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The effects of diatom abundance and biogenic silica (BSi) deposition on the population growth of tintinnid ciliates were investigated using incubations of sub-surface waters (10 m depth) of Suruga Bay, Japan in April and November 2018. Seawater for incubation was pre-filtered using a 200-µm mesh to remove mesozooplankton grazers. Initial concentrations of dissolved inorganic nitrogen were similar in both seasons, but silicic acid and phosphate were higher in April than in November. This allowed us to observe the growth of planktonic communities under varied silicic acid availability and explore the effects of BSi accumulation and food availability on the growth of tintinnids. Phytoplankton blooms dominated by diatoms formed in both, April and November incubations, but their biomass was higher in April than in November, demonstrating the effects of nutrients, particularly silicic acid, on diatom growth. The BSi concentration increased in both incubations but was higher in April than in November, confirming the effects of diatom abundance and size on BSi deposition. Tintinnid biomass also increased in both incubations but was higher in April than in November, showing that the biomass of tintinnid was affected by the BSi concentration. Species composition of diatoms affected the species composition of tintinnids by providing selected material for the construction of their lorica. Moreover, the results showed that the food supply mainly provided by pico-nanoflagellates via microbial loop and detritus may limit tintinnids’ population growth in natural planktonic ecosystems and this demonstrates tintinnids’ role as top predators in the microbial loop

Ocean surface acidification due to increasing atmospheric CO2 concentration is currently attracting much attention. Coccolithophores distribute widely across the world's oceans and represent a carbon sink containing about 100 million tonnes of carbon. For this reason, there is concern about dissolution of their shells, which are made of calcium carbonate, due to decreasing pH. In this study, intracellular calcification, photosynthesis, and mass transport through biomembranes of Emiliania huxleyi were modelled numerically for understanding biological response in calcifying organisms. Unknown parameters were optimised by a generic algorithm to match existing experimental results. The model showed that the production of calcium carbonate rather than its dissolution is promoted under an acidified environment. Calcite remains at saturation levels in a coccolith even when it is below saturation levels in the external seawater. Furthermore, a coccolith can dissolve even in water where calcite saturation exceeds 1, because the saturation may be below the threshold level locally around the cell membrane. The present model also showed that the different calcification rates of E. huxleyi with respect to rising CO2 concentrations reported in the literature are due to differences in experimental conditions; in particular, how the CO2 concentration is matched. Lastly, the model was able to reproduce differences in calcification rates among coccolithophore species. The above biochemical-kinetic model was then incorporated into an ecosystem model, and the behaviour of coccolithophores in the ecosystem and the influence of increases in CO2 concentration on water quality were simulated and validated by comparison with existing experimental results. The model also suggests that increased CO2 concentration could lead to an increase in the biomass ratio of coccolithophores to diatoms at high CO2 concentrations, particularly in oligotrophic environments, and to a consequent decrease in pH due to calcium dissolution.

This study explored the physiological responses of the coral Pocillopora damicornis to high nitrate concentrations and thermal stresses. The expression of heat shock proteins Hsp60 and Hsp32, Symbiodiniaceae density, Chl a concentration, Fv/Fm, H2O2 scavenging, and caspase 3 activity varied during 60 h incubations at 28 °C or 32 °C, ambient or high nitrate (~10 μM) concentrations, and their combinations. In combined stresses, corals showed a rapid and high oxidation level negatively affecting the Symbiodiniaceae density and Chl a concentration at 12 h, followed by caspase 3 and Hsps upregulations that induced apoptosis, bleaching and tissue detachment. Corals under thermal stress showed the highest oxidation and upregulation of Hsps and caspase 3 resulting in coral discoloration. High nitrate treatment alone did not seriously affect the coral function. Results showed that combined stress treatment severely affected coral physiology and, judging from the condition of detached tissues, these corals might have lower chances to recover.

Marine phytoplankton production as well as biomass is globally significant. This study hypothesized that a mild increase in nutrients concentrations (by a factor 1–2 higher) from artificial upwelling in oligotrophic water can alter phytoplankton dynamics (biomass, composition and size), and consequently, phytoplankton-derived particulate organic carbon flux. Primary production, carbon biomass of different planktonic groups, and organic carbon remineralization were examined by incubating seawater collected from two oceanographic stations in the vicinities of Ikitsuki Island, Japan, in 2004 and 2005. Station C, located near to and downstream of an artificial seamount that generates upwelling, had higher nutrient concentrations and biomass (Chl. a and carbon) than Station O-2, which was upstream and far from the seamount. Phytoplankton biomass and primary production rates remained higher during incubation for station C than for station O-2 in both 2004 and 2005. Phytoplankton composition also differed between the two stations. Picophytoplankton contributions to total biomass were smaller at station C than at station O-2 while those of micro- and nanophytoplankton were higher at station C. The results of this study indicate that even a small increase in nutrient availability in oligotrophic waters can alter productivity, biomass, and phytoplankton composition. Additionally, around 4.0% of net primary production was estimated to escape from grazers and remineralization, instead sinking into deep ocean layers in the form of less easily degraded particles. The difference in net primary productivity between Stns. C and O-2 gave an estimation of excess production at Stn. C resulting from upwelled nutrients. Owing to this 1.3 to 1.5 mg more carbon m − 2 d − 1 is likely to be exported at Stn. C compared to Stn. O-2.

Chlorophyll a fluorescence is increasingly being used as a rapid, non-invasive, sensitive and convenient indicator of photosynthetic performance in marine autotrophs. This review presents the methodology, applications and limitations of chlorophyll fluorescence in marine studies. The various chlorophyll fluorescence tools such as Pulse-Amplitude-Modulated (PAM) and Fast Repetition Rate (FRR) fluorometry used in marine scientific studies are discussed. Various commonly employed chlorophyll fluorescence parameters are elaborated. The application of chlorophyll fluorescence in measuring natural variations, stress, stress tolerance and acclimation/adaptation to changing environment in primary producers such as microalgae, macroalgae, seagrasses and mangroves, and marine symbiotic invertebrates, namely symbiotic sponges, hard corals and sea anemones, kleptoplastic sea slugs and giant clams is critically assessed. Stressors include environmental, biological, physical and chemical ones. The strengths, limitations and future perspectives of the use of chlorophyll fluorescence technique as an assessment tool in symbiotic marine organisms and seaplants are discussed.

