ALBERT

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 2022.

Description: Dispersion in estuaries sets the length of salinity intrusion and the horizontal mixing rate of waterborne constituents, including larvae, nutrients, sediments, and contaminants. While bulk calculations of dispersion are readily estimated using traditional field measurements, the mechanisms contributing to the total dispersion are difficult to identify because they require high temporal and spatial resolution to measure. Recent advances in field techniques and numerical modeling have enabled the isolated study of various mechanisms contributing to dispersion, many of which vary on tidal time-scales and over small spatial scales. The objective of this thesis is to use a combination of high-resolution field measurements and numerical modeling to determine the mechanisms of dispersion that maintain the salt balance in the North River (Marshfield, MA), a tidally-dominated salt marsh estuary with complex topography. First, a field campaign was conducted to determine the dispersion associated with the out-of-phase exchange between tributary creeks and the main channel. Then, numerical simulations of an idealized estuary were conducted and a novel quasi-Lagrangian approach was applied to analyze the sources of dispersive salt fluxes throughout the estuary. A second field campaign was conducted to evaluate the spatial variability of shear dispersion, particularly near regions of abrupt topographic variations. The key result from this thesis is obtained through the first application of the theoretical moving plane framework of Dronkers & van de Kreeke (1986), which confirms quantitatively that all landward salt flux at a fixed location must result from spatial correlations in velocity and salinity within a tidal excursion of the fixed location. Based on this result, the sources of the landward salt flux can be directly identified based on the spatial and tidal variations of shear dispersion, which can vary strongly due to its dependence on the local tidal currents, along-channel salinity gradient, and bathymetry. This thesis identifies and quantifies various mechanisms of topographically-induced tidal dispersion and thus highlights the dominant role of topography in controlling the processes that contribute to mixing and transport in short, tidally-energetic estuaries.

Description: The work presented in this thesis was funded largely by the National Science Foundation through a Graduate Student Research Fellowship (No. 1122374) in addition to NSF Grants OCE-1634490 and OCE-2123002. Additional funding was also provided from WHOI through the Michael J. Kowalski Fellowship for Ocean Science & Engineering and from MIT through an OGE Diversity Fellowship.

Description: Dataset: Intra-annual salinity and temperature variation in four regions across latitude

Description: Temperature and salinity measurements from coastal sites across a latitudinal gradient spanning the subarctic to the tropics. Environmental variables were obtained at 1 meter below the water surface and are represented in biweekly periods for one year. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/863108

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1434528

Description: Dataset: CTD AR29, RB1904 and TN3638

Description: CTD casts from the first, second and third cruises of the SPIROPA project. The first cruise (AR29), took place aboard the R/V Neil Armstrong in April 2018, the second cruise (RB1904) on the Ronald H. Brown in May 2019 and the third cruise (TN368) took place on the R/V Thomas G. Thompson cruise in July of 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/807119

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657803

Description: Dataset: BLOOFINZ-GoM flow cytometry abundance

Description: Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/835414

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1851558, National Oceanic and Atmospheric Administration (NOAA) NA16NMF4320058

Description: Dataset: CTD AR29 and TN368: Diatom Hotspot Data

Description: CTD casts from the first cruise and third cruises of the SPIROPA project. The first cruise (AR29 Transect 24), took place aboard the R/V Neil Armstrong in April 2018 and the third cruise (TN368) took place on the R/V Thomas G. Thompson cruise in July of 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/807119

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657803

Description: Dataset: Coral Associated Microbes on Mo'orean Coral Reefs

Description: Three species of coral, plus water and sediment, were sampled at 21 sites around the island of Mo’orea, French Polynesia during the dry and rainy seasons in 2017 and 2018. Coral associated microbes (bacteria and archaea) were investigated and their community composition characterized through sequencing of the 16S rRNA gene. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/845039

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1635798, NSF Division of Ocean Sciences (NSF OCE) OCE-1635913

Description: Dataset: CTD Profile Casts

Description: CTD Depth Profile Cast Data for the InVirT-2019-BATS (Bermuda Atlantic Time Series) project taken in the on board of the R/V Atlantic Explorer AE1926 in 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/835593

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1829636

Description: Dataset: CTD Data from IFCB Sampling

Description: CTD casts associated with IFCB (Image Flow CytoBot) sampling events taken at Palmer Deep Station on February 8 and March 7 2020. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/865030

