Comparison of nonlinear and linear PCA on surface wind, surface height, and SST in the South China Sea

We compared nonlinear principal component analysis (NLPCA) with linear principal component analysis (LPCA) with the data of sea surface wind anomalies (SWA), surface height anomalies (SSHA), and sea surface temperature anomalies (SSTA), taken in the South China Sea (SCS) between 1993 and 2003. The SCS monthly data for SWA, SSHA and SSTA (i.e., the anomalies with climatological seasonal cycle removed) were pre-filtered by LPCA, with only three leading modes retained. The first three modes of SWA, SSHA, and SSTA of LPCA explained 86%, 71%, and 94% of the total variance in the original data, respectively. Thus, the three associated time coefficient functions (TCFs) were used as the input data for NLPCA network. The NLPCA was made based on feed-forward neural network models. Compared with classical linear PCA, the first NLPCA mode could explain more variance than linear PCA for the above data. The nonlinearity of SWA and SSHA were stronger in most areas of the SCS. The first mode of the NLPCA on the SWA and SSHA accounted for 67.26% of the variance versus 54.7%, and 60.24% versus 50.43%, respectively for the first LPCA mode. Conversely, the nonlinear SSTA, localized in the northern SCS and southern continental shelf region, resulted in little improvement in the explanation of the variance for the first NLPCA.

Factors influencing the climatological mixed layer depth in the South China Sea: numerical simulations

The mixed layer depth (MLD) in the upper ocean is an important physical parameter for describing the upper ocean mixed layer. We analyzed several major factors influencing the climatological mixed layer depth (CMLD), and established a numerical simulation in the South China Sea (SCS) using the Regional Ocean Model System (ROMS) with a high-resolution (1/12A degrees x1/12A degrees) grid nesting method and 50 vertical layers. Several ideal numerical experiments were tested by modifying the existing sea surface boundary conditions. Especially, we analyzed the sensitivity of the results simulated for the CMLD with factors of sea surface wind stress (SSWS), sea surface net heat flux (SSNHF), and the difference between evaporation and precipitation (DEP). The result shows that of the three factors that change the depth of the CMLD, SSWS is in the first place, when ignoring the impact of SSWS, CMLD will change by 26% on average, and its effect is always to deepen the CMLD; the next comes SSNHF (13%) for deepening the CMLD in October to January and shallowing the CMLD in February to September; and the DEP comes in the third (only 2%). Moreover, we analyzed the temporal and spatial characteristics of CMLD and compared the simulation result with the ARGO observational data. The results indicate that ROMS is applicable for studying CMLD in the SCS area.

Variability of surface circulation in the South China Sea from satellite altimeter data

11-year satellite altimeter sea surface height (SSH) anomaly data from January 1993 to December 2003 are used to present the dominant spatial patterns and temporal variations of the South China Sea (SCS) surface circulation through Empirical Orthogonal Function (EOF) analysis. The first three EOF modes show the obvious seasonal variations of SSH in the SCS. EOF mode one is generally characterized by a basin-wide circulation. Mode two describes the double-cell basin scale circulation structure. The two cells were located off west of the Luzon Island and southeast of Vietnam, respectively. EOF mode three presents the mesoscale eddy structure in the western SCS, which develops into a strong cyclonic eddy rapidly from July to September. EOF mode one and mode three are also embedded with interannual signals, indicating that the SCS surface circulation variation is influenced by El Nino events prominently. The strong El Nino of 1997/98 obviously changed the SCS circulation structure. This study also shows that there existed a series of mesoscale eddies in the western SCS, and their temporal variation indicates intra-seasonal and interannual signals.

Highly nonlinear internal solitary waves over the continental shelf of the northwestern South China Sea

Large amplitude internal solitary waves (ISWs) often exhibit highly nonlinear effects and may contribute significantly to mixing and energy transporting in the ocean. We observed highly nonlinear ISWs over the continental shelf of the northwestern South China Sea (19A degrees 35'N, 112A degrees E) in May 2005 during the Wenchang Internal Wave Experiment using in-situ time series data from an array of temperature and salinity sensors, and an acoustic Doppler current profiler (ADCP). We summarized the characteristics of the ISWs and compared them with those of existing internal wave theories. Particular attention has been paid to characterizing solitons in terms of the relationship between shape and amplitude-width. Comparison between theoretical prediction and observation results shows that the high nonlinearity of these waves is better represented by the second-order extended Korteweg-de Vries (KdV) theory than the first-order KdV model. These results indicate that the northwestern South China Sea (SCS) is rich in highly nonlinear ISWs that are an indispensable part of the energy budget of the internal waves in the northern South China Sea.