Urea is an unstable and intermediate organic nitrogenous compound present in coastal environments and is derived from the excretion of some aquatic organisms and wastewater discharges. Urea plays an important role in the nitrogen cycle, where it is utilized by algae, including diatoms. However, there are very limited relevant data on the production, consumption, and degradation of urea because of the lack of appropriate measurement techniques. The conventional method is based on the formation of a colored product when urea reacts with diacetyl monoxime in a sulfuric acid solution. We examined the optimal conditions for the formation of the colored product; specifically, we evaluated different temperatures (22–80 °C), reaction times, mixing ratios of color reagents, and sample storage times. Application of the single mixed color-developing reagent (COLDER) at 70 °C resulted in the optimal formation of the colored product within a short reaction time of 60 min. This method was then used to measure dissolved urea in different coastal environments. The concentrations detected were as follows: 0.65–0.72, 0.49–0.58, and 1.09–2.28 µM urea-N at coral reef, seagrass, and mangrove sites, respectively. Our results showed high precision (SD = 0.02, CV = 1.2%), a low detection limit (0.03 µM urea-N), and a high recovery rate (94–99%). In summary, this high-temperature procedure for urea measurements should be valuable for obtaining high-precision data that can further the understanding of urea dynamics and its role in coastal ecosystems.

The feeding strategies of Montipora digitata and Porites lutea, two dominant corals in the Okinawan reefs, were investigated. The focus was on pico- and nanoplankton feeding efficiencies, using 6-h incubations. Although healthy M. digitata consumed from 72% to 87% more pico-nanoplankton cells than P. lutea, feeding rates of bleached corals of both species were similarly low at heat stress (33 °C). Heterotrophic carbon acquisition with respect to dark respiration varied from 3% to 65% in M. digitata and from 7% to 68% in P. lutea. A decrease in the feeding efficiency of bleached M. digitata under heat stress shows its vulnerability to water heating events. Feeding rates of P. lutea were low under all conditions and treatments; therefore, this species is less vulnerable to heat stress due to the strategy of meeting metabolic costs by using translocated organic matter from endoliths and selecting pico-nanoplankton cells with a high C/N ratio.

Elevated seawater temperatures in the summer months of 2010 were associated with widespread coral mortality in Thailand. A large number of corals at Mu Ko Surin died following the bleaching event. Understanding of the recruitment of corals would improve our ability to predict the potential for coral recovery from the impacts of bleaching events, as well as the interpretation of spatio-temporal variability in coral community structure. This study aims to examine the composition, abundance and growth rate of juvenile corals and the potential of reef recovery at Mu Ko Surin in order to help to understand how reefs react to major disturbances. We found that the densities of coral recruits varied among years and study sites. In the year 2011, coral recruitments ranged between 0.18 ± 0.02 to 1.67 ± 0.07 recruits per m2 for 10 study sites. While in 2012, the monitoring revealed a range between 0.96 ± 0.16 and 2.19 ± 0.21 recruits per m2 from 5 study sites. Fungia, Acropora, Porites and Favites were the dominant groups of coral recruits. In terms substrate forms, they were significant differences between sampling years but the preferential dominant substrate forms did not differ. The Acropora recruits at Ko Torinla showed normal distributions of size class during the two periods. Their ranges in 2011 and 2012 were 4–30 and 13–54 mm, respectively. Six species of Acropora recruits, i.e. Acropora intermedia, A. nasuta, A. cerealis, A. subulata, A. muricata and A. latistella were found. They showed diverse growth rates due to the spatial distribution of 2.11 ± 0.59 to 7.47 ± 1.37 cm per year. This study provides useful data in terms of coral recruitment and recovery from degradation and disturbance, especially from temperature changes induced by coral bleaching. The findings suggest that there is the possibility for coral recovery around Mu Ko Surin following the 2010 bleaching event.

The Okhotsk Sea is considered the only ventilation source area for North Pacific Intermediate Water (NPIW), which is widely distributed in the low and middle latitudes of the North Pacific. Previous studies have confirmed high levels of dissolved organic carbon (DOC) in NPIW, yet the amounts and the processes driving DOC export from the Okhotsk Sea are poorly understood. In this study, concentrations of DOC and dissolved organic nitrogen (DON) were measured in the western Okhotsk Sea during the summer of 2006, and additional DOC measurements were made during the late spring of 2010. Results indicate that DOC transport to the intermediate waters (26.7–27.0 σθ) occurs through two processes. The first process involves the spread of water discharged from the continental shelf (Dense Shelf Water), which contributes to a DOC and turbidity maxima in the 250–300 m layer of Okhotsk Sea Mode Water (OSMW) located off the eastern Sakhalin coast. The second process involves diapycnal mixing in the Kuril Basin and the Bussol’ Strait, where DOC is transported to a depth greater than 800 m. The ratio of DOC:DON in OSMW was significantly higher in the Kuril Basin and Bussol’ Strait than off of the Sakhalin coast, which suggests that the transport of terrigenous organic matter from the bottom occurs in the former regions. DOC and DON efflux from the Okhotsk Sea to the intermediate layer in the North Pacific water (26.7–27.0 σθ) were estimated to be 68–72 Tg C yr−1 and 5.4 Tg N yr−1, respectively, for which the DOC transported by diapycnal mixing accounts for 37%. We conclude that diapycnal mixing in the Kuril Basin and Bussol’ Strait regions could play a significant role in regulating the quality and quantity of DOC exported to the intermediate water in the North Pacific.

