The inventory and chemical characterization of dissolved proteins in oceanic waters

One-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and high resolution two-dimensional electrophoresis (2-DE) were applied to separate protein molecules in dissolved organic matter (DOM) from oceanic waters. Results were: (1) The 2-DE distinguished a total of 412 protein spots in 10 samples from five water columns over the Pacific, although fewer than 30 proteins were resolved as bands from the identical samples by SDS-PAGE. (2) Major and ubiquitous protein bands (34 and 39 kDa proteins) on the SDS-PAGE gel were resolved into horizontally spread arrays (trains) of spots on the 2-DE gels, indicating that these bands were a mixture of protein species that have the same molecular weight (MW) but different isoelectric points (pIs). (3) Proteins that exhibited such electrophoretic patterns on the 2-DE gels were glycosylated with variable linkages between the sugar and polypeptide chains. (4) N-terminal amino-acid sequencing demonstrated that individual spots within each train of spots had identical N-terminal amino-acid sequences.The N-terminal amino-acid sequences of the 39 and 34 kDa glycoprotein spots in samples collected at different sites were also identical. Protein isoforms with the same amino-acid sequence but different glycosylation profiles, termed glycoforms, were often observed on the 2-DE gel. Thirty-one and 24 spots on the 2-DE gels were glycoforms of two glycoproteins with MWs of 39 and 34 kDa, respectively; they were one protein species. The glycoforms of the 39 kDa protein were identified as a low molecular weight alkaline phosphatase (L-AP) of Pseudomonas aeruginosa PAO1 by a homology search through five amino-acid sequence databases. The present and earlier work indicates that all identified source organisms of dissolved proteins belong to the Pseudomonas group. We propose the hypothesis that proteins associated with membrane vesicles liberated from a minor member of the bacterioplankton assemblage, the marine Pseudomonas group, are one of the important sources of dissolved proteins in oceanic waters. This hypothesis may apply to the source pathway and survival not only of proteins and also to the universally occurring bacterial peptidoglycan and lipopolysaccharide components in DOM.     

An East-West Comparison of the Transition Zone Coastal Pelagic Nekton of the North Pacific Ocean

During the 1980s and 1990s, scientific research cruises were conducted in both the eastern and western boundary regions of the North Pacific Ocean. The main purpose of these cruises was to examine the abundance and distribution patterns of juvenile salmon in coastal waters. These studies created one of the most extensive databases ever collected on the species composition of coastal Transition Zone epipelagic nekton in the North Pacific Ocean. Catch data from two purse seine and two surface trawl surveys (one each from off northern Japan and eastern Russia and off the West Coast of the U.S.) were examined using multivariate techniques to analyze the community structure of nektonic cephalopods, elasmobranchs, and teleosts in the coastal zone during the summer and autumn months. Juvenile salmonids are generally among the most common species caught, but in terms of overall abundance, other potential competitors with juvenile salmon, such as small squids and clupeoid fishes predominated the catches. Species diversity and dominance varied among areas and gear types. Distinct assemblages were found in each area, but the two regions had closely related species occupying similar ecological positions in each habitat. This revised version was published online in August 2006 with corrections to the Cover Date.     

Mean circulation induced over bottom topography by mesoscale variabilities in the Kuroshio Extension

Circulation could be generated over bottom topography by vertical shrinking or stretching of a water parcel, in which potential vorticity is conserved. The water parcel moves up or down over the bottom topography yielding shrinking or stretching. In addition to a prevailing current which advects the water parcel in one direction, an oscillatory motion can also induce shrinking and stretching, and circulation is consequently generated over the bottom topography, once it is averaged in time. A two-layer quasi-geostrophic model has been used to reproduce mesoscale variabilities both in and under the Kuroshio Extension around the Shatsky Rise. A combination of TOPEX and ERS altimeters provided information on an eddy field near the sea surface, while a data assimilation method was used to reconstruct the flow field below the main thermocline. Among various mesoscale processes associated with the Kuroshio, it is remarkable that topographic Rossby waves trapped over the Shatsky Rise are generated by the upper-layer mesoscale variability. A persistent anticyclonic circulation is produced on the Shatsky Rise through a water parcel moving up and down over the bottom slope, and is consistent with the observed density anomaly in the WOA94.     