Observations of Kuroshio intrusion into the South China Sea

To discuss the intrusion of the Kuroshio into the SCS, we examined the mixing between the North Pacific and South China Sea (SCS) waters based on in-situ CTD data collected in August and September 2008 and the moored ADCP data taken from mid September 2008 to early July 2009. The CTD survey included four meridional sections from 119A degrees E to 122A degrees E around the Luzon Strait, during which pressure, temperature, and salinity were measured. The CTD data show that the isopycnal surface tilted from the SCS to the North Pacific; and it was steeper in the lower layers than in the upper ones. Meanwhile, we found strong vertical mixing taken place in the areas near 121A degrees E. The Kuroshio in high temperature and salinity intruded westward through Luzon Strait. The frequency of buoyancy was one order of magnitude greater than that of the common ones in the ocean, suggesting stronger stratification in the northeastern SCS. On the other hand, the long-term ADCP data show that before late October 2008, the direction of water flow in the SCS was eastward, and from November 2008 to late February 2009, it turned northwestward in the layers shallower than 150 m, while remained unchanged in deep layers from 200 to 450 m. From March to June 2009, the direction shifted with increasing depth from northward to southward, akin to the Ekman spiral. EOF analysis of the current time series revealed dominant empirical modes: the first mode corresponded to the mean current and showed that the Kuroshio intrusion occurred in the upper layers only from late December to early March. The temporal coefficient of the first and the second mode indicated clearly a dominant signal in a quasi-seasonal cycle.

Submesoscale activity over the shelf of the northern South China Sea in summer: simulation with an embedded model

We applied a primitive equation ocean model to simulate submesoscale activities and processes over the shelf of the northern South China Sea (NSCS) with a one-way nesting technology for downscaling. The temperature and density fields showed that submesoscale activities were ubiquitous in the NSCS shelf. The vertical velocity was considerably enhanced in submesoscale processes and could reach an average of 58 m per day in the subsurface. At this point, the mixed layer depth also was deepened along the front, and the surface kinetic energy also increased with the intense vertical movement induced by submesoscale activity. Thus, submesoscale stirring/mixing is important for tracers, such as temperature, salinity, nutrients, dissolved organic, and inorganic carbon. This result may have implication for climate and biogeochemical investigations.

A study of internal solitary waves observed on the continental shelf in the northwestern South China Sea

Based on in-situ time series data from the acoustic Doppler current profiler (ADCP) and thermistor chain in Wenchang area, a sequence of internal solitary wave (ISW) packets was observed in September 2005, propagating northwest on the continental shelf of the northwestern South China Sea (SCS). Corresponding to different stratification of the water column and tidal condition, both elevation and depression ISWs were observed at the same mooring location with amplitude of 35 m and 25 m respectively in different days. Regular arrival of the remarkable ISW packets at approximately the diurnal tidal period and the dominance of diurnal internal waves in the study area, strongly suggest that the main energy source of the waves is the diurnal tide. Notice that the wave packets were all riding on the troughs and shoulders of the internal tides, they were probably generated locally from the shelf break by the evolution of the internal tides due to nonlinear and dispersive effects.

A new empirical model for retrieving sea surface salinity in L band

Sea surface salinity is a key physical parameter in ocean science. It is important in the ocean remote sensing to retrieve sea surface salinity by the microwave probe technology. Based on the in situ measurement data and remote sensing data of the Yellow Sea, we have built a new empirical model in this paper, which can be used to retrieve sea surface salinity of the Yellow Sea by means of the brightness temperature of the sea water at L-band. In this model, the influence of the roughness of the sea surface is considered, and the retrieved result is in good agreement with the in situ measurement data, where the mean absolute error of the retrieved sea surface salinity is about 0.288 psu. This result shows that our model has greater retrieval precision compared with similar models.