Scleractinian corals host photosynthetic endosymbionts, making direct measurement of the host respiration rate via incubation methods based on O2 consumption impossible. We tested the use of the respiratory electron transport system activity (ETSA) for measuring host potential respiration. The applied method, modified from a previous study, is based on the re - duction of (4-iodophenyl)-3-(4-nitrophenyl)-5-phenyl-2H-tetrazolium chloride (INT) to formazan. After the development of a protocol suitable for corals, the method was tested on 5 different spe- cies. Metabolism, including photosynthesis, dark respiration and light and dark calcification, was measured through incubation. Host and zooxanthellae fractions were separated and their ETSAs, protein contents and zooxanthellae densities were measured. Mean ETSA/dark respiration (ETSA/R) ratios for host corals ranged from 1.7 ± 0.2 to 3.5 ± 0.6, while ratios for zooxanthellae ranged from 3.7 to 7.8. The high ratios observed for zooxanthellae indicate that their respiration may be 5 times higher under light conditions than in the dark. Considering the obtained ratios, host respiration in light could increase at most by a factor of 3.5 compared with dark respiration rates. Ratios close to 1 were found for some specimens, which suggests that higher respiration rates under light compared with dark conditions are not possible. Therefore, increased respiration in light cannot explain the observed enhancement of calcification under light conditions. ETSA was correlated with zooxanthellae density, suggesting adaptation of the levels of host ETS enzymes to the amount of translocated photosynthetates under optimal conditions. Estimated dark host respiration was correlated with photosynthesis, which suggests that it is determined mainly by the amount of energy available but also the amount of electron transport system enzymes. This constrains the amount of ATP available for calcification. Hence, we propose a mechanism by which respiration limits the calcification rate.

Increasing seawater temperatures and CO2 levels associated with climate change affect the shallow marine ecosystem function. In this study, the effects of elevated seawater temperature and partial pressure of CO2 (pCO2) on subtropical sediment systems of mangrove, seagrass, and coral reef lagoon habitats of Okinawa, Japan, were examined. Sediment and seawater from each habitat were exposed to four pCO2-temperature treatments, including ambient pCO2- ambient temperature, ambient pCO2-high temperature (ambient temperature + 4°C), high pCO2 (936 ppm)-ambient temperature, and high pCO2-high temperature. Parameters including primary production, nutrient flux, pigment content, photosynthetic community composition, and bacterial abundance were examined. Neither high temperature nor high pCO2 alone impacted mangrove and seagrass sediment primary production significantly (Tukey's test, P > 0.05). However, the combined stress significantly (Tukey's test, P < 0.01) increased primary production in these two habitats. In sediments from the coral reef lagoon, single and combined stress treatments induced a shift from heterotrophy to autotrophy. Significant increases in net primary production (Tukey's test, P < 0.01), and gross primary production (Tukey's test, P < 0.05) under the combined stress suggested that benthic microalgae in mangrove and seagrass sediments were more responsive to high temperature and pCO2 conditions than those in coral reef lagoon sediments. Additionally, combined stress significantly increased the sediment chlorophyll a content (Tukey's test, P < 0.05) in all habitats. These increases were associated with increased net primary production, indicating that combined stress stimulates primary production activity by the photosynthetic benthic microalgae in all habitats. Diatom activity increased, as silicate uptake increased in all habitats. Microbial abundance significantly increased under the combined stress treatment (Tukey's test, P < 0.01), but did not exceed autotrophic activity. Respiration did not change significantly in any of the three habitats (Tukey's test, P > 0.05) under the combined stress, suggesting that heterotrophic processes were less affected by the combined stress than autotrophic processes. In summary, mangrove and seagrass sediments minimize the negative impacts of elevated temperature and pCO2 via increased primary production and carbon storage. Lagoonal sediments also act as a carbon sink under temperature and ocean acidificationstress.

We examined the production and partitioning of organic carbon under different inorganic nitrogen concentrations and phytoplankton composition by incubating unaltered seawater collected from 10, 100, 400 and 700 m depths off Suruga Bay, Japan. Particulate organic carbon (POC) accounted for 60–112% of net accumulated total organic carbon (TOC) during exponential growth and blooms of phytoplankton in all incubations regardless of the concentrations of nutrients and the forms of dissolved inorganic nitrogen (DIN) as well as the composition and size of phytoplankton. After the blooms of phytoplankton, microzooplankton (mainly ciliates) (>20 μm) increased rapidly in majority of incubations. This suggests that a large fraction of new production may also be transferred to higher trophic levels rather than immediately exported. After the depletion of initial DIN, accumulation of both POC and dissolved organic carbon (DOC) increased. DOC accounted for major fraction of TOC in most of the incubations. Continued accumulation of high C/N organic matter implies that recycling through the food web is not necessarily the dominant fate of organic carbon produced under low DIN condition but rather that a major fraction of the organic carbon is exported to deep water through sinking.

This ten-year study examined the morphological, physiological, and ecological characteristics of coral growth anomalies on Acropora cytherea on Amuro Island, Okinawa, Japan. The objectives of the study were to assess whether the growth anomalies, identified as diffuse disruptions on the skeleton: (i) were more prevalent on large colonies than on small colonies, (ii) were more common near the center of the colonies than peripherally, (iii) affected colony growth and mortality, and (iv) affected coral-colony fecundity and photosynthetic capacity. We hypothesized that the growth anomalies were signs of the onset of aging. The growth anomalies were more prevalent on colonies >2 m diameter, and were concentrated near the central (older) portions of the colonies. The growth anomalies were also associated with reduced productivity and dysfunctional gametogenesis. Still, the growth anomalies did not appear to affect colony survival. The contact experiments showed that the growth anomalies were not contagious, and were most likely a sign of aging that was exacerbated by thermal stress.

