ALBERT

Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.

Description: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.

Description: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanographic Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2019.

Description: Marine microbes are key drivers of biogeochemical transformations within the world’s oceans. Although seawater appears uniform at scales that humans often interact with and sample, the world that marine microbes inhabit can be highly heterogeneous, with numerous biological and physical processes giving rise to resource hotspots where nutrient concentrations exceed background levels by orders of magnitude. While the impact of this microscale heterogeneity has been investigated in the laboratory with microbial isolates and theoretical models, microbial ecologists have lacked adequate tools to interrogate microscale processes directly in the natural environment. Within this thesis I introduce three new technologies that enable interrogation of microbial processes at the microscale in natural marine communities. The IFCB-Sorter acquires images and sorts individual phytoplankton cells, directly from seawater, allowing studies exploring connections between the diversity of forms present in the plankton and genetic variability at the single-cell level. The In Situ Chemotaxis Assay (ISCA) is a field-going microfluidic device designed to probe the distribution and role of motility behavior among microbes in aquatic environments. By creating microscale hotspots that simulate naturally occurring ones, the ISCA makes it possible to examine the role of microbial chemotaxis in resource acquisition, phytoplankton-bacteria interactions, and host-symbiont systems. Finally, the Millifluidic In Situ Enrichment (MISE) is an instrument that enables the study of rapid shifts in gene expression that permit microbial communities to exploit chemical hotspots in the ocean. The MISE subjects natural microbial communities to a chemical amendment and preserves their RNA in a minute-scale time series. Leveraging an array of milliliter-volume wells, the MISE allows comparison of community gene expression in response to a chemical stimulus to that of a control, enabling elucidation of the strategies employed by marine microbes to survive and thrive in fluctuating environments. Together, this suite of instruments enables culture-independent examination of microbial life at the microscale and will empower microbial ecologists to develop a more holistic understanding of how interactions at the scale of individual microbes impact processes in marine ecosystems at a global scale.

Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.

Description: I’d like to thank the Gordon and Betty Moore Foundation, the National Science Foundation, and NSERC for funding portions of my research.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2019.

Description: This thesis addresses the dynamics of estuarine networks, based on hydrographic observations in Newark Bay, a sub-estuarine network connected to the Hudson River estuary through New York Harbor. Estuarine networks differ from simple estuaries in that they may have multiple connections to the ocean, multiple freshwater sources, and often contain complex junctions between estuarine segments. The Newark Bay estuarine network is connected to the sea through two tidal straits, and is fed by multiple internal and external sources of fresh water. The estuarine network is also naturally divided into a series of reaches, each of which is characterized by a different cross-sectional geometry. This thesis focuses on the hydrographic variability and varying exchange flow within the Newark Bay estuarine network. Shipboard hydrographic measurements reveal the time-dependent formation of salinity fronts between reaches of the estuary. Each front is generated by a different mechanism; however, all are generated by tidal flow through channel junctions during ebb tide, and are advected landward during flood tide. Mooring-based measurements confirm that these fronts form during nearly every tidal cycle, and that the fronts are associated with substantial changes in local salinity on tidal timescales. The effect of tidal processes, such as frontal advection, on the exchange flow is investigated by applying the isohaline total exchange flow (TEF) framework to mooring-based observations in multiple reaches of the estuarine network. This reveals that over half of the exchange flow is driven by tidal processes at all sites within the estuary. Both the TEF-based salt balance and the standard Eulerian salt balance indicate that tidal processes are also responsible for at least half of the landward salt flux at most sites within the estuary; TEF and Eulerian salt balances are nearly identical. Tidal processes within the estuary are in large part associated with fronts. The large influence of tidal processes on the exchange flow in Newark Bay is thus likely due to the prevalence of channel junctions within the estuarine network.

Description: The studies contained in this thesis were largely funded as part of a National Science Foundation Coastal SEES project (Grant OCE-1325136), which was developed to investigate the effects of anthropogenic modifications on the physical processes in estuaries. Additional funding was provided by the J. Seward Johnson Fund at Woods Hole Oceanographic Institution, and by Hudson River Foundation Graduate Fellowship GF/01/17.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Oceanography/Applied Ocean Science and Engineering at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2019.