Description: NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1745009, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1744884, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1745011, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1745018, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1745023, NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) OPP-1745081

Description: Dataset: CTD AR29 and TN368

Description: CTD casts from the first cruise and third cruises of the SPIROPA project. The first cruise (AR29), took place aboard the R/V Neil Armstrong in April 2018 and the third cruise (TN368) took place on the R/V Thomas G. Thompson cruise in July of 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/807119

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1657803

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: Dataset: Site data, hydrographic measurements and seagrass cover

Description: Sampling sites, hydrographic measurements and percent cover of seagrass sampled at the southern Aransas Bay (Redfish Bay area), northern Corpus Christi Bay (Redfish Bay area) and East Flat region of Corpus Christi bay between November 2017 and December 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/814871

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1807143

Description: Dataset: MO - biogeochemical and microbial field surveys

Description: Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013. This dataset includes water samples collected from 2009-2013 at the Bermuda Hydrostation that were analyzed for DOC, POC, bacterial abundance, leucine, and thymidine incorporation. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543314

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004

Description: Dataset: Diatom Matrix RNAseq

Description: Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/818765

Description: NSF Division of Integrative Organismal Systems (NSF IOS) IOS-1656311

Description: Dataset: Wetz-783256-Sonde

Description: Bottom and surface water quality sonde data of the Guadalupe Estuary site (Texas) between August 2017 and December 2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/787319

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1760006

Description: Dataset: In situ biogeochemical time-series in Bermuda 2017

Description: In situ biogeochemical measurements including pCO2, pH, alkalinity, oxygen, temperature and salinity for a time-series in Bermuda, September 2017. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/783568

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1459255

Description: Dataset: Mumford Cove Monitoring Data

Description: Despite their importance for research and environmental protection, there's still a shortage of high quality and high-resolution temperature, pH, and oxygen data particularly in shallow coastal habitats. We monitor five important environmental parameters (i.e., depth, temperature, salinity, pH, and dissolved oxygen) at 30 minute intervals in Mumford Cove, CT (41 degrees 19'25"N, 72 degrees 01'07"W), a small (2 km N-S × 0.5 km E-W), shallow (1-5m), cone-shaped embayment opening to northeastern Long Island Sound, with protected marsh habitat along its western side, marsh and beach habitat along its eastern side, and an extensive seagrass (Zostera marina) cover. Continuous monitoring is achieved by swapping identical and recalibrated probes (Eureka Manta Sub2) every 3-5 weeks. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/659874

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1536336

Description: Dataset: Wetz-783256-Discrete

Description: Discrete hydrographic measurements of Lavaca-Colorado, Guadalupe and Nueces Estuaries on the Texas coast between August 2017 and January 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/787316

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1760006

Description: Dataset: Inside and Outside Kelp Forest Mooring

Description: Data from moored instruments (pH, dissolved oxygen, temperature, salinity, PAR, pressure) at 9 depths outside (36° 37.342’ N, 121° 54.049’ W) and inside the kelp canopy (36° 37.297’ N, 121° 54.102’ W.) at Hopkins Marine Station, recorded between June and October 2018. The tidal depth of the kelp canopy mooring ranges from 8 to 11 meter. The outside mooring is located 115m north and offshore from the kelp forest, the tidal range is 16 to 9 meters. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822549

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1737096, NSF Division of Ocean Sciences (NSF OCE) OCE-1737176

Description: Dataset: Discrete Seawater Samples

Description: Discrete seawater samples collected at the surface, 1 m below the surface, and 1 m above the bottom two times a week at each mooring (Kelp and Outside) from June 12, 2018 to August 3, 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/826410

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1737096, NSF Division of Ocean Sciences (NSF OCE) OCE-1737176

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: Dataset: UW FHL Temperature & Salinity

Description: Hourly seawater temperature and salinity values taken by an SBE 37 MicroCAT at UW FHL (University of Washington, Friday Harbor Laboratories) in Friday Harbor between January 1, 2010 and January 1, 2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/775732

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1041213

Description: Dataset: Montagna-783256-Hydrography

Description: The effects of Hurricane Harvey were studied. This dataset includes hydrographic measurements (temperature, salinity, oxygen, pH, refraction) from San Antonio Bay, northwest Gulf of Mexico estuaries along the Texas coast. They were taken during eleven quarterly sampling trips on a small boat, Feb. 2017 - July 2019. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/784614

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1760006

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 June 2019.

