Seagrass productivity is largely limited by nutrient and light availability. However, increasing evidence suggests that sedimentary geochemical processes may play an essential role in seagrass productivity/health. Much of this work has been largely phenomenalistic and has not clearly identified the spatio-temporal behavior of the major geochemical parameters involved in diagenesis of seagrass sediments. In this study, a much broader range of both dissolved and solid phase chemical parameters in eelgrass vegetated sediments was investigated. Parallel measurements were made on adjacent unvegetated sediments (<10 m) to more clearly refine the specific influences of seagrass (Zostera marina) on chemical gradients in associated sediments. Previous studies have pointed strongly toward diurnal ??ventilation?? of sediments vegetated with seagrass by the exudation of photosynthetically produced oxygen. However, strong lateral variability of sediment geochemical parameters among and between seagrass vegetated and unvegetated sediments made the observation of diurnal effects sufficiently difficult. Changes resulting from temporal variability were difficult to discern within the spatial variability. A critical question that is often not dealt with in the study of the early diagenesis of sediments is what spatial and temporal sampling intervals are required to account for the dominant source of variability. The auto-covariance function (ACF) was used to determine the optimum scaling length for sample intervals (?x) of ?H2S and Fe2+. Characteristic scale lengths obtained for sediments from seagrass environments are not significantly different from those observed for unvegetated sediments and averaged 13.7?? 2.2 mm. Lateral variations in our scales analyses showed that scale length approximated our sampling interval and that lateral sampling intervals were smaller than the vertical sampling intervals. Our results indicate that macrofauna dwelling in the sediment, the seagrass root/rhizomes, and aggregations of bacteria, microalgae, and meiofauna may be responsible for the vertical and lateral variability. Model calibrations and sensitivity analyses from a sediment-seagrass diagenetic model revealed that changes in physical parameters of the sediments (irrigation, advection, and porosity, for example) had the greatest effect on organic carbon and total dissolved sulfides. This study revealed that sedimentary geochemical parameters that are both vertically and laterally heterogeneous may also affect seagrass productivity.

Marine aggregates are an important means of carbon transfers downwards to the deep ocean as well as an important nutritional source for benthic organism communities that are the ultimate recipients of the flux. During these last 10 years, data on size distribution of particulate matter have been collected in different oceanic provinces using an Underwater Video Profiler. The cruise data include simultaneous analyses of particle size distributions as well as additional physical and biological measurements of water properties through the water column. First, size distributions of large aggregates have been compared to simultaneous measurements of particle flux observed in sediment traps. We related sediment trap compositional data to particle size (d) distributions to estimate their vertical fluxes (F) using simple power relationships (F=Ad^b). The spatial resolution of sedimentation processes allowed by the use of in situ particle sizing instruments lead to a more detailed study of the role of physical processes in vertical flux. Second, evolution of the aggregate size distributions with depth was related to overlying primary production and phytoplankton size-distributions on a global scale. A new clustering technique was developed to partition the profiles of aggregate size distributions. Six clusters were isolated. Profiles with a high proportion of large aggregates were found in high-productivity waters while profiles with a high proportion of small aggregates were located in low-productivity waters. The aggregate size and mass flux in the mesopelagic layer were correlated to the nature of primary producers (micro-, nano-, picophytoplankton fractions) and to the amount of integrated chlorophyll a in the euphotic layer using a multiple regression technique on principal components. Finally, a mesoscale area in the North Atlantic Ocean was studied to emphasize the importance of the physical structure of the water column on the horizontal and vertical distribution of particulate matter. The seasonal change in the abundance of aggregates in the upper 1000 m was consistent with changes in the composition and intensity of the particulate flux recorded in sediment traps. In an area dominated by eddies, surface accumulation of aggregates and export down to 1000 m occured at mesoscale distances (<100 km).

Thesis (MS)--Montana State University--Bozeman, 2008. / Typescript. Chairperson, Graduate Committee: Mark L. Skidmore. Includes bibliographical references.