Description: Submesoscale ocean dynamics and instabilities, with characteristic scales 0.1–10 km, can play a critical role in setting the ocean’s surface boundary layer thickness and associated density stratification. Submesoscale instabilities contribute to lateral stirring and tracer dispersal. These dynamics are investigated in the Bay of Bengal, motivated by the upper ocean’s potentially coupled interactions with Monsoon winds and convection. The region’s excess precipitation and runoff generates strong salinity gradients that typically set density fronts and stratification in the upper 50 m. Since we cannot synoptically measure currents containing fast-evolving and oscillating components across the submesoscale range, we instead analyze passive tracer distributions (spice ⌘ density-compensated temperature (T) and salinity (S) anomalies), identifying signatures of flows and testing dynamical theories. The analysis is based on over 9000 vertical profiles of T and S measured along ⇠4800 km of ship tracks in the Bay of Bengal during ASIRI and MISO-BOB expeditions in 2013, 2015, and 2018. Observations in the surface mixed layer reveal ⇠1 km scale-selective correlation of surface T and S, with compensation reducing cross-front density gradients by ⇠50%. Using a process study ocean model, we show this is caused by submesoscale instabilities slumping fronts, plus surface cooling over the resultant enhanced salinity stratification, potentially thwarting the forward cascade of energy. In the stratified interior, we present a spectral analysis of horizontal spice variance statistics from wavenumber k ⇠0.01 cpkm to ⇠1 cpkm. At scales 〈10 km, stratified layers that are closer to the surface exhibit redder passive tracer spectra (power spectra k−3, gradient spectra k−1) than predicted by quasi-geostrophic or frontogenetic theories. Complimentary observations reveal spice patterns with multiple, parallel, ⇠10 m thin layers, crossing isopycnals with O(10−4) slopes, coherent over at least 30–80 km, with coincident layers of stratification anomalies. Comparison with shear measurements, and a numerical process study, suggest that both submesoscale sheared eddies, and thin near-inertial waves, form such layers. Fast formation timescales and large aspect ratios suggest they enhance horizontal mixing by shear dispersion, reducing variance at ⇠1–10 km scales.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Physical Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2019.

Description: The Galápagos Cold Pool (GCP) is a region of anomalously cold sea surface temperature (SST) just west of the Galápagos Archipelago. Modeling studies have shown that the GCP is maintained by wind- and current-driven upwelling. The Galápagos Archipelago lies on the equator, in the path of the Pacific Equatorial Undercurrent (EUC) as it flows eastward across the Pacific at the depth of the thermocline. It is hypothesized that the EUC upwells into the GCP as it reaches the topographical barrier of the Galápagos Archipelago. The path of the EUC in the vicinity of the archipelago is not well understood. The ‘Repeat Observations by Gliders in the Equatorial Region’ (ROGER) program deployed a fleet of Spray autonomous underwater gliders in the region just west of the Galápagos Archipelago from 2013 – 2016 with the goal of continuously occupying three transects that form a closed area, with the archipelago as the eastern boundary. Gliders obtained subsurface measurements of temperature, salinity, and velocity with unprecedented temporal and spatial resolution. These measurements are used to observe the path of the EUC as it bifurcates into a north and south branch around the Galápagos Archipelago. Net horizontal transport into the volume defined by the closed area formed by the glider transects is used to estimate an average vertical velocity profile in the region of the GCP, indicating upwelling in the upper 300 m. The bifurcation latitude of the EUC, estimated to be approximately 0.4∘S from volume transport as a function of salinity, is coincident with the meridional center of the archipelago, suggesting the bifurcation latitude is topographically controlled. Ertel potential vorticity and a Bernoulli function are qualitatively conserved, supporting an inertial model of the EUC. Average spectral variance from Argo profiling float observations is used to show that tropical instability waves propagate with frequency and wavelength consistent with linearized, equatorial 𝛽-plane model results and may impact the GCP, according to their vertical structure.

Description: Funding for my thesis research was provided by the National Science Foundation (grants OCE-1232971 and OCE-1233282), the NASA Earth and Space Science Fellowship Program (grant 80NSSC17K0443), the J. Seward Johnson Fund, and the Karen L. Von Damm Fellowship.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2016

Description: Eddies in the ocean move westwards. Those shed by western boundary currents must then interact with continental shelf-slope topography at the western boundary. The presence of other eddies and mean lows complicates this simple picture, yet satellite images show that mesoscale eddies translating near the shelfbreak routinely affect the continental shelves of the Mid-Atlantic Bight, the Gulf of Mexico etc. The consequent cross-shelfbreak transports are currently of unknown importance to shelf budgets of heat, salt and volume. Thus motivated, this thesis uses idealized continuously stratified numerical experiments to explore eddy-slope interactions under four questions: 1. Can the continental slope prevent an eddy from reaching the shelfbreak? 2. What is the structure of the eddy-driven offshore low? 3. How is the continental shelf affected by an eddy at the shelfbreak? 4. Given surface observations, can one estimate the volume of water transported across the shelfbreak? The experiments show that the efficiency of Rossby wave radiation from the eddy controls whether it can cross isobaths: by radiating energy the eddy becomes shallow enough to move into shallower water. For wide continental slopes, relative to an eddy diameter, a slope can prevent an anticyclone from reaching the shelfbreak by shutting down such radiation. For narrow continental slopes, the interaction repeatedly produces dipoles, whose cyclonic halves contain shelf-slope water stacked over eddy water. The formation of such cyclones is explained. Then, the structure of shelf lows forced by the eddy are studied: their vertical structures are rationalized and scalings derived for their cross-isobath scales; for example, the extent to which the eddy influences the shelf. A recipe for estimating cross-isobath transports based on eddy surface properties is put forward. Finally, the findings are tested against observations in the Middle Atlantic Bight of the northeastern United States.