Description: Global patterns of ocean salinity arise from the exchange of freshwater between the sea surface and the atmosphere. For a quasi-steady state system, these surface fluxes are balanced by compensating transports of salt in the ocean interior. In a warming climate, the atmosphere holds additional water vapor which acts to intensify the global water cycle. Amplified freshwater fluxes are then absorbed at the surface and propagate along ocean circulation pathways. Here, we use coupled model results from the CMIP5 experiment to identify coherent responses in the atmospheric water cycle and in ocean salinity patterns. Some aspects of the response are consistent across models, while other regions show large inter-model spread. In particular, the salinity response in the North Atlantic subpolar gyre, where the mean salinity plays a role in maintaining high surface density for deep-water formation, has low confidence in CMIP5 models. To understand how differences in ocean circulation may affect this response, we use two techniques to diagnose the role of salt transports in the present-day climate. The first is a salt budget within the surface mixed layer, which identifies major transport processes. The second is a Lagrangian particle tracking tool, used to understand the regional connectivity of water masses. From this analysis, we find that anomalous freshwater signals become well mixed within the ocean gyres, but can be isolated on larger scales. The subpolar Atlantic salinity response generally shows freshening at the surface, but is sensitive to the transport of anomalously salty water from the subtropics, a largely eddy-driven process. As CMIP5 models use a range of eddy parameterizations, this is likely a source of uncertainty in the salinity response. Finally, we investigate the effect of salinity changes on the deep overturning cells and other circulations, and find a complex influence that also depends on the details of advective pathways. In a warming scenario, water cycle amplification actually works to strengthen the Atlantic meridional overturning circulation due to the influence of enhanced subtropical evaporation.

Description: Funding for this thesis was provided by NASA grant NNX12AF59GS03, a NASA Earth and Space Science Fellowship award 80NSSC17K0372, and the WHOI Academic Programs Office.

Description: Dataset: McMurdo Sound CTDs

Description: CTD data were collected as part of an ecosystem study in McMurdo Sound, which is located at the southern extent of the Ross Sea in the Southern Ocean. The major goal of this multi-disciplinary project was to assess the influence of top−down forcing (predation) on pelagic zooplankton and fish. During the first year (3 November 2012 – 21 January 2013), the CTD was deployed through ice core holes in the fast ice (sea ice attached to land), sampling from near surface to depths between 97 and 175 m. Stations were located along a transect in the middle of McMurdo Sound, perpendicular to the fast ice edge. In the second year (17 November 2014 – 1 January 2015), CTD casts were deployed between 100 and 254 m in depth, at stations along the fast ice edge, and along three transects into the fast ice along the eastern side of McMurdo Sound (Ross Island), in the middle of the Sound, and on the western side of the Sound. Chlorophyll fluorescence sensor measurements on the CTD casts were only made during the 2014/2015 field expedition. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/680929

Description: NSF Division of Polar Programs (NSF PLR) PLR-0944511

Description: Dataset: Physical monitoring data

Description: Despite their importance for research and environmental protection, there’s still a shortage of high quality and high-resolution temperature, pH, and oxygen data particularly in shallow coastal habitats. We monitor five important environmental parameters (i.e., depth, temperature, salinity, pH, and dissolved oxygen) at 30 minute intervals in Mumford Cove, CT (41°19’25”N 72°01’07”W), a small (2 km N-S × 0.5 km E-W), shallow (1-5m), cone-shaped embayment opening to the northeastern Long Island Sound, with protected marsh habitat along its western side, marsh and beach habitat along its eastern side, and an extensive seagrass (Zostera marina) cover. Continuous monitoring is achieved by swapping identical and recalibrated probes (Eureka Manta Sub2) every 3-5 weeks. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/659874