Microbes, including Bacteria, are globally important mediators of elemental transformations in the marine water column, but not until recently has their biomass been suggested to contribute significantly to carbon export flux. Here I characterize lipid and carbon isotopic signatures in marine particulate organic matter (POM) explicitly at microbial size scales, and I quantitatively explore how these signatures are transferred down the water column. In the North Pacific Subtropical Gyre (NPSG) an isotopically-enriched pool of submicron POM appears to dominate export to mesopelagic depths, supporting recent observations that bacterioplankton communities contribute to export flux in proportion to their biological abundance. In the Eastern Tropical North Pacific (ETNP) complex pathways emerge for the flux of POM to the deep ocean. I use the largest data set to date for natural \(^{13}C\) signatures of individual water column lipids to reveal that submicron and larger-size suspended POM size classes are isotopically distinct. Results point to de novo production of lipids above and within the oxygen minimum zone. I develop quantitative models to deconvolve the signatures of sinking and in situ sources of these lipids. Results converge on a best-fit model for downward flux in the ETNP that includes both surface-derived and sub-photic zone lipids. Overall results from the modern ocean suggest that approximately half of total suspended POM is submicron in size, much of it is bacterial in origin, and despite the small size of this material, it participates dynamically in water column export flux. These results also suggest some revised interpretations of organic matter signatures in the geologic record. I formulate a quantitative model of marine microbial production and degradation, and reproduce "inverse" isotopic signatures found in lipids and organic matter preserved in Proterozoic sedimentary rocks. Results suggest that the disappearance of this inverse \(^{13}C\) pattern was a consequence of the shift from Bacteria to Eukarya as dominant producers of marine autotrophic biomass. Together, results of this thesis reveal that heterogeneity in the isotopic signatures of marine suspended POM is associated with particle size, and by extension, must be a function of the composition of the total planktonic community. / Earth and Planetary Sciences

During the synthesis of secretory and membrane proteins, polypeptides move through a universally conserved protein-conducting channel, formed by the Sec61/SecY complex that is located in the eukaryotic endoplasmic reticulum membrane or the prokaryotic plasma membrane. The channel operates in two different modes depending on its binding partners. In co-translational translocation, a pathway found in all organisms, the channel associates with a translating ribosome. In post-translational translocation, the channel cooperates with either the Sec62–Sec63 complex in eukaryotes or the SecA ATPase in bacteria. Despite tremendous progress in our understanding of protein translocation over the past decades, many questions about its mechanism remain to be answered. These include (1) how the channel maintains the membrane barrier for small molecules while transporting large proteins, (2) what is the functional implication of channel oligomerization, and (3) how the channel interacts with binding partners and polypeptide substrates during translocation. To address these questions, we developed a novel in vivo method to generate both co- and post-translation translocation intermediates in intact Escherichia coli cells, such that polypeptide chains are only partially translocated through the channel. Using this method, we first demonstrated that a translocating polypeptide itself blocks small molecules from passing through an open SecY channel. A hydrophobic pore ring surrounding the polypeptide chain is vital for maintaining the membrane barrier during translocation. Next, we examined the importance of SecY oligomerization in protein translocation. Crosslinking experiments showed that SecY molecules interact with each other in native membranes, but that this self-association is greatly decreased upon insertion of polypeptide substrates. We also showed that SecY mutants that cannot form oligomers are still functional in vivo. Collectively, our data indicate that a single copy of SecY is sufficient for protein translocation. Finally, we isolated an intact co-translational translocation intermediate from E. coli cells and analyzed its structure by cryo-electron microscopy. An initial map shows a translating ribosome containing all three tRNAs is bound to one copy of the SecY channel. Analysis of a large dataset is ongoing in order to understand the structural basis of how the channel interacts with the ribosome and translocating nascent chain.