Synechococcus is widely distributed in the world's ocean surfaces, and is often found in sediment traps. However, its distribution and ecological importance have not been well studied in meso- and bathypelagic waters. We measured Synechococcus abundance in the Suruga Bay (central Japan) and the subtropical NW Pacific. Synechococcus abundance at depths of 200 m and below var- ied from 2.4 to 190 cells ml -1 , but was in proportion to the surface abundance, suggesting transport of epipelagic populations to greater depths. Surprisingly, Synechococcus was evenly distributed from 200 m down to 1420 m (Suruga Bay) or to 2000 m (subtropical NW Pacific), regardless of season. The contribution of deep Synechococcus to the total population was highest in spring in the Suruga Bay (36 to 77%), and lowest in summer in the Suruga Bay (1 to 9%) and in the subtropical NW Pacific (4 and 10%). These results suggest effective transport of Synechococcus cells down the water column during productive seasons by attachment to large particles and limited transport under oligotrophic and stratified conditions. Deep Synechococcus abundance decreased from fall to winter in the Suruga Bay, though in filtered deep seawater it did not significantly decrease for 30 d in the dark, and it increased in a light/dark cycle. Our investigations show that the standing stock of Synechococcus has been significantly underestimated in previous studies of epipelagic waters conducted during produc- tive seasons and that Synechococcus seems to be grazed and to contribute to biogeochemical cycles in the dark ocean.

Studies in epipelagic waters report higher heterotrophic microbial biomass in the productive high latitudes than in the oligotrophic low latitudes; however, biogeographical data are scarce in the deep ocean. To examine the hypothesis that the observed latitudinal differences in heterotrophic microbial biomass in the epipelagic zone also occur at depth, abundance and biomass of heterotrophic prokaryotes, nanoflagellates (HNF), and ciliates were determined at depths of 5-5000 m in the central Pacific between August and September of 2005. Heterotrophic microbial biomass increased from the tropical to the subarctic region over the full water column, with latitudinal differences in prokaryotic biomass increasing from 2.3-fold in the epipelagic zone to 4.4-fold in the bathypelagic zone. However, the latitudinal difference in HNF and ciliate biomass decreased with depth. In the mesopelagic zone, the vertical attenuation rate of prokaryotic abundance, which was calculated as the linear regression slope of log-log plot of abundance versus depth, ranged from -0.55 to -1.26 and was more pronounced (steeper slope) in the lower latitudes. In contrast, the vertical attenuation rate of HNF in the mesopelagic zone (-1.06 to -1.27) did not differ with latitude. In the subarctic, the attenuation rate of HNF was 1.7 times steeper than for prokaryotes. These results suggest the accumulation of prokaryotes in the deep subarctic Pacific, possibly due to low grazing pressure. Although the vertical attenuation rate of ciliates was steepest in the bathypelagic zone, HNF abundance did not further decrease at depths below 1000 m, except for at 2000 m where HNF was lowest across the study area. Ciliate abundance ranged 0.3-0.8 cells l -1 at 4000 m, and were below the detection limit ( < 0.1 cells l -1 ) at 5000 m. To our knowledge, this study presents the first data for ciliates below 2000 m.

Production (abundance and biomass) and net calcification rates of the coccolithophorid Pleurochrysis carterae under different partial pressures of CO2 (pCO2) were examined using short (15, 24 and 39 h), long (7 d) and dark (7 d) incubation experiments. Short incubations were conducted at ambient, 500 and 820 ppm pCO2 levels in natural seawater that was enriched with nutrients and inoculated with P. carterae. Long incubations were conducted at ambient and 1200 ppm pCO2 levels in natural seawater (0.2 µm filtered as well as unfiltered) that was enriched with nutrients and inoc- ulated with P. carterae. Dark incubations were conducted at ambient and 1200 ppm pCO2 in unfil- tered seawater that was inoculated with P. carterae. The abundance and biomass of cocco- lithophorids increased with pCO2 and time. The abundance and biomass of most noncalcifying phytoplankton also increased, and were hardly affected by CO2 inputs. Net calcification rates were negative in short incubations during the pre-bloom phase regardless of pCO2 levels, indicating dis- solution of calcium carbonate. Further, the negative values of net calcification in short incubations became less negative with time. Net calcification rates were positive in long incubations during blooms regardless of pCO2 level, and the rate of calcification increased with pCO2. Our results show that P. carterae may adapt to increased (~1200 ppm) pCO2 level with time, and such increase has little effect on the ecology of noncalcifying groups and hence in ecosystem dynamics. In dark incuba- tions, net calcification rates were negative, with the magnitude being dependent on pCO2 levels.

Global environmental changes are recently occurring faster than any other time. The resulting combinations of natural and anthropogenic disturbances are strongly affecting coral reef communities. Coral damage can be caused by both abiotic factors (temperature, sedimentation, nutrients inputs, ultraviolet radiation) and biotic factors (predation, overgrowth of algae, infectious diseases). These factors acting mostly in synergy had resulted in worldwide coral reef deterioration. Coral bleaching is the most impacting process that is affecting coral survival under elevated sea surface temperature and high irradiance scenario. Bleaching is well known to occur around the world; however, its mechanism is not well understood. This is due to the high complexity of the “coral holobiont” (coral in symbiosis with its zooxanthellae and a microbial community that maintains a delicate balance to keep the coral health). In this chapter a novel point of view of bleaching mechanism using micro/nano-size scales is presented: (1) the study of pigment dynamics during thermal-induced bleaching revealed that bleaching is a detoxification strategy to avoid the formation of reactive oxygen species (ROS), (2) the synergistic action of thermal stress with pathogenic bacteria exacerbates the bleaching process, and (3) the synergistic effect of thermal stress in a nitrate-enriched environment can impede the recovery of corals after a bleaching event, turning the corals to be more susceptible to other environmental or anthropogenic stressors.

We examined the flows of nitrogen in two batch incubations of plankton assemblages under controlled conditions, using mesopelagic seawater from different depths. Observations included concentrations of nutrients, organic matter (particulate and dissolved) and plankton (biomass by species). Because nitrogen flows were not observed directly (as is generally the case), we examined them using a multi-element ecosystem model developed to simulate these experiments. Dynamic changes in the observed bulk POC/PON ratio (C/N ratio of particulate organic matter, POM) were consistent with a quota model for phytoplankton. To relate these changes to the regeneration of nitrogen, we included such a quota model and all major planktonic groups observed. By assimilating the data (all observations of carbon and nitrogen concentrations, including living carbon biomasses) into the model using the Monte Carlo Markov Chain, we accurately simulated the changes in bulk POC/PON ratio and its difference between incubations. Changes in phytoplankton composition dominated the changes in bulk POC/PON ratio. Bacteria dominated the regeneration of nitrogen in both incubations, and changes in bacterial regeneration strongly affected the bulk POC/PON ratio. After nitrate depletion, gross nitrogen regeneration varied inversely with observed POC/PON ratio and was constrained by this ratio. Thus, we have demonstrated a powerful new approach to constraining the flows of nutrients through ecosystems. Our results suggest that simultaneous observations of POC and PON could place an additional constraint on the supply of inorganic nitrogen in models of the oligotrophic ocean.

