines the creation of a data file. Field names include scientificName that represents the lowest level taxonomic classification (e.g., genus if not certain of species, family if not certain of genus) and scientificNameID, the unique identifier from a reference database such as the World Register of Marine Species or AlgaeBase. The data table described here includes the field names associatedMedia, scientificName/ scientificNameID for both automated and manual identification, biovolume, area_cross_section, length_representation and width_representation. Additional steps that instruct the user on how to format their data for a submission to the Ocean Biodiversity Information System (OBIS) are also included. Examples of documentation and data files are provided for the user to follow. The documentation requirements and data table format are approved by both NASA’s SeaWiFS Bio-optical Archive and Storage System (SeaBASS) and the National Science Foundation’s Biological and Chemical Oceanography Data Management Office (BCO-DMO).