Description: I acknowledge high-performance computing support from Yellowstone (ark:/85065/d7wd3xhc) provided by NCAR’s Computational and Information Systems Laboratory, sponsored by the National Science Foundation. The research presented here was funded by National Science Foundation grants OCE-1059632 and OCE-1433953. Funding support from the Academic Programs Oice, WHOI is also gratefully acknowledged.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2014

Description: Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, 〉1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highly-similar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation.

Description: I also gratefully acknowledge the WHOI Ocean Ventures Fund, which provided funding for the sequencing of over 250 viral genomes of the Nahant Collection and thereby contributed immensely to the impact of the thesis work presented here. Work presented in this thesis was also made possible by support from National Science Foundation grant DEB 0821391, National Institute of Environmental Health Sciences grant P30- ES002109, the Moore Foundation and the Broad Institute’s SPARC program.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2013

Description: The interpretation of echoes collected by active remote-sensing systems, such as sonar and radar, is often ambiguous due to the complexities in the scattering processes involving the scatterers, the environment, and the sensing system. This thesis addresses this challenge using a combination of laboratory and fi eld experiments, theoretical modeling, and numerical simulations in the context of acoustic scattering by marine organisms. The unifying themes of the thesis are 1) quantitative characterization of the spectral, temporal, and statistical features derived from echoes collected using both broadband and narrowband signals, and 2) the interpretation of echoes by establishing explicit links between echo features and the sources of scattering through physics principles. This physics-based approach is distinct from the subjective descriptions and empirical methods employed in most conventional fisheries acoustic studies. The fi rst part focuses on understanding the dominant backscattering mechanisms of live squid as a function of orientation. The study provides the first broadband backscattering laboratory data set from live squid at all angles of orientation, and conclusively con firms the fluidlike, weakly-scattering material properties of squid through a series of detailed comparisons between data and predictions given by models derived based on the distorted-wave Born approximation. In the second part, an exact analytical narrowband model and a numerical broadband model are developed based on physics principles to describe the probability density function of the amplitudes of echo envelopes (echo pdf) of arbitrary aggregations of scatterers. The narrowband echo pdf model signi cantly outperforms the conventional mixture models in analyzing simulated mixed assemblages. When applied to analyze fish echoes collected in the ocean, the numerical density of sh estimated using the broadband echo pdf model is comparable to the density estimated using echo integration methods. These results demonstrate the power of the physics-based approach and give a rst-order assessment of the performance of echo statistics methods in echo interpretation. The new data, models, and approaches provided here are important for advancing the eld of active acoustic observation of the ocean.

Description: Taiwan Merit Scholarship (NSC-095-SAF-I-564-021-TMS), Office of Naval Research (ONR; grants N00014-10-1-0127, N00014-08-1-1162, N00014-07-1-1034), National Science Foundation (NSF; grant OCE-0928801), Naval Oceanographic Offi ce (grant N62306007-D9002), WHOI Ocean Life Institute, and the WHOI Academic Programs O ffice funds.

Description: Submitted in partial fulfillment of the requirements for the degree of Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 1988

Description: A portion of the northeast Pacific ocean was chosen within which to evaluate and use altimetric data from the U.S. Navy Geodetic Satellite GEOSAT. The zero-order accuracy of the major GEOSAT geophysical data record (GDR) channels was verified, and occasional gaps in the altimeter coverage were noted. GEOSAT'S 17-day repeat orbit allowed use of collinear-track processing to create profiles of the difference between the sea surface height along a given satellite repeat, and the mean sea surface height along that repeat's groundtrack. Detrending of sea surface bias and tilt on each repeat reduced orbit and other long wavelength errors in the difference profiles. The corrections provided on the GEOSAT GDR were examined for their effects on the difference profiles of three test arcs. It was found that only the ocean tide, electromagnetic bias, and inverted barometer corrections varied enough over the arc lengths (~4400 km) to have any noticeable effect on the difference profiles. Only the ocean tide correction was accurate enough to warrant using it to adjust the sea surface heights. The recommended processing of GEOSAT data for the area included making the ocean tide correction, three-point block averaging successive sea surface heights, and forming the mean height profiles from 18 repeat cycles (to reduce aliasing of the M2 tidal component). A set of difference proftles for one GEOSAT arc indicated that a reasonable estimate of GEOSAT's system precision was -4.5 cm (RMS). The mid wavelength range (100-500 km) of these profiles was found to be the only range in which oceanic mesoscale features could be separated from altimeter errors. Mean alongtrack wavenumber spectra of oceanic variability for two GEOSAT arcs were compared with a SEASAT-derived regional spectrum of Fu (1983). Agreement was good, with GEOSAT showing less system noise at short wavelengths, and greater oceanic variability at long wavelengths. The GEOSAT spectra were fit well by a k-1.5 slope at wavelengths from 100 to 1000 km. Sea surface temporal variability as a function of location was compared with the SEASAT results of Cheney et al. (1983). Qualitative agreement was excellent and quantitative differences were largely accounted for. GEOSAT picked up the variability of the major current systems of the northeast Pacific, including the Alaskan, Californian, and North Equatorial currents. Error bounds on GEOSAT-derived oceanic variability showed that the effects of uncorrected electromagnetic bias, inverted barometer, and wet troposphere were significant. Further work in the areas of error modelling, orbit determination, and geoid calculation were called for.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 1984