Vertical and seasonal characteristics of biogenic silica (BSi) dissolution in seawater were investigated by multiple dissolution experiments using seawater collected from surface and mesopelagic layers in Suruga Bay during the period 2002–2004. The dissolution rate coefficients calculated based on temporal changes of BSi concentration varied with the season of sample collection. They ranged from 0.023–0.057 day − 1 for surface samples and 0.0018–0.0025 day − 1 for mesopelagic samples for temperatures approaching in situ conditions. Experiments at various temperatures confirmed that BSi dissolution depends on temperature in natural seawater. Dissolution rate coefficient (day − 1 ) of BSi correlated significantly with temperature (°C), and Q 10 was 2.6. Addition of bioavailable organic matter to low-bioactivity seawater enhanced the protease activity and abundance of bacteria, and increased BSi dissolution rate by a factor of 1.4–2.0. There is clear evidence that BSi dissolution is accelerated by bacterial activity and potentially limited by bioavailable organic matter in natural seawater. Dissolution rates and total decreases of BSi concentration were lower during experiments using mesopelagic samples than in those using surface samples. This suggests that dissolution of BSi varies with depth and that BSi in the mesopelagic water is more resistant to the dissolution than that in the surface water. This lower dissolution rate was caused by lower temperature and lower bacterial activity due to less bioavailable organic matter in mesopelagic water. Our results provide a mechanistic understanding of variations in silica cycling within the seasonally and vertically differing marine environment.

We investigated the water structure and nutrient distribution in the Suruga Bay from April 2000 to July 2002, especially the Offshore Water, which occupies a large part of the bay. The maximum salinity in the upper 200 m varied between 34.49 and 34.71, indicating a temporal change in the influence of Kuroshio Water on the Offshore Water. Seasonal variation in nutrient concentrations was largest from surface to 50 m. On the other hand, the variance in nutrient concentrations within each season was largest in the subsurface layer of 100–300 m in spring, summer and fall. In the Offshore Water, the change of nutrients was negatively correlated with that of salinity in each season. This suggests that an increasing intrusion of saline water brings about a lower nutrient concentration in the Offshore Water. Likewise, negative correlations were observed between the change of the maximum salinity and chlorophyll a (Δ [chl.a-int])/nutrients integrated in the upper 200 m. Δ[chl.a-int] was significantly correlated with the changes of nitrate and phosphorus, but there were no significant correlations between Δ[chl.a-int] and the change of silicate. These results suggest that the concentrations of chlorophyll a and nutrients in the Offshore Water were decreased due to the increasing intrusion of Kuroshio Water. The Offshore Water is likely to be related to the regulation of primary production by nitrate.

The concentration of dissolved organic carbon (DOC) was measured every few months from September 2000 through October 2001 at a coastal location in the center of Suruga Bay, Japan (34°51′N, 138°38′E). Water samples were collected three times per day (midday, night and predawn). DOC concentrations ranged from 91.3 to 45.2 μM C on the surface to 100 m depth. Diel variation in DOC concentrations, among the three sampling times, was greater in the upper 20 m, with a maximum difference of 21.7 μM C in July 2001, and reflected in diel DOC inventory variations from the surface to 50 m. Diel variations were controlled by both physical and biological factors. DOC concentrations were significantly correlated with potential density in the deeper layers (100–1000 m), indicating that the distribution of DOC concentrations in the deeper layer was mainly due to mixing. Most DOC concentrations in the upper layer (0–50 m) did not display the same relationship as in the deeper layer. Using the relationship with potential density at 100–1000 m, the DOC concentration in the upper layer, due simply to mixing, was calculated. The difference between the calculated and observed DOC was used to estimate biological contribution. The biological contributions to the DOC inventory in the upper layer (0–50 m) were found greatly in November 2000 and April 2001. This indicates that excess DOC accumulated, by biological processes, in the upper layer during these periods. In November 2000, the excess DOC in the inventory was constant throughout the sampling days (0.36–0.37 mol C m −2 ), whereas diel variations of DOC in the vertical profile were large and contrary to the variation between 10 and 20 m. This suggests that the excess DOC was contributed biologically during daytime in the uppermost layer and reached to the 50 m depth by deeper mixing. As a result, the inventory appeared to be stable over a day because of the compensating effects of DOC production and consumption throughout 50 m. In contrast, in spring and summer, there was a distinct diel inventory decrease in the nighttime, with apparent rates ranging from −0.61 to −0.35 μM C h −1 . It is probable that the DOC, which accumulated during the daytime, was mostly labile, with a turnover time of a few hours. The results indicate that the dynamics of diel DOC variations varied seasonally, and suggest that these variations need to be considered when estimating seasonal DOC pools in the coastal ocean.

We conducted experiments at Fukido mangrove, northeastern Ishigaki Island, Okinawa, Japan in March 1999, to quantify the nitrogen cycle for simulations of nitrogen cycling and export. We measured concentrations of TON (total organic nitrogen), nitrate (NO3– + NO2–), ammonia (NH4+) in the creek water, and as physical parameter, measured flow rate and water level. Concentrations of TON and NO3– + NO2– were higher at high tide and lower at low tide, whereas NH4+ concentration had an opposite trend. Export flux of NO3– + NO2– was positive (62 mol·d–1) but export of TN (total nitrogen) was estimated –21 mol·d–1, so that Fukido mangrove is a source of nitrogen to its coastal community. And we constructed a model of nitrogen cycle and simulated the export fluxes. Simulated TON export was only 6.6%. In the simulations, the vegetation was a net sink for nitrogen, meaning that it is string nitrogen as biomass. There is no mechanism to input into the ecosystem in this model. Nitrogen fixation may be a significant source of nitrogen to the mangrove ecosystem, and we will need to conduct more studies to clarify here its role in the nitrogen cycle.