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1536336

Description: Dataset: qPCR

Description: These data include the quantification of specific microbial taxa within the sediments collected during Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea. DNA was extracted from the interior of frozen whole round cores sampled from Little Belt, Anholt Loch, Landsort Deep, and Bornholm Basin at The University of Tennessee. For a more detailed description of drill sites, access the data set, "IODP-347 drill site locations". Primers specifically targeting the 16S rRNA gene of bacteria, archaea, anaerobic methane oxidizers (ANME-1), and Miscellaneous Crenarchaeota Group (MCG; taxonomically reassigned as the Bathyarchaeota phylum of Archaea) were used to assess abundance of these microbial groups. Abundance data was generated using quantitative-PCR (qPCR) and a non-specific, intercalating DNA stain, SYBR Green. Values were compared against a standard curve to generate copies/uL. These data were collected by Alex Shumaker as part of Dr. Karen Lloyd and Dr. Andrew Steen’s project funded by the National Science Foundation entitled, "Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea". For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641358

Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1431598

Description: Dataset: Inferno vent plume proteins-Av1

Description: Proteins identified from the black smoker chimney Inferno hydrothermal vent plume waters at Axial Seamount, an active volcano along the Juan de Fuca Ridge spreading center, were identified using tandem mass spectrometry (MS/MS). These data are reported as Supplementary Table 3 and discussed in the on-line publication “Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean” by Mattes, et al., 2013. doi for that publication: 10.1038/ismej.2013.113. This is the first of two replicate datasets. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/627835

Description: NSF Ocean Sciences (NSF OCE) OCE-1232840

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 sinking flux of particles is an important removal mechanism of carbon from the surface ocean as part of the biological pump and can play a role in cycling of other chemical species. This work dealt with improving methods of measuring particle export and measuring export on different scales to assess its spatial variability. First, the assumption of 238U linearity with salinity, used in the 238U–234Th method, was reevaluated using a large sample set over a wide salinity range. Next, neutrally buoyant and surface-tethered sediment traps were compared during a three-year time series in the subtropical Atlantic. This study suggested that previously observed imbalances between carbon stocks and fluxes in this region are not due to undersampling by traps. To assess regional variability of particle export, surface and water-column measurements of 234Th were combined for the first time to measure fluxes on ~20 km scales. Attempts to relate surface properties to particle export were complicated by the temporal decoupling of production and export. Finally, particle export from 234Th was measured on transects of the Atlantic Ocean to evaluate basin-scale export variability. High-resolution sampling through the water-column allowed for the identification of unique 234Th features in the intermediate water column.

Description: I was supported by NASA Headquarters under the NASA Earth and Space Science Fellowship Program (Grant NNX10AO72H). Specific projects were funded by grants from the National Science Foundation, including Carbon Flux Through the Twilight Zone – New Tools to Measure Change (OCE-0628416), WAPflux – New Tools to Study the Fates of Phytoplankton Production in the West Antarctic Peninsula (ANT-0838866), and GEOTRACES Atlantic Section: Trace Element Sources and Sinks Elucidated by Short- Lived Radium and Thorium Isotopes (OCE-0925158).

Description: This is the first volume of an international scientific journal that is dedicated to issues of geoethics and geological culture. Its goal is to inform the Italian and international scientific communities about what emerged at the GeoItalia 2011 conference, attended by not only Italian geoscientists. At this conference, the geoscientists questioned their role in society and the responsibilities that they have to assume as scholars of the planet Earth and experts of the territory. They highlighted the need for rediscovery of the cultural values of geology as a science that can contribute to the construction of correct social knowledge, and the need to be aware that geoethics cannot exist without a real awareness among geoscientists of the cultural value of the Earth sciences.

Description: Published

Description: 331

Description: 5.9. Formazione e informazione

Description: JCR Journal

Description: open

Description: Prof. Giulio Giorello is amongst the most prominent philosophers of science in Italy and in the world. He is currently Professor of the Philosophy of Science at the University of Milan, Director of the Series ‘Science and Ideas’ (Raffaele Cortina Books Editor), and Literary Journalist of the cultural pages of the Corriere della Sera, one of the most important of the Italian newspapers. In this keynote presentation, in interview form, he talks about the value that the Earth sciences have had through history, framing this group of disciplines in ethical and epistemological terms, and highlighting some important elements that have to be considered in geological activities.