Description: The distribution and feeding behavior of bacterivorous micro flagellates (2-20 μm protozoa) and their ingestion by copepods were examined in an attempt to assess the importance of these protozoa as a trophic link between planktonic bacteria and zooplankton. The abundance of microflagellates relative to other picoplankton (0.2-2.0 μm) and nanoplankton (2-20 μm) populations in water samples in the North Atlantic and in Lake Ontario and on macroaggregates in the North Atlantic was determined using direct microscopical and culture estimation techniques. Seasonal, vertical and geographical changes in the density of microflagellates were generally not greater than one order of magnitude. Microscopical counts of heterotrophic nanoplankton (presumably microflagellates) typically ranged from a few hundred to a few thousand m1-1 for a variety of planktonic environments. They constituted approximately 1/3 to 1/2 of the nanoplankton in the euphotic zone and dominated the nanoplankton in the aphotic zone. Most Probable Number (MPN) estimation of the density of bacterivorous protozoa indicated that microflagellates were, on average, an order of magnitude more abundant than bacterivorous ciliates and amoebae. MPN and direct microscopical counts of microflagellates differed by as much as 104. This discrepancy was smaller in eutrophic environments (e.g. Continental Shelf and Lake Ontario) and on macroscopic detrital aggregates. All microbial populations enumerated were highly concentrated on macroscopic detrital aggregates relative to their abundance in the water surrounding the aggregates. Enrichment factors (the ratio of abundance of a population on a macroaggregate to its abundance in the surrounding water) increased along a eutrophic-to-oligotrophic gradient because of the combined effects of an increased abundance of microorganisms on macroaggregates in oligotrophic environments and a decreased abundance in the surrounding water in these same environments. Average enrichment factors for direct microscopical counts of heterotrophic nanoplankton (range = 17-114) were not as large as enrichment factors observed for MPN estimates of the number of bacterivorous microflagellates (range = 273-18400). Microflagellates numerically dominated the bacterivorous protozoa cultured from macroaggregates by one to two orders of magnitude, but ciliates and amoebae were also highly enriched on macroaggregates. Microenvironments are therefore a potentially important aspect for the ecology of planktonic microorganisms. Observations on the microbial colonization of mucus sloughed by ctenophores and discarded appendicularian houses suggest that these materials may be important sources of macroaggregates. Batch and continuous culture experiments were conducted with clonal cultures of microflagellates to test their ability to grow on various types and densities of bacteria. The doubling time of Monas sp. 1 ranged from 43 hr (when fed the cyanobacterium Synechococcus Strain WH 8101) to 6.9 hr (when fed the heterotrophic bacterium Serratia marinorubra). Cell yields (i.e. the conversion of bacterial biomass into protozoan biomass) of Monas sp. 1 fed two species of heterotrophic bacteria were greater than yields for the microflagellate fed two species chroococcoid cyanobacteria (range = 7-68%). Cell yields of two other species of microflagellates (Monas sp. 2 and Cryptobia maris) were 48% and 61%, respectively, on the bacterium Pseudomonas halodurans. Microflagellates grew in continuous culture at concentrations of bacteria which were lower than bacterial densities required for the growth of ciliates as shown by other investigations. Therefore, microflagellates appear to be well-adapted for grazing bacterioplankton. Microflagellates were also investigated for their ability to graze bacteria attached to particles. Bodo nanorensis and Rhynchomonas nasuta both showed a marked ability to graze attached bacteria and a limited ability to graze unattached cells. These results suggest that microflagellates may also be important consumers of bacteria attached to particles in the plankton and may explain the highly elevated densities of microflagellates on macroaggregates. Grazing experiments performed with the copepod Acartia tonsa indicated that heterotrophic microflagellates were ingested by the copepods at rates comparable to the ingestion of phytoplankton of similar size. The presence of heterotrophic microflagellates did not depress filtration rates of the copepods, and one species (Cryptobia maris) appeared to be selectively grazed. Survival of A. tonsa on a diet of heterotrophic microflagellates was similar to survival on a diet of phytoplankton and was significantly longer than survival of starved Controls or copepods fed only bacteria. Due to their ability to grow at in-situ densities of planktonic bacteria, their relatively high cell yields, and their acceptability as food for zooplankton, it is concluded that bacterivorous microflagellates may constitute an important trophic link between bacteria and zooplankton. This link may provide a mechanism whereby organic material and energy from the detrital food chain can be returned to the classical phytoplankton-copepod-fish food chain.

