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<p>While much is known about the abundance and genetic diversity of environmental microbial communities, little is known about their taxon-specific activity. In this thesis I address this gap using a model marine microbe, the cyanobacterium <italic>Prochlorococcus spp.</italic>, which numerically dominates tropical and subtropical open oceans and encompasses a group of genetically defined clades that are ecologically distinct. Ribosomal RNA is a promising indicator of in situ activity because of its essential role in protein synthesis as well as its phylogenetic information, which could be used to distinguish clades among mixed populations. Here I show that, in a laboratory system the specific growth rate of representative <italic>Prochlorococcus</italic> strains could be quantitative predicted from cellular rRNA content (assessed by RT-qPCR), cell size (assessed by flow cytometry) and temperature. Applying this approach in the field, I show unique clade-specific activity patterns for <italic>Prochlorococcus</italic>. For example, vertically within the euphotic zone, eHL-II activity is strongly impacted by light and is consistent with patterns of photosynthesis and on a horizontal transect from Hawaii to San Diego, eHL-I and eHL-II activities exhibit significant transitions and appear to be regulated by temperature, nutrient and vertical mixing gradients. Using ribosomal tag pyrosequencing of DNA and RNA, I have extended our observation to the Eubacterial community and described the biomass distribution (rDNA) and activity (rRNA) patterns from two representative depths (25 and 100 m) at a well-studied oligotrophic ocean station. These results show that for some populations the abundances and activities are significantly uncoupled, which suggests substantial top-down controls or physical transport processes. Further exploring the taxon-specific activity patterns along with abundances and environmental variables across time and space is essential to better understanding the dynamics of a complex microbial system as well as predicting the consequences of environmental change.</p> / Dissertation

<p> The Coastal and Marine Ecological Classification Standard (CMECS) provides a comprehensive framework of common terminology for organizing physical, chemical, biological, and geological information about marine ecosystems. Federally endorsed as a dynamic content standard, all federally funded data must be compliant by 2018; however, applying CMECS to deep sea datasets and underwater video have not been extensively examined. The presented research demonstrates the extent to which CMECS can be applied to deep sea benthic habitats, assesses the feasibility of applying CMECS to remotely operated vehicle (ROV) video data in near-real-time, and establishes best practices for mapping environmental aspects and observed deep sea habitats as viewed by the ROV&rsquo;s forward-facing camera. All data were collected during 2014 in the Northern Gulf of Mexico by the National Oceanic and Atmospheric Administration&rsquo;s (NOAA) ROV <i> Deep Discoverer</i> and ship <i>Okeanos Explorer.</i></p>