Description: Published

Description: 343-346

Description: 5.9. Formazione e informazione

Description: JCR Journal

Description: open

Description: The international debate in the field of geoethics focuses on some of the most important environmental emergencies, while highlighting the great responsibilities of geoscientists, whatever field they work in, and the important social, cultural and economic repercussions that their choices can have on society. The GeoItalia 2009 and 2011 conferences that were held in Rimini and Turin, respectively, and were organized by the Italian Federation of Earth Science, were two important moments for the promotion of geoethics in Italy. They were devoted to the highlighting of how, and with what tools and contents, can the geosciences contribute to the cultural renewal of society. They also covered the active roles of geoscientists in the dissemination of scientific information, contributing in this way to the correct construction of social knowledge. Geology is culture, and as such it can help to dispel misconceptions and cultural stereotypes that concern natural phenomena, disasters, resources, and land management. Geological culture consists of methods, goals, values, history, ways of thinking about nature, and specific sensitivity for approaching problems and their solutions. So geology has to fix referenced values, as indispensable prerequisites for geoethics. Together, geological culture and geoethics can strengthen the bond that joins people to their territory, and can help to find solutions and answers to some important challenges in the coming years regarding natural risks, resources, and climate change. Starting from these considerations, we stress the importance of establishing an ethical criterion for Earth scientists, to focus attention on the issue of the responsibility of geoscientists, and the need to more clearly define their scientific identity and the value of their specificities.

Description: Published

Description: 335-341

Description: 5.9. Formazione e informazione

Description: JCR Journal

Description: open

Description: Franco Ferrarotti, Professor emeritus at ‘La Sapienza’ University of Rome; since winning the first Chair in this discipline in Italy in 1961, he has been considered the Father of Italian Sociology. An independent Member of Italian Parliament in the third government (1958-1963), a member of the New York Academy of Sciences, and a ‘visiting Professor’ at many universities in Europe, North America, Russia, Japan and Latin America. Franco Ferrarotti has taught and still teaches in Europe and America, and he has received many awards throughout his career. In this interview, he talks about the social aspects and consequences of Earth sciences studies.

Description: Published

Description: 347-348

Description: 5.9. Formazione e informazione

Description: JCR Journal

Description: open

Description: We argue here that the introduction of an ethical code of conduct that follows the example of the Hippocratic Oath of physicians will help geologists to acquire binding awareness of their professional and social responsibilities. The ethical behavior and obligations of modern geologists involve, but are not limited to, the following issues: correct land/ environment use and management; respect of truth and science; and protection of the Earth systems, on both the local and global scales, and therefore, of our well-being. We believe that for geoligists, the explicit acceptance of an ethical code will help to promote: (i) an awareness of their social role, expertise and sense of belonging to a professional community; (ii) an understanding of the expectations of citizens and society; and (iii) cultural growth, with better use of research and implementation of scientific and professional skills. All this should enhance the public recognition of the social mission of geologists, which is essential for the well-being of society. Therefore, we suggest that like in the majority of medical schools, ethical training should be a part of the university curriculum for students in geology.

Description: Published

Description: 365-369

Description: 5.9. Formazione e informazione

Description: JCR Journal

Description: open

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 Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2009

Description: Mechanisms for the tidal component of salt flux in the Hudson River estuary are investigated using a 3D numerical model. Variations with river discharge, fortnightly tidal forcing, and along channel variability are explored. Four river discharge conditions were considered: 1200 m3 s-1, 600 m3 s-1, 300 m3 s-1, 150 m3 s-1. Tide-induced residual salt flux was found to be variable along the channel, with locations of counter-gradient flux during both neap and spring tide. The magnitude of tidal salt flux scales with the river flow and has no clear dependence on the spring-neap tidal forcing. The diffusive fraction, ν, has a value of -0.25 to 0.46 in the lower estuary, increasing to -0.23 to 1 near the head of salt. The phase lag between tidal salinity and velocity is analyzed at three cross-sections with: large positive, negative, and weak tidal salt flux. The composite Froude number, G2, is calculated along the channel and indicates nearly ubiquitous supercritical flow for maximum flood and ebb during both neap and spring tides. Subcritical flow occurs during slack water and at geographically locked locations during neap floods. Application of two-layer, frictional hydraulic theory reveals how variations in channel width and depth generate tidal asymmetries in cross-sectional salinity, the key ingredient of tidal salt flux.