Description: This research was supported by National Science Foundation grants OCE80-2444l and OCE82-l4928 and Ocean Industry Program grant 4473 awarded to Dr. Laurence P. Madin, NSF Doctoral Dissertation grant OCE8l-l299l, the Woods Hole Oceanographic Institution Education Program and the Wood Hole Oceanographic Institution Biology Department.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2009

Description: Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn’t directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation.

Description: National Science Foundation (NSF) Biocomplexity Program Grant (OCE-0323332); the Center for Microbial Oceanography Research and Education (C-MORE), an NSF Science and Technology Center (EF-0424599); the Woods Hole Oceanographic Institution (WHOI) Ocean Life Institute (OLI) grant to J. Waterbury, and the WHOI Academic Programs Office.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2009.

Description: This thesis examines the nature of eddy-mean flow interactions in western boundary current jets and recirculation gyre dynamics from both theoretical and observational perspectives. It includes theoretical studies of eddy-mean flow interactions in idealized configurations relevant to western boundary current jet systems, namely (i) a study of the mechanism by which eddies generated from a localized forcing drive mean recirculation gyres through the process of nonlinear rectification; and (ii) a study of the role of eddies in the downstream evolution of a baroclinic jet subject to mixed instabilities. It also includes an observational analysis to characterize eddy-mean flow interactions in the Kuroshio Extension using data from the downstream location of maximum eddy kinetic energy in the jet. New insights are presented into a rectification mechanism by which eddies drive the recirculation gyres observed in western boundary current systems. Via this mechanism, eddies drive the recirculations by an up-gradient eddy potential vorticity flux inside a localized region of eddy activity. The effectiveness of the process depends on the properties of the energy radiation from the region, which in turn depends on the population of waves excited. In the zonally-evolving western boundary current jet, eddies also act to stabilize the unstable jet through down-gradient potential vorticity fluxes. In this configuration, the role of eddies depends critically on their downstream location relative to where the unstable time-mean jet first becomes stabilized by the eddy activity. The zonal advection of eddy activity from upstream of this location is fundamental to the mechanism permitting the eddies to drive the mean flows. Observational results are presented that provide the first clear evidence of a northern recirculation gyre in the Kuroshio Extension, as well as support for the hypothesis that the recirculations are, at least partially, eddy-driven. Support for the idealized studies’ relevance to the oceanic regime is provided both by indications that various model simplifications are appropriate to the observed system, as well as by demonstrated consistencies between model predictions and observational results in the downstream development of time-mean and eddy properties.

Description: Funding was for this research and my education was provided by the MIT Presidential Fellowship and NSF grants OCE-0220161 and OCE-0825550. The financial assistance of the Houghton Fund, the MIT Student Assistance Fund, and WHOI Academic Programs is also gratefully acknowledged.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2008

Description: The subtidal circulation of the southeast Greenland shelf is described using a set of highresolution hydrographic and velocity transects occupied in summer 2004. The main feature present is the East Greenland Coastal Current (EGCC), a low-salinity, highvelocity jet with a wedge-shaped hydrographic structure characteristic of other surface buoyancy-driven currents. The EGCC was observed along the entire Greenland shelf south of Denmark Strait, while the transect north of the strait showed only a weak shelf flow. This observation, combined with evidence from chemical tracer measurements that imply the EGCC contains a significant Pacific Water signal, suggests that the EGCC is an inner branch of the polar-origin East Greenland Current (EGC). A set of idealized laboratory experiments on the interaction of a buoyant current with a submarine canyon also supported this hypothesis, showing that for the observed range of oceanic parameters, a buoyant current such as the EGC could exhibit both flow across the canyon mouth or into the canyon itself, setting the stage for EGCC formation. Repeat sections occupied at Cape Farewell between 1997 and 2004 show that the alongshelf wind stress can also have a strong influence on the structure and strength of the EGCC and EGC on timescales of 2-3 days. Accounting for the wind-induced effects, the volume transport of the combined EGC/EGCC system is found to be roughly constant (~2 Sv) over the study domain, from 68°N to Cape Farewell near 60°N. The corresponding freshwater transport increases by roughly 60% over this distance (59 to 96 mSv, referenced to a salinity of 34.8). This trend is explained by constructing a simple freshwater budget of the EGCC/EGC system that accounts for meltwater runoff, melting sea-ice and icebergs, and net precipitation minus evaporation. Variability on interannual timescales is examined by calculating the Pacific Water content in the EGC/EGCC from 1984-2004 in the vicinity of Denmark Strait. The PW content is found to correlate significantly with the Arctic Oscillation index, lagged by 9 years, suggesting that the Arctic Ocean circulation patterns bring varying amounts of Pacific Water to the North Atlantic via the EGC/EGCC.