Radium isotopes in coastal and open ocean surface waters of the Western North Pacific

Using manganese-impregnated fiber extraction and high-efficiency gamma counting techniques, we measured the distribution of ²²⁸Ra and ²²⁶Ra in surface waters near the coast of Japan and in the western North Pacific. There is no evidence in our data that any significant amount of ²²⁸Ra is added to open ocean surface waters from the coastal waters around Tokyo Bay. High ²²⁸Ra concentrations (> 10 dpm/10³ kg), were observed along the Kuroshio Current as compared to < 2.5 dpm/10³ kg between 10° and 30°N of the central gyre, and hence the major source of ²²⁸Ra in the surface water is likely to be the East Asian continental shelf zones. A simple one-dimensional eddy diffusion and advection model is used to explain the observed decrease of ²²⁸Ra from coast to the open ocean. The model results indicate two mixing regimes across the Kuroshio Current System with apparent eddy diffusion coefficients of K_y = 4 × 10⁵ cm² s⁻¹ at distance y < 200 km from the coast, and K_y = 4 × 10⁷ cm² s⁻¹ at y > 200 km. Along 40°N where an eastward flow of the ‘Kuroshio Extension’ prevails, an advective flow of > 0.1 knot is consistent with the observation of nearly constant ²²⁸Ra along the track.The geographical distribution pattern of ²²⁸Ra is clearly different from that of atmospherically derived ²¹⁰Pb. Thus the ²²⁸Ra in surface water serves as a useful tracer that accompanies fluvially and coastally derived elements during their subsequent lateral transport toward the central gyre.     

Precipitation of authigenic uranium in suboxic continental margin sediments from the Okinawa Trough

Concentrations of U and Th isotopes in Okinawa Trough and East China Sea sediment cores were determined by isotope dilution inductively coupled plasma-mass spectrometry (ID-ICP-MS) to investigate the behavior of redox sensitive uranium in suboxic hemipelagic sediments and determine their significance in oceanic uranium balance. ²³⁸U concentrations and ²³⁸U/²³²Th activity ratios in the East China Sea sediments showed no remarkable variation with depth. However, ²³⁸U and ²³⁸U/²³²Th ratios in the Okinawa Trough sediments were low in the surface oxidizing layer but increased where the suboxic condition was encountered. The distribution profiles of ²³⁰Th and ²³²Th concentrations were relatively constant with depth in both the Okinawa Trough and East China Sea sediment cores. These results suggested that there has been post-depositional precipitation of authigenic uranium within the suboxic Okinawa Trough sediment column. The post-depositional precipitation rates of authigenic uranium were estimated to be 47 ± 5 to >62 ± 8 ng cm⁻² yr⁻¹; these rates were comparable to those previously reported for several anoxic sediments. A mechanism controlling precipitation of uranium may be the downward diffusion of uranium U(VI), reduction to U(IV) and finally precipitation onto the solid phase. The accumulation rate of uranium for the Okinawa Trough sediments was approximately eight times higher than the world average rate reported for suboxic sediments. This removal of uranium in the oceanic budget increases the importance of the suboxic sediment sink.     

An Ecosystem Model Including Nitrogen Isotopes: Perspectives on a Study of the Marine Nitrogen Cycle

We have developed an ecosystem model including two nitrogen isotopes (¹⁴N and ¹⁵N), and validated this model using an actual data set. A study of nitrogen isotopic ratios (δ¹⁵N) using a marine ecosystem model is thought to be most helpful in quantitatively understanding the marine nitrogen cycle. Moreover, the model study may indicate a new potential of δ¹⁵N as a tracer. This model has six compartments: phytoplankton, zooplankton, particulate organic nitrogen, dissolved organic nitrogen, nitrate and ammonium in a two-box model, and has biological processes with/without isotopic fractionation. We have applied this model to the Sea of Okhotsk and successfully reproduced the δ¹⁵N of nitrate measured in seawater and the seasonal variations in δ¹⁵N of sinking particles obtained from sediment trap experiments. Simulated δ¹⁵N of phytoplankton are determined by δ ¹⁵N of nitrate and ammonium, and the nitrogen f-ratio, defined as the ratio of nitrate assimilation by phytoplankton to total nitrogenous nutrient assimilation. Detailed considerations of biological processes in the spring and autumn blooms have demonstrated that there is a significant difference between simulated δ¹⁵N values of phytoplankton, which assimilates only nitrate, and only ammonium, respectively. We suggest that observations of δ ¹⁵N values of phytoplankton, nitrate and ammonium in the spring and autumn blooms may indicate the ratios of nutrient selectivity by phytoplankton. In winter, most of the simulated biogeochemical fluxes decrease rapidly, but nitrification flux decreases much more slowly than the other biogeochemical fluxes. Therefore, simulated δ¹⁵N values and concentrations of ammonium reflect almost only nitrification. We suggest that the nitrification rate can be parameterized with observations of δ¹⁵N of ammonium in winter and a sensitive study varying the parameter of nitrification rate.     

Large kinetic power in FRII radio jets

We investigate the total kinetic powers (L _j) and ages (t _age) of powerful jets of four FR II radio sources (Cygnus A, 3C 223, 3C 284, and 3C 219) by the detail comparison of the dynamical model of expanding cocoons with observed ones. It is found that these sources have quite large kinetic powers with the ratio of L _j to the Eddington luminosity (L _Edd) resides in 0.02<L _j/L _Edd<10. Reflecting the large kinetic powers, we also find that the total energy stored in the cocoon (E _c) exceed the energy derived from the minimum energy condition (E _min): 2<E _c/E _min<160. This implies that a large amount of kinetic power is carried by invisible components such as thermal leptons (electron and positron) and/or protons.