Coral reef seawater samples from Bora Bay off Miyako Island in Okinawa, Japan were incubated with an initial volume of 20 liters. The degradation of organic carbon in this seawater was monitored for more than three months in dark, unstirred polycarbonate vessels by measuring the concentration of organic carbon in the seawater. The concentration of organic carbon gradually decreased to the background level of the refractory organic matter. The ratio of labile organic carbon to total organic carbon was about 30% in the water within the reef, and 10% in the water outside. The concentration of inorganic nutrients gradually increased with the degradation of the organic matter. In terms of the cell density and cell biomass of bacteria, the doubling rate was initially about twice a day and then declined during the incubation. Rate of degradation of labile organic carbon was about 20mmol C/m2/day in the reef. It was much smaller than the respiration rate reported for the whole coral reef community. This indicates that benthos like corals plays a major role in carbon dynamics in the coral reef. The result that the refractory organic concentration in the reef is lower than that in the outer sea indicates that the coral reef has the role of carbon sink in that organic carbon might be absorbed to the sedimentation particle.

Decomposition experiments were conducted on cultured phytoplankton (Skeletonema costatum) in seawater containing decomposer and consumer of size less than 500 µm. We determined the decomposition rates of bulk particulate organic matter (POM), the ratio of labile to semi-refractory fractions in the POM, and the POM carbon/ nitrogen (C/N) ratio during decomposition. To identify the kinetic mechanisms involved in the reactions of different order (e.g., first- and second-order), we studied the sensitivity of reaction rates to the initial concentration of POM, ranging from 2.4 to 71 mg-C L−1. The results showed that decomposition consists of two first-order reactions: decomposition of labile and of semi-refractory particulate organic carbon (POC). The decomposition rate constants found for labile (0.13 day−1 at 20°C), and semi-refractory POC (0.008 day−1 at 20°C), and the carbon weight ratio of semi-refractory POC (13% at 20°C), were insensitive to the initial organic matter concentration. The time-dependence of the C/N ratio was also independent of this initial concentration. The decomposition rate constants and the content of semi-refractory POC did not change, regardless of the absence or presence of 25–500 µm organisms in natural seawater.

Dissolved organic carbon (DOC) concentrations in surface waters of the Pacific Ocean during October–November, 1995, were determined using a high-temperature combustion method. The DOC in the surface mixed-layer was approximately homogeneous with a concentration between 55 and 89 µmol C l−1. This homogeneity indicates that there is a strong control of the vertical distribution of DOC by mixing processes. The DOC concentrations in the mixed-layer in the subtropical region were up to 27 µmol C l−1 higher than in the tropical region. This difference reflects the subtropical accumulation and the tropical export of DOC. There is a significant positive correlation between DOC and chlorophyll a concentrations in the mixed-layer of the North Pacific subtropical region, suggesting that phytoplankton is the primary source of DOC accumulated in this region. Calculations using simple box models suggest that DOC export in the tropical region (0–50 m depth, 10°N-10°S, along 160°W) occurs primarily by poleward advection at a rate of 0.5–3 mmol C m−2day−1. A comparison with estimates of the export rate of particulate organic carbon published in previous studies leads us to conclude that DOC export may contribute less to the carbon budget in the tropical region than has recently been supposed.

Measured changes in dissolved oxygen (DO) concentrations in a coral reef at Miyako Island are markedly different from the diurnal sinusoidal pattern expected if biological processes are dominant. We were able to resolve this paradox by constructing a simple model that combines the influences of organic production and air-sea exchange with water flow and mixing through the reef system. The model successfully replicates the observed DO behavior, suggesting that the simple flow system we propose adequately accounts for these water advection effects. Our optimized estimates of gross production and respiration on the reef flat are 13 m and 5.2 g C m -2 d -1 ,giving a P:R ratio of 2.5. We obtained best fits to the data in the lagoon with a production rate of 4.9 g C m -2 d -1 and a respiration rate of 5.2 g C m -2 d -l for a P :R ratio of 0.9.

A new methodology is proposed for the evaluation of metabolic parameters in coral reef ecosystems using a simple model which combines the metabolic activity with a simplified water flow system. The concentration time profile resulting from running the model for DO are compared with continuously observed data taken at a site in Miyako Island and the metabolic rates are obtained by fitting the model to the data using a four parameter optimization routine. The model yields an excellent fit to the observed data (r > 0.9) using a set of easily obtained flow and tidal information. It is concluded thus that the factors governing concentration changes of biologically mediated substrates are sufficiently simulated in the model and mass fluxes can be predicted with accuracy between the coral reef ecosystem and its interfaces with the ocean and the atmosphere.

Biological studies were carried out in Bora Bay, Miyako Island, near Okinawa Japan, with the object to understand the structure and physiology of a coral reef ecosystem, with especial emphasis on the carbon cycle and CO2 fixation. Food web of the coral reef ecosystem at Bora Bay shows some remarkable patterns with cyanobacteria, epiphytic microalgae, sea weed and zooxanthellae as primary producers rather than phytoplankton. The importance of the microbial loop as an organic source and the rapid decomposition and recycling rates is another pattern to be considered.

Only about half of all the CO2 that has been produced by the burning of fossil fuels now remains in the atmosphere. The CO2 missing from the atmosphere is the subject of an important debate. One of the great possibility of the missing CO2 is to know the pool and turn-over time of oceanic organic carbon, especially dissolved organic carbon in the carbon cycle. Measurement of dissolved organic carbon in seawater has been much argued for a long time. An essential discussion is described in relation to the understanding “Nature”.