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / "August, 1998." / Includes bibliographical references (p. 219-254). / Two cytochrome P4501A-dependent mechanisms of aryl hydrocarbon receptor (AhR) agonist toxicity were examined in the marine teleost scup (Stenotomus chrysops), alteration of arachidonic acid (AA) metabolism and production of reactive oxygen species (ROS). In scup hepatic microsomes, cytochrome P450s including CYP1A and CYP2B-like proteins catalyzed regioselective metabolism of AA to eicosatrienoic and hydroxyeicosatetraenoic acids. Benzo[a]pyrene (BP) treatment induced liver microsomal AA metabolism, but that effect varied with season. Endogenous AA epoxides were recovered from scup liver, heart, and kidney, and their composition in the liver was altered by treatment with BP or 2,3,7,8-tetrachlorodibenzo-p-dioxin. In scup and mammals, the formation of ROS was stimulated by binding of 3,3',4,4-tetrachlorobiphenyl (TCB) to CYP1A, apparently CYP1A1. Attack of that ROS inactivated scup CYP1A. ROS release and inactivation of CYPlA were stimulated only by substrates of CYP1A that are slowly metabolized. In vivo, 3,3',4,4',5- pentachlorobiphenyl (PeCB) potently induced CYPlA mRNA, protein and catalytic activity at low doses (0.01-0.1 mg/kg), suppressed induction of CYPlA protein and catalytic activity at a high dose (1 mg/kg) and transiently induced oxidative stress in scup liver. The suppression of CYP1A induction was organ-dependent, with hepatic CYP1A being most susceptible to inactivation. The results suggest that ROS could be involved in the in vivo suppression of scup liver CYP1A by planar halogenated aromatic hydrocarbons. The reactive oxygen sensitive transcription factor, nuclear factor-KB (NF-KB), was characterized in scup. An NF-KB consensus binding sequence bound specifically to 3 proteins in scup liver, heart and kidney. One protein was recognized by an antibody to mammalian p50. Injection alone appeared to activate NF-KB. BP did not increase the activation of NF-KB, and PeCB activated NF-KB in only 1 of 2 experiments. Last, CYP1A induction in endothelial cells of the American eel (Anguilla rostrata), a site which may be particularly susceptible to alterations in AA metabolism and ROS production, was described. Eel liver CYPlA responded to BP, 13-naphthoflavone and TCB in a dose-dependent fashion, and induction was correlated with hepatic inducer concentration. Endothelial CYP1A was inducible in a number of organs and was metabolically active. In the rete mirabile, penetration of endothelial CYP1A induction increased with increasing dose of AhR agonists, corresponding with an increase in inducer concentration. A transition from endothelial to epithelial staining occurred in the gill, heart and kidney at high inducer doses. / by Jennifer Joy Schlezinger. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), February 2001. / Includes bibliographical references. / by Nicole Jane Poulton. / Ph.D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 27-33). / The colonization dynamics and life histories of pioneer species are vital components in understanding the early succession of nascent hydrothermal vents. The reproductive ecology of pioneer species at deep-sea hydrothermal vents may provide insight into their dispersal, population connectivity, and ability to colonize after disturbance. An opportunity to study the reproductive traits of two pioneer gastropod species, Ctenopelta porfera and Lepetodrilus tevnianus, presented itself in 2006 after an eruption on the East Pacific Rise (EPR) eliminated vent communities near 9°50'N. Standard histological techniques were used to determine whether reproductive characteristics, such as timing of gamete release, fecundity, or time to maturation, differed from other vent gastropods in ways that might explain arrival of these two species as early colonizers. Both species exhibited two-component oocyte size frequency distributions that indicated they were quasi-continuous reproducers with high fecundity. In C. porifera, the oocyte size distributions differed slightly between two collection dates, suggesting that environmental cues may introduce some variability in gamete release. In samples collected within one year of the estimated eruption date, individuals in populations of both C. porfera and L. tevnianus were reproductively mature. The smallest reproducing C. porifera were 4.2 mm (males) and 5.4 mm (females) in shell length, whereas reproductive L. tevnianus were smaller (2.3 and 2.4 mm in males and females respectively). Most Cporifera in the population were large (> 6.0 mm) compared to their settlement size and reproductively mature. In contrast, most L tevnianus were small (< 1.0 mm) and immature. Reproductive traits of the two species are consistent with opportunistic colonization, but are also similar to those of other Lepetodrilus species and peltospirids at vents, and do not explain why these particular two species were the dominant pioneers. It is likely that their larvae were in high supply immediately after the eruption due to oceanographic transport processes from remote source populations. / by Skylar Bayer. / S.M.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references. / by Gorka Sancho. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 1998. / Includes bibliographical references (leaves 179-199). / by Marjorie Frances Oleksiak. / Ph.D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 47-54). / At deep-sea hydrothermal vents chemolithoautotrophic microbes mediate the transfer of geothermal chemical energy to higher trophic levels. To better understand these underlying processes and the organisms catalyzing them, this research used DNA Stable Isotope Probing (SIP) combined with Catalyzed Activated Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to identify the microorganisms chemoautotrophically supporting the food web at a diffuse flow hydrothermal vent. Both anaerobic and aerobic shipboard incubations containing various augmented electron donor and acceptor species showed that Epsilonproteobacteria were the dominant chemoautotrophs with greater than 70% of the cells counted within the first 24 hours. 13C DNA SIP identified unique organisms not previously characterized from low temperature diffuse flow venting: green sulfur bacteria (Chlorobi-like organisms) possibly utilizing photoautotrophy, aerobic Lutibacter litoralis-like organisms growing under anaerobic conditions, and Epsilonproteobacterial Thioreductor sp. at temperatures above maximum known tolerances. This research illustrates both the promise and pitfalls of the SIP technique applied to hydrothermal systems, concluding that timing of the incubation experiments is the critical step in eliminating undesired 13C labeling. These results set the stage for a more thorough future examination of diffuse flow microorganisms by presenting interesting questions that second generation experiments could be designed to answer. / by Kevin Patrick Richberg. / S.M.

Thesis (Ph.D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology, and the Woods Hole Oceanographic Institution), 2002. / Includes bibliographical references. / Predictions of chlorophyll concentration from satellite ocean color are an indicator of phytoplankton primary productivity, with implications for foodweb structure, fisheries, and the global carbon cycle. Current models describing the relationship between optical properties and chlorophyll do not account for much of the optical variability observed in natural waters, because of the presence of seawater constituents that do not covary with phytoplankton pigment concentration. In an attempt to better understand variability in these models, the contributions of seawater constituents to ocean optical properties were investigated. A combination of Mie theory and flow cytometry was used to determine the diameter, complex refractive index (n+n'i), and optical cross-sections of individual particles, based on a method developed in the laboratory using phytoplankton cultures. Individual particle measurements were used to interpret variability in concurrently measured bulk optical properties in New England continental shelf waters in two seasons. The summed contribution to scattering of individual particles in the size range of 0.1-50 Cpm accounted for approximately the entire scattering coefficient measured independently using bulk methods. In surface waters in both seasons, the large diameters and n' of eukaryotic phytoplankton caused them to be the main particle contributors to both absorption and scattering. Minerals were the main contributor to backscattering, bb, in the spring, whereas in the summer both minerals and detritus contributed to bb. Synechococcus and heterotrophic bacteria were less important optically, contributing <11% each to attenuation in either season. / (cont.) The role of seawater constituents in determining remote sensing reflectance, Rrs, was determined using radiative transfer theory. Seasonal differences in the spectral shape of Rrs were contributed to approximately equally by eukaryotic phytoplankton absorption, dissolved absorption, and non-phytoplankton bb. A higher inverse wavelength dependence of non-phytoplankton bb in the summer was caused by the contribution of small detritus, in contrast to larger minerals in the spring. Measurements of bb and Rrs were compared to values from bio-optical models based on chlorophyll concentration. Differences in measured and modeled bb and Rrs were caused by higher dissolved absorption and higher backscattering efficiencies and scattering by non-phytoplankton than were assumed by the model. / by Rebecca E. Green. / Ph.D.