Distinguishing marine and freshwater animals in the fossil record is a long-standing problem in paleontology. The physiological tolerances of extinct animals usually are inferred from environmental indicators and/or on the physiology of nearest living relatives. These types of evidence are often ambiguous and may be confounded by factors such as post-mortem transport and polymorphism in the living relatives. A solution to this problem is to combine these types of data with analyses of the oxygen isotope compositions of the phosphate (δ¹⁸O(p)) and the carbon isotope compositions of the carbonate (δ¹³C(sc)) of teeth and bones, to determine whether the ingested water and diet, respectively, were fresh or marine. The power of this approach is illustrated here in a study of the early evolution of cetaceans (whales, dolphins and porpoises). Changes in δ¹⁸O(p) and δ¹³C(sc) of the teeth and bones of early cetaceans documented here indicate that fully marine cetaceans existed by the middle Eocene and that some species exploited both marine and freshwater environments. This isotopic approach requires the avoidance of isotopically altered specimens. For this reason, the second component of this work deals with criteria for recognizing isotopically altered fossils. In contrast to one recent study, I found a positive correlation between δ¹⁸O(p) and δ¹⁸O(sc) not only in mammals but also in fish and reptiles. This correlation can be used as a test of whether the original isotopic composition is preserved in fossil specimens. Another approach to this problem is to make analyses of samples taken along growth transect of a fossil tooth or bone. Growth-transect analyses could resolve whether within-species isotopic variation represents differences in preservation or ontogenetic shifts in diet or habitat. In support of this goal, a new method for the analysis of phosphate oxygen is presented. This new method differs from all previous methods in that it involves no chemical reaction, but rather high-temperature (>725°C) equilibrium oxygen isotope exchange between CO₂ and Ag₃PO₄ As the amount of CO₂ is controlled by the analyst, small phosphate samples may be analyzed, making this method potentially useful for growth-transect analyses.

No description available.

Field and laboratory experiments were conducted with the following ten cultivars of rice: Lebonnet, Lemont, Dawn, Katy, Della, IR36, Mars, Brazos, Labelle and Jasmine. For each variety, components of biomass, root porosity and methane emission were observed throughout the entire growing season and yield was determined at harvest. Methane emission differed among cultivars by as much as a factor of 2.4 and resulted in two distinct emission groups. Significant differences were also found for biomass among cultivars, although these differences did not coincide with the differences that were observed for emission among cultivars. Methane emission correlated strongly with aboveground live vegetative biomass within most varieties until heading and among cultivars within emission groups to heading. Emissions showed less correlation with biomass during ripening and may have been affected by other factors within the system at this time. Methane emission appeared to be consistently proportional to grain production among cultivars, when determined per gram biomass, and may be related through processes of carbohydrate partitioning. Root porosity did not appear to be associated with observed differences or trends in methane emission.

Increasing levels of atmospheric CO2 threaten to change the earth's climate and diversity in numerous adverse ways. This thesis explores aspects of two potential types of terrestrial sinks in East Texas, plantation rotation management and reforestation. I used a simple method of employing government GIS and tabular data for calculating and visualizing the size of those sinks, which could store an additional 2.3 to 98 million Mg C aboveground. The uncertainty of these values is high because of data inadequacies and also uncertainty about future land use trends. The mitigative powers of these sinks are discussed, as is their potential application in newly forming carbon credit programs such as the Chicago Climate Exchange.

Three experiments focused on the contribution of rice productivity to methane emission were conducted in Texas flooded rice paddy soils during 1994-95 growing seasons. Measurements of methane emission from different rice paddy soils during 1991-92 growing seasons (Sass et al., 1994) and from ten different cultivars in 1993 growing season (Willis, 1995; Sass and Fisher, 1995) were cited to quantify the relationships of methane emission with soil, rice cultivar and grain yield. Under the similar soil sand content and agronomic management regime, total seasonal methane emission was positively correlated with rice grain yield and aboveground biomass at harvest. Linear relationships of daily methane emission with aboveground vegetative biomass and root biomass were also observed. On a carbon to carbon basis, the ratio of methane emission to rice net primary productivity was dependent on soil and rice variety, and increased with rice plant development. Models emphasized the contributions of rice plants to the processes of methane production, oxidation and emission and also the influence of environmental factors were developed to predict methane emission from flooded rice fields. Relative effects of soil texture, soil temperature and rice variety on methane production/emission were quantified by three dimensionless indices: soil index, temperature index and variety index, respectively. Model validation against observations from various regions of the world, including Italy, China, Indonesia, Philippines and USA demonstrated that methane emission can be predicted from rice growth and development, cultivar character, soil texture and temperature, and organic matter amendments. Of these, rice growth and development is a principal parameter governing the processes of methane production, oxidation and emission in irrigated rice paddies. Model estimates suggest that annual amount of methane emitted from Chinese rice fields ranges from 7.03 to 13.32 Tg CH$\sb4$ yr$\sp{-1}$ with an average value of 9.45 Tg CH$\sb4$ yr$\sp{-1}$ under permanent irrigation and the majority of methane was emitted in the region located at latitude between 25$\sp\circ$ and 32$\sp\circ$ N. Comparisons of estimated with the observed emissions show that the estimates were in general close to the measurements at most locations.