Behavior of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) in coral reef waters in relation with biological processes was studied with incubation experiments and field observations in May 2008 and 2009 at the fringing reef of Sesoko Island, Okinawa, Japan. Reef sea water (RSW) and coral mucus added RSW collected from Acropora digitifera (AcrRSW) and Montipora digitata (MonRSW) were incubated for one day in situ and then for 77 days in the laboratory under dark condition . The results indicated that the behavior of DON was different compared to that of DOC in RSW and mucus added (AcrRSW and MonRSW) during dark incubation. Concentration of DON increased from 8.3 µM to 11.8 µM for AcrRSW and 4.0 µM to 15.4 µM for MonRSW during dark incubation period. The increasing rates for DON in AcrSRW and MonRSW were 0.05 µM day -1 and 0.1 µM day -1 respectively. On the other hand DOC concentration decreased from 129.0 µM to 75.0 µM for AcrRSW and 75.1 µM to 64.7 µM for MonRSW, with decreasing rates of 0.7 µM day -1 and 0.1 µM day -1 respectively. We assume that the increase of DON may be determined by difference between rates of inputs of organic matter mainly from mucus and rate of degradation of dissolved organic matter in the water column. These results suggest that recycling of DON is slow than that of DOC in coral reef ecosystem.

A direct comparison is presented here between dissolved organic carbon (DOC) analyses done with the historical routine wet chemical oxidation method (persulfate oxidation), the high temperature catalytic oxidation method of Sugimura and Suzuki (MRI instrument), and a commercial high temperature combustion analyzer (Shimadzu instrument). The sample set used for the comparison included stations in a tidal urban river, the salinity gradient of an estuary, and continental shelf and slope waters, including those to a depth of 2000 m. Both high temperature combustion methods measured considerably more DOC (1.5 to 3.5 times) in the coastal waters than did the conventional persulfate method. In the fresh water and estuary, the commercial instrument measured only slightly higher values than did the conventional method, while the MRI instrument measured almost twice the concentration. Throughout all the environments, the MRI instrument measured about twice the concentration measured by the commercial instrument. An inverse linear correlation can be demonstrated between DOC and apparent oxygen utilization with data from each of the methods, but it is argued that this does not necessarily imply ‘oceanographic consistency’.

The recent studies on the behavior, role, and characteristics of DON (dissolved organic nitrogen), including nitrogen fixation and organic nitrogen compounds in corals and coral reefs were reviewed. DON is one of the important components as well as DOC for understanding biogeochemical cycling and ecosystem function in coral reefs. Recent results and views have been integrated into a new concept for the nitrogen cycle in coral reefs.

Publisher Summary This chapter evaluates the effectiveness of an artificial marine structure as an upwell-generator to enhance oceanic CO 2 sequestration in the coastal areas of Japan. Results suggest that the processes responsible for vertical mixing between shallow waters and bottom waters were vertical shear of currents, internal wave breaking, and entrainment. It also found evidence that neap tides may enhance the mixing. The upwelling generated by the artificial marine structure, increased nutrient supply to the shallow layer. Coccoid pico-cyanobacteria represented about 25% to 30% of the total biomass produced during incubation. Diatoms of small size were abundant, among which Chaetoceros compressum and other Chaetoceros species predominated. Net organic production estimated over the year is 470 gC m -2 yr -1 using 1300 mgC m -2 day -1 . This value is the same order of magnitude as net organic production in temperate forests and mangroves. This, together with the contribution from forestation, could help enable Japan to reach its CO 2 -reduction target as set in the Kyoto Protocol. It is concluded that the use of marine biota, natural energy and this artificial upwelling system contributes effectively to increased CO 2 fixation.

Publisher Summary The traditional notion that coral reefs sustain high rates of gross primary productivity is valid, but the contribution of various sources and variations in productivity among reef zones are still emerging into a coherent picture. A rich variety of symbiotic zooxanthellae, phytoplankton, seagrasses, and macro- and micro-algae living in and on hard substrata and unconsolidated sediments contribute to production of fixed carbon on a coral reef. A large part of the organic matter produced within coral reef metabolisms is as particulates and dissolved forms. Dissolved organic matter (DOM) is produced largely through its direct excretion by plants and corals, which comprise up to 20-30% of their primary production. The particulate organic matter is formed from the disintegrated faces of phytophages, from the crushed tallom of dead macmphytes, as well as from the microbial and algae biomass washed out from sediments and perphytoton by surf. Although these organic matters and nutrient cycles among the different organisms keep the maintenance of coral reef ecosystem, little is known on the behavior of organic matters. The fate of organic matter within coral reef is due to the organic production, decomposition, and export of organic matter to open ocean from coral reef with tidal cycle. This chapter reports the experimental results and also estimated increase of CO2 fixation rates by worldwide coral reef ecosystems, considering the effect of flow rates of sea water outside coral reefs.

OCEANIC dissolved organic carbon (DOC) is one of the Earth's largest carbon reservoirs, but until recently its role in the carbon cycle has been neglected. New methodology1, however, has led to larger estimates of DOC concentrations and also to renewed interest in the biochemical lability of DOC2. Previous work found that the mean age of DOC in the surface ocean was > 1,000 years3. To examine the lability of DOC in greater detail, we have conducted experiments to estimate DOC turnover rates in the upper ocean. We directly observed rapid DOC turnover by bacterioplank-ton during the spring phytoplankton bloom in the North Atlantic ocean. Potential turnover rates, measured in 0.8-um filtered samples, ranged from 0.025 to 0.363 per day, and were consistent with bacterial biomass production and uptake of dissolved nitrogen (NH+4, NO-3 and urea). Our results indirectly suggest that cycling of dissolved organic nitrogen (DON) differs from that of DOC. The high estimates of DOC concentrations and turnover rates repeated here, if found to be general, would seem to demand changes in models4 of carbon cycling and of the ocean's role in buffering increases in atmospheric CO2.