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 January 1977

Description: Millimeter scale fluctuations in refractive index recorded with a freely sinking shadowgraph system are correlated with finestructure profiles of temperature, salinity and density and compared to models of ocean turbulence. Images with vertically aligned periodic structure, called bands, are identified as salt fingers, while others with chaotic structure are turbulent. Images are found on interfaces that are 1-10m thick and have gradients at least several times the mean. From 6 profiles in the Mediterranean Outflow region of the eastern North Atlantic between 1.0 and 1.9 km depth, 398 interfaces have been identified and a significant fraction (about 1/3) of these have detectable images. High contrast images, including bands, are most often found below warm, saline intrusions and within stepped structure where there is a regular sequence of homogeneous mixed layers separated by interfaces. As the interfacial salinity gradient increases in the sense that allows salt finger convection, the fraction of interfaces with images increases. The horizontal spacing of bands (~5 mm) is consistent with calculated salt finger diameter. The calculated and observed length of ocean salt fingers (10-20 cm) is a small fraction of the interface thickness. High levels of small scale variability in the shadowgraphs is reflected in high levels of variance in the finestructure band of the temperature spectra. The temperature gradient spectra have a slope of -1, indicative of turbulence affected by buoyancy forces, and there is a relative peak at a wavelength near the observed salt finger length. The high contrast images are found at interfaces within the enhanced mean salinity gradient below saline intrusions. For very strong salinity gradients there is a solitary interface with intense images, but for weaker mean gradients the convection takes the form of stepped structure. The steps may evolve from the solitary interface as the salinity gradient is run down by salt finger convection. This study identifies parts of the ocean where salt finger convection is prevalent and includes the first comprehensive description of salt fingers in the ocean. Existing models of salt fingers are evaluated in light of ocean observations, and models of ocean turbulence are compared to measurements.

Description: Support from ONR contract N00014-66-C0241 NR. 083-004 is also 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 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 2003

Description: This thesis utilizes field data from the Fraser River Estuary, a highly stratified system located in southwestern British Columbia, Canada, to investigate the nature of mixing processes in a highly stratified environment, and to extend two-dimensional hydraulic theory to a three dimensional environment. During the late ebb, a stationary front exists at the Fraser mouth. Although densimetric Froude numbers in the vicinity of the front are supercritical in a frame of reference parallel to the local streamlines, the front itself is oriented such that the value of the Froude number is equal to the critical value of unity when taken in a frame of reference perpendicular to the front. This observation presents a robust extension of established two-dimensional, two-layer hydraulic theory to thee dimensions, and implies similarity with trans-sonic flows, in that a Froude angle can be used to identify critical conditions in a manner similar to the Mach angle. Mixing processes were evaluated at the mouth during the late ebb using a control volume approach to isolate mean vertical entrainment processes from turbulent processes, and quantify the vertical turbulent salt and momentum fluxes. Observed turbulent dissipation rates are high, on the order of 10-3 m2s.3, with vertical entrainment velocities on the order of 2x10-3 m's'l. Mixing efficiencies, expressed as flux Richardson numbers, are confined within a range from 0.15 to 0.2, at gradient Richardson number values between 0.2 and 0.25. These results are consistent with previous laboratory studies, but represent energetic conditions that are several orders of magnitude higher. In the estuarine channel, the variability of mixing processes was investigated through the tidal cycle using control volume and overturn scale methods. Spatially, mixing was observed to be more intense near a width constriction on the order of25%. Temporally, more dominant mixing was observed during ebbs, due to increases in both vertical shear and stratification. Mixing is active and important throughout the tidal cycle, and was found to be the dominant process responsible for removing salt from the estuarine channel during the ebb.

Description: This research was funded by Office of Naval Research grants N000-14-97-10134 and N000-14-97-10566, National Science Foundation grant OCE-9906787, a National Science Foundation graduate fellowship, 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 2000

Description: The variability of salt transport determines the variation of the length of the salinity intrusion and the large-scale density gradient in an estuary. This thesis contains three studies that address salt transport and the salt balance. The variation of salt transport with the depth, the along-channel salinity gradient, and the amplitude of the tidal velocity is investigated with analytic and numerical models. The results indicate that salt transport increases dramatically during stratified periods when vertical mixing is weak. Analysis of salt transport from observations in the Hudson Estuary show that stratified periods with elevated estuarine salt transport occur in five-day intervals once a month during apogean neap tides. Oscillatory salt transport, which is hypothesized to be primarily caused by lateral exchange and mixing of salt, appears to play a more minor role in the salt balance of the estuary. The salt balance of the estuary adjusts very little to the spring-neap modulation of salt transport but adjusts rapidly to pulses of freshwater flow. A simple model is used to investigate the process and time scales of adjustment of the salt balance by connecting variations of salt transport to the variations of freshwater flow and vertical mixing. The results show the length of the salinity intrusion adjust via advection to rapid and large increases in freshwater flow. The salinity intrusion adjusts more rapidly to the spring-neap cycle of tidal mixing the higher the freshwater flow.