Description: Funding for the cruise and analysis was provided by National Science Foundation grant OCE-0450658, which along with NSF grant OCE- 0095427 provided funds for my tuition and stipend as well.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution August 1980

Description: Observational evidence of seasonal variability below the main thermocline in the eastern North Atlantic is described, and a theoretical model of oceanic response to seasonally varying windstress forcing is constructed to assist in the interpretation of the observations. The observations are historical conductivity-temperature-depth data from the Bay of Biscay region (2° to 20°W, 42° to 52°N), a series of eleven cruises over the three years 1972 through 1974, spaced approximately three months apart. The analysis of the observations utilizes a new technique for identifying the adiabatically leveled density field corresponding to the observed density field. The distribution of salinity anomaly along the leveled surfaces is examined, as are the vertical displacements of observed density surfaces from the leveled reference surfaces, and the available potential energy. Seasonal variations in salinity anomaly and vertical displacement occur as westward propagating disturbances with zonal wavelength 390 (±50) km, phase 71 (±30) days from 1 January, and maximum amplitudes of ±30 ppm and ±20 db respectively. The leveled density field varies seasonally with an amplitude corresponding to a thermocline displacement of ±15 db. The observations are consistent with the predictions of a model in which an ocean of variable stratification with a surface mixed layer and an eastern boundary is forced by seasonal changes in a sinusoidal windstress pattern, when windstress parameters calculated from the observations of Bunker and Worthington (1976) are applied.

Description: This work was supported by the Office of Naval Research under contract N00014~76-C-197, NR 083-400.

Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution April 1978

Description: The structure of the membrane-free nucleoid of Escherichia coli and of unfolded chromosomal DNA was investigated by sedimentation on neutral sucrose gradients after irradiation with 60Co gamma-rays and ultraviolet light (2S4nm). Irradiation both in vivo and in vitro was used as a molecular probe of the constraints on DNA~packaging in the bacterial chromosome. The extremely gentle lysis and unfolding procedures which were developed yielded undamaged, replicating genomes, thus permitting direct measurement of the formation and repair of DNA double-strand breaks at biologically-significant doses of ionizing radiation. In vitro UV-irradiation of nucleoids resulted in an increase in the observed rate of sedimentation due to the formation of an unknown photo-product. In contrast, UV-irradiation of wild-type cells in vivo showed evidence of the formation of incision breaks which resulted in the relaxation of supercoiling in the nucleoid. Strand breakage was also observed following in vivo UV-irradiation of a uvrB-5 strain, but at a lower rate and also accompanied by considerable unfolding of the chromosome. Such lesions may have been the result of direct photochemical reactions in the nucleoid, or enzyme activity associated with a uvr-independent mode of repair. The number of domains of supercoiling was estimated at 170 per genome equivalent of DNA based on measurements of relaxation caused by single-strand break formation in in vivo- and in vitro-gamma-irradiated folded chromosomes. Similar estimates based on the target size of RNA molecules responsible for maintaining the compact packaging of the nucleoid predicted negligible unfolding due to the formation of RNA single-strand breaks at doses up-to 10 Krad, and were born out by experimental measurements. Unfolding of the nucleoid in vitro by limit-digestion with RNase or by heating at 70° resulted in DNA complexes with sedimentation coefficients of 1030±59S and 625±15S respectively. The difference in these rates was apparently due to more complete deproteinization and thus less mass in the heated material. These structures are believed to represent intact, replicating genomes in the form of complex-theta structures containing 2-3 genome equivalents of DNA. The rate of formation of double-strand breaks was determined from molecular weight measurements of thermally unfolded chromosomal DNA gamma-irradiated in vitro. Break formation was linear with dose up to 10 Krad, resulting in 0.27 double-strand breaks per kilorad per genome equivalent of DNA and requiring 1080 eV/double-strand break. The influence of possible non-linear DNA conformations of these calculations is discussed. Repair of ionizing radiation damage to folded chromosomes was observed within 2-3 hours of post-irradiation incubation in growth medium. A model based on recombinational repair is proposed to explain the formation of 2200-2300S material during early stages of incubation and subsequent changes in the gradient profiles. Such behavior is not observed for post-irradiation incubation of wild-type cells in buffer or for a recA-13 strain incubated in growth medium. Association of unrepaired DNA with plasma membrane is proposed to explain the formation of a peak of rapidly sedimenting material (〉〉3100S) during the later stages of repair. Direct evidence of repair of double-strand breaks during post-irradiation incubation in growth medium was obtained from gradient profiles of DNA from RNAse-digested chromosomes. The sedimentation coefficient of broken molecules was restored to the value of unirradiated DNA after 2-3 hours of incubation, and the fraction of the DNA repaired in this fashion was equal to the fraction of cells which survived at the same dose. An average of 2.7 double-strand breaks per genome per lethal event was observed, suggesting that 1-2 double-strand breaks per genome are repairable in this strain of E. coli.