[1] An evaluation of DOC export with the formation of North Pacific Intermediate Water is presented. Data from sites representing the relevant North Pacific water masses (subtropical, subpolar, and subtropical transitional) are used to demonstrate the process. We suggest that dissolved organic carbon (DOC)-replete Oyashio (subpolar) water mixes with DOC-depleted Kuroshio (subtropical) water in the mixed water region east of Japan. The new intermediate water, formed at a rate of 2–5 Sv, exports DOC at 13 ± 6 Tg DOC yr � 1 . On the basis of these findings we present an alternative model to explain the 14 C-DOC age gradient recently reported for intermediate depths of the North Pacific. INDEX TERMS: 4806 Oceanography: Biological and Chemical: Carbon cycling; 4805 Oceanography: Biological and Chemical: Biogeochemical cycles (1615); 4283 Oceanography: General: Water masses; KEYWORDS: dissolved organic carbon; DOC; North Pacific Intermediate Water; carbon export; carbon

A method is described for the rapid, precise determination of non-volatile dissolved organic carbon in seawater in concentrations between 0 and 2000 μM. The oxidation is carried out on a platinum catalyst at 680 °C under an oxygen atmosphere after the sample has been freed of inorganic carbon, and the concentration of the CO 2 generated is measured with a non-dispersive IR gas analyzer. The determination can be carried out on board ship with a precision of ±2% using a sample volume of 200 μl. The results obtained using this method are of a much higher value than those obtained using persulfate oxidation methods. The molecular weight dependency of the results clearly indiates that the above discrepancy is caused by the low oxidation efficiency of the persulfate oxidation method against high-polymer organic matter dissolved in seawater. The results reveal that the concentration of dissolved organic carbon in surface water is about 300 μM and decreases with depth. An examination of molecular weight distribution indicates that the concentration of high-polymer organic carbon decreases rapidly from surface to deeper layers, with molecular weight ranging from 1.8 x 10 3 to 6 x 10 4 Dalton. It is noted that there is an inverse correlation between the concentration of dissolved organic carbon and apparent oxygen utilization (AOU). Frozen or acidified preservation of unfiltered samples does not give reliable results. An essential requirement for dissolved carbon analysis is membrane filtration just after sampling and real-time analysis on board. Because of the well-defined principle of the oxidation process, its reliability, the ease of sample handling and of the analytical procedure on board or in the land laboratory, and the consistency of the oceanographic parameters, this method is much more suitable for the analysis of marine dissolved organic carbon than the methods used previously.

Dissolved and particulate forms of mercury in seawater were determined. To avoid errors due to adsorption, total mercury was collected on XAD-2 resin after converting inorganic mercury to oxinate immediately after sampling. The organic mercury was trapped directly on XAD-2 resin. Both total and organic mercury adsorbed on XAD-2 resin were finally reduced to metallic mercury, which was determined by the cold vapor AAS method. In the temperature zone in the western North Pacific, total mercury is 14 ng l−1 in surface waters and 6 ng l−1 between 500 and 5,000 m. Organic and particulate mercury are 7 ng l−1 in surface waters and 2 ng l−1 between 500 and 5,000 m. Particulate forms are 3 to 10% of the total. Organic mercury comprises one-third to a half of the total. The molecular weight of organic mercury compounds was determined to be about 9 × 103, indicating its proteinaceous nature.

In order to clarify the chemical forms of minor metallic elements occurring in the ocean, a new method of separation of organic compounds of metals in sea water by using XAD-2 resin was contrived. By applying the new method of determination, it is found that, (1) More than 80 % of V, Fe, Cd and Cu dissolved in sea water are present in organic forms regardless of the depth; (2) A most part of Co and Pb are present in organic forms near the surface, but they change into inorganic forms in the deep layer up to 50 to 60%; (3) Of the total amounts of dissolved Al, Ni, Zn, Ag, Mo, and U, less than 30 % are present in organic forms in sea water anywhere in the ocean; (4) Up to 45% of Se is in organic forms.

A new method of determination of selenium and separation of Se(IV) and Se(VI) in sea water is described. The selenium is determined by fluorometric method using Se-DAN complex in cyclohexane media. Prior to the fluorometric determination, Se(IV) is separated from sea water by means of Se(IV)-DDTC complex which is adsorbed on the macroreticular resin. As to the separation of the total selenium from sea water sample, the reduction and coprecipitation method is used. Se(VI) is determined with the same method as used for the total selenium after the separation of Se(IV). The average recoveries are 92.5±1.3% for Se(IV) and 97.4±0.9% for ∑Se. The standard deviation of analytical results is below 10%.

By using the new fluorometric method of determination of the total selenium (Σ Se), Se (IV) and Se (VI), the content of selenium in sea weter was determined in the western North Pacific. Results showed that the content ofΣ Se in surface water ranged from 0.06 to 0.12μg l−1, while in deeper layers, the content increased to 0.20μg l−1. It was found that Se (IV) showed rather uniform distribution with depth, while Se (VI) increased with depth to about three times that in the surface. The ratio of Se (IV) to theΣ Se ranged from 0.5 to 0.8 in the surface and 0.4 to 0.6 in the deep. The coexistence of the hexa- and tetravalent ions of selenium was confirmed both in surface and deep layers. Some results of observations on the content of selenium in the coastal areas of Japan were also reported.

A detailed examination of a high-temperature catalytic oxidation method for liquid samples in the analysis of total nitrogen dissolved in seawater is reported. The nitrogenous compounds in liquid samples are oxidized on a platinum catalyzer at 680°C under oxygen atmosphere and the generated NO 2 is absorbed into a chromogenic reagent, followed by a spectrophotometric determination. The results of this method are much higher than those of wet oxidation methods. Molecular size dependency of the results clearly indicates that the above discrepancy is caused by the low oxidation capacity of the wet oxidation method against high-polymer organic matter dissolved in seawater. The results revealed that the concentration of total nitrogen in seawater is nearly constant from surface to bottom, ranging from 30 to 40 μM 1 −1 , which organic nitrogen concentration higher in the surface layer, and a rapid decrease with depth. An examination of molecular size distribution indicates that the concentration of high-polymer organic nitrogen decreases rapidly from surface to deeper layers, with molecular sizes ranging from 5 × 10 3 to 3 × 10 4 . Because of the well-defined principle of the oxidation process, its reliability, ease of sample handling and of analytical procedure on board or in the land laboratory, the present method is much more suitable for the marine analytical chemistry of total and organic nitrogen than the other previous methods.