Description: The National Science Foundation provided support through a National Science Foundation Graduate Fellowship and NSF Grant OCE94-15617. Grants from the Hudson River Foundation (HRF Grant 006j96A) and the Office of Naval Research (Grant Number N00014-97-1-0134) have also contributed towards the work in this thesis. This work is also partially the result of research sponsored by NOAA National Sea Grant College Program Office, Department of Commerce, under Grant No. NA46RG0470, Woods Hole Oceanographic Institution (WHOI) Sea Grant project no. R/O-30.

Description: Red Pompeian paintings, very famous for their deep intensity, are currently suffering from darkening. The origins of this darkening degradation are not clearly identified yet and remain a major issue for curators. In the specific case of cinnabar (HgS)-based red pigment, a photoinduced conversion into black metacinnabar is usually suspected. This work is focused on the blackening of red cinnabar paintings coated on a sparry calcite mortar. Different samples exhibiting different levels of degradation were selected upon visual observations and analyzed by synchrotron-based microanalytical techniques. Atomic and molecular compositions of the different debased regions revealed two possible degradation mechanisms. On one hand, micro X-ray fluorescence elemental maps show peculiar distributions of chlorine and sulfur. On the other hand, X-ray absorption spectroscopy performed at both Cl and S K-edges confirms the presence of characteristic degradation products: (i) Hg- Cl compounds (e.g., corderoite, calomel, and terlinguaite), which may result from the reaction with exogenous NaCl, in gray areas; (ii) gypsum, produced by the calcite sulfation, in black coatings. Metacinnabar is never detected. Finally, a cross section was analyzed to map the in-depth alteration gradient. Reduced and oxidized sulfur distributions reveal that the sulfated black coating consists of a 5-ím-thick layer covering intact cinnabar.

Description: Published

Description: 7484-7492

Description: reserved

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: Submitted in partial fulfillment of the requirements for Master of Science at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2005

Description: A moored profiler record from the western tropical North Atlantic provides the first continuous time series of temperature, salinity and velocity profiles in a thermohaline staircase. Variations in the intensity of layering and the evolution of layer properties are well documented during the 4.3 month record. Such staircases are the result of strong salt fingering at the interfaces between the mixed layers, and these data provide unique insights into the dynamics of salt fingers. In particular, a striking linear correlation between the temperature and salinity of the layers may be interpreted as resulting from vertical salt finger flux divergences. Data from this record allow new interpretations of previous work on this topic by McDougall (1991).

Description: This research was supported by the National Science Foundation under grants OCE-0081502 and OCE-0350743

Description: When the U. S. Bureau of Fisheries, in cooperation with the Museum of Comparative Zoology, commenced the oceanographic survey of the Gulf of Maine in the summer of 1912 (Bigelow, 1925-1927), it was in the hope that this might later be extended to the coastal waters thence southward; eventually even as far as the Gulf of Mexico. Cruises carried out in connection with investigations of the biology of the mackerel, by the Fisheries' steamer "Albatross II" from 1927 to 1932, supplemented by those of the research ship "Atlantis" of the Woods Hole Oceanographic Institution, have made it possible to extend the detailed examination of the physical oceanography of the continental shelf as far as the offing of Chesapeake Bay, and to the offing of Cape Hatteras for some of the months. The present account of the temperature of the region will, it is hoped, be followed shortly by corresponding accounts of salinity, of circulation and of the dominant planktonic communities.

Description: The present paper forms a sequel to the account of the temperature of the same region (Bigelow, 1933)... the continental shelf between the offings of Cape Cod (longitude about 70°) and Chesapeake Bay;-extended southward, for occasional months, to the offing of Cape Hatteras; and with such discussion of conditions along the continental slope as is justified by occasional profiles.