Description: The series of observations described in this report were planned with the double purpose of measuring the evaporation and transport of water vapor from the ocean into an unstable atmosphere, and of studying the diffusion processes operating in air of this stability class. Measured values of the evaporation from ocean surfaces were conspicuously absent from the meteorological literature until Craig and Montgomery (1949) published values for hydrostatically stable air. The present set of measurements extends our knowledge to include evaporation into a hydrostatically unstable air mass. In addition to evaporation values at the surface, net transports of water vapor at many levels up to 2000 meters have been measured.

Description: With the advance in knowledge of oceanic circulation there now exists a demand for additional identifying properties which will serve to trace the origin and movements of water masses in the sea, and to check earlier conclusions based entirely on temperature and salinity distribution. Of all the known identifying properties (except temperature and salinity) oxygen appears to be the most useful, not only because of the ease with which it can be accurately measured at sea, but also because of the large amount of data available on its distribution in the open ocean.

Description: With the opening of the Woods Hole Oceanographic Institution in July 1931, there was inaugurated a program of investigations in the deep waters of the western North Atlantic for which there had long been a great need. In contrast to most deep-sea investigations, which have had to be planned as single expeditions, the Institution was able to initiate a general program which could be carried out gradually in order to take advantage of knowledge gained during the course of the work. Suffcient funds having been provided for the continuous operation of its research vessel "Atlantis," work could be planned for all seasons of the year. Although these investigations have not been in progress for long and new data are continually being brought in by the "Atlantis," there are several reasons that make it seem desirable at this time to publish a preliminary report based on the completed temperature and salinity observations. In the first place, the problem of oceanic circulation is such that we cannot hope for a satisfactory solution for a long time to come. Moreover, it would be unwise to allow too much data to accumulate, because several years may pass before we can arrive at more important conclusions. Secondly, both the chemical and biological programs undertaken at the same time, require as a background the general scheme of circulation in the western North Atlantic as well as the distribution of temperature and salinity. It is, in fact, the necessity of taking into consideration the movements of the sea water which ties together the whole subject of oceanography. Therefore, it is the duty of those interested in ocean circulation to make available their findings as soon as possible for investigators of other problems in the same area. The "Atlantis" temperature and salinity observations discussed in these pages were planned with two main purposes in view. The first objective was an intensive study of seasonal changes along sections running from the southwestern corner of Nova Scotia to Bermuda and from Bermuda to the mouth of Chesapeake Bay.! This, of course, included an examination of fluctuations in the Gulf Stream, as well as of the variations in the water masses on each side of it. Second, there has been planned and partly carried out, a more general survey of the western North Atlantic, where accurate, deep stations have been sadly lacking.

Description: During the past four years a deliberate effort has been made at the Woods Hole Oceanographic Institution to devise methods of kinematic observation generally suited to the needs of oceanographers. One result of this work, the electromagnetic method, has been brought from the experimental stage to one of useful maturity. Many of the theoretical potentialities of the method are still to be explored and developed. Nevertheless it seems likely that this remaining work may be done more soundly if present developments of the theory and instrumentation are made available for use and evaluation by, others. These studies in methods of kinematic observation have been supported mainly under the provisions of Bureau of Ships Contract NObs-2083, and Office of Naval Research Contract N6onr-277-1. This support and the assistance of the Naval Ordnance Laboratory, the Hydrographic Office (Oceanographic Division), the United States Coast Guard, and the David Taylor Model Basin of the United States Navy is gratefully acknowledged.

Description: The New York Bight consists of the waters lying between Cape May, New Jersey, and Montauk Point, Long Island. A portion of the general southwesterly current known as the Coastal Drift lies in the seaward part of the Bight. Inshore from the Coastal Drift is an area of complex hydrography where the combined outflows of the Hudson River and other rivers enter the sea. In the region where the New Jersey and Long Island coastlines converge, an area 25 nautical miles on each side has been studied at all seasons of the year. This area extends from Sandy Hook southward to a point off Seaside Heights, eastward to 73°15' W longitude, north to the Long Island shore, and westward to Rockaway Inlet. The depth of water in the area averages about 90 feet, except in the innermost part of the Hudson Canyon which runs roughly northwest-southeast across most of the survey area. In the Canyon, depths in excess of 240. feet are found within the limits of the area studied. The hydrographic conditions in the area are in essence similar to those off the mouths of other large rivers. The combined flows of the Hudson and other rivers entering the surveyed area discharge enough fresh water annually to replace about one-half of the total volume of water under the 600 square miles of sea surface extensively surveyed. The salinity within the area is nearly as high as that of adjacent coastal water, however, and the actual quantity of river water within the area at any time rarely exceeds one percent of the total volume of water. Quantitative evaluation of these factors has led to the conclusion that there is an active circulation within the area which rapidly disperses the introduced river effluent. Many surveys of coastal and estuarine waters have been made. Outstanding among these are the survey of the River Tees, (1931, 1935), of the Tamar Estuary, (Hartley and Spooner, 1938; Milne, 1938), and of Alberni Inlet, (Tully, 1949). The general principles of estuarine circulations may be summarized as follows: In order to remove the added river water there must be a non-tidal drift of mixed water in a net seaward direction. When river flow remains constant, a steady state distribution of fresh and salt water throughout the estuary is attained, and at such times the net transport of river water seaward through any complete cross section of the estuary exactly equals the contribution of fresh water from the river during the same interval of time. As the mixture containing the river water moves seaward it gets progressively more saline, as additional sea water is entrained. In order to provide this sea water there must be a counter drift having a net flow in a landward direction. Superimposed on these necessary parts of the circulation are tidal and wind currents. The velocities of the tidal currents are commonly much greater than the velocity of the non-tidal drift, making the latter difficult to measure directly. It can be inferred, however, from the distribution of river water, as derived from the salinity distribution. Using the river water in this way we have evaluated the exchanges of the waters within the New York Bight. Tully (1949) has analyzed the circulation in Alberni Inlet by similar methods. Tidal current measurements made by the Coast and Geodetic Survey at various locations in the northwestern corner of the surveyed area are summarized by Marmer (1935). At Scotland Lightship, which is the location of the stations at the western end of Section A in Figure 1, the total excursion which results from the flood or ebb tidal currents is less than two miles. The currents at Ambrose Lightship, about five miles to the eastward, produce displacements only about half as great. The tidal displacements throughout the rest of the area are presumed to be less than these. The pattern of distribution of properties will be displaced, therefore, a distance less than ±1 mile at various stages of the tide. This distance is small in comparison to the size of the area surveyed, especially when considering the fact that distances between stations ranged from 5 to 8 miles. It was unnecessary, therefore, to attempt to take comparable stations at similar stages of the tide. Other considerations, beside its interesting hydrography, have contributed to the choice of this area for study. Because it is adjacent to centers of dense population and heavy industrial concentration, the New York Bight serves the conflicting purposes of waste disposal and recreation. Sewer effluents and industrial wastes enter the area by way of the rivers. Sewage sludges are barged out and dumped within the region studied. During the period covered by our surveys, The National Lead Company commenced operations to barge and discharge at sea the waste from its titanium plant at Sayreville, New Jersey. Since iron was a major constituent of this waste, analyses for iron in the water were made at each station, and the results have been valuable in checking the rate of the circulation which was computed from the distribution of river effluent. The New York Bight is also used extensively for recreational purposes. Because the area is readily and cheaply accessible by public transportation it must serve the recreational demands of a large part of the population of metropolitan New York. Sport fishing, bathing and boating are the principal recreational activities. Small but valuable commercial fisheries for shellfish and fin-fish also exist. The purpose of this study was to investigate the hydrographic processes in the New York Bight since they have an important bearing on the general problems of coastal oceanography and a knowledge of them should lead to a more successful evaluation and utilization of the area for the diverse purposes it must serve.

Description: This paper is a discussion of possible discrepancies in computations of ocean currents (based on horizontal variations of dynamic topography calculated from arbitrary deep lying reference surfaces), because of time variations of temperature and salinity at fixed depths in the sea (illustrated for a 24-hour period at "Atlantis" Station 2639). The results contained herein, while based chiefly on information from the western North Atlantic, are of general applicability, since time variations of the same order of magnitude have been observed over extensive areas of the Atlantic ocean. In selecting material for analysis of dynamic situations in the region concerned, consideration has been given only to those favorably located stations from which the structural features could most conveniently be obtained for illustrating the points in question.