Phylogenetic position and morphology of thecae and cysts of Scrippsiella (Dinophyceae) species in the East China Sea

Resting cysts of the marine phytoplanktonic dinoflagellate Scrippsiella spp. are encountered in coastal habitats and shallow seas all over the world. Identification of Scrippsiella species requires information on cyst morphology because the plate pattern of the flagellated cell is conserved. Cysts from sediments of the East China Sea were identified based on traits from both the cysts and the thecal patterns of germinated cells. Calcareous cysts belonged predominantly to S. trochoidea (F. Stein) A. R. Loebl., S. rotunda J. Lewis, and S. precaria Montresor et Zingone. The former two species also produced smooth and noncalcified cysts in the field. A new species, S. donghaienis H. Gu sp. nov, was obtained from six noncalcified cysts with organic spines. These cysts are spherical, full of pale white and greenish granules with a mesoepicystal archeopyle. The vegetative cells consist of a conical epitheca and a round hypotheca with a plate formula of po, x, 4', 3a, 7 '', 6c (5c + t), 6 s, 5''', 2'''' and are morphologically indistinguishable from S. trochoidea. Results of internal transcribed spacer (ITS) sequence comparisons revealed that S. donghaienis was distinct from the S. trochoidea complex and appeared nested within the Calciodinellum/Calcigonellum clade. Culture experiments showed that the presence of a red body in the cyst and the shape of the archeopyle were constant within cell lines from one generation to the next, while the morphological features of the cyst wall, such as calcification and spine shape, appeared to be phenotypically plastic.

Feeding and egg production of the planktonic copepod Calanus sinicus in spring and autumn in the Yellow Sea, China

Shipboard incubations were conducted in spring (April) and autumn (October/November) 2006 to measure the feeding and egg production rates (EPR) of Calanus sinicus in the Yellow Sea, China. The ingestion rate (2.08-11.46 and 0.26-3.70 mu g C female(-1) day(-1) in spring and autumn, respectively) was positively correlated with microplankton carbon concentrations. In the northern part of the Yellow Sea, feeding on microplankton easily covers the respiratory and production requirements, whereas in the southern part in spring and in the frontal zone in autumn, C. sinicus must ingest alternative food sources. Low ingestion rates, no egg production and the dominance of the fifth copepodite (CV) stage indicated that C. sinicus was in quiescence inside the Yellow Sea Cold Bottom Water (YSCBW) area in autumn. Calanus sinicus ingested ciliates preferentially over other components of the microplankton. The EPR (0.16-12.6 eggs female(-1) day(-1) in spring and 11.4 eggs female(-1) day(-1) at only one station in autumn) increased with ciliate standing stock. Gross growth efficiency (GGE) was 13.4% (3-39%) in spring, which was correlated with the proportion of ciliates in the diet. These results indicate that ciliates have higher nutrient quality than other food items, but the low GGE indicates that the diet of C. sinicus is nutritionally incomplete.

Relationships between nitrogen and phosphorus forms and ratios and the development of dinoflagellate blooms in the East China Sea

During late spring and early summer of 2005, large-scale (> 15 000 km(2)), mixed dinoflagellate blooms developed along the the coast of the East China Sea. Karenia mikimotoi was the dominant harmful algal bloom species in the first stage of the bloom (late May) and was succeeded by Prorocentrum donghaiense approximately 2 wk later. Samples were collected from different stations along both north-south and west-east transects, from the Changjiang River estuary to the south Zhejiang coast, during 3 cruises of the Chinese Ecology and Oceanography of Harmful Algal Blooms Program, before and during the bloom progression. Nitrogen isotope tracer techniques were used to measure rates of NO3-, NH4+, urea, and glycine uptake during the blooms. High inorganic nitrogen (N), but low phosphorus (P) loading from the Changjiang River led to high dissolved inorganic N:dissolved inorganic P ratios in the sampling area and indicate the development of P limitation. The rates of N-15-uptake experiments enriched with PO43- were enhanced compared to unamended samples, suggesting P limitation of the N-uptake rates. The bloom progression was related to the change in availability of both organic and inorganic N and P. Reduced N forms, especially NH4+, were preferentially taken up during the blooms, but different bloom species had different rates of uptake of organic N substrates. K mikimotoi had higher rates of urea uptake, while P. donghaiense had higher rates of glycine uptake. Changes in the availability of reduced N and the ratios of N:P in inorganic and organic forms were suggested to be important in the bloom succession. Nutrient ratios and specific uptake rates of urea were similar when compared to analogous blooms on the West Florida Shelf.

Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical-biogeochemical model study

To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical - biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air-sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)(4), and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS-CoSiNE model favourably reproduces many of the observed features, such as ChI a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0-125 m) varies seasonally, with the highest value of 386 mg C m (-2) d (-1) during winter and the lowest value of 156 mg C m (-2) d (-1) during early summer. The annual mean value is 196 mg C m (-2) d (-1). The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m (-2) d (-1) which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.

Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea

Magnetotactic bacteria are a heterologous group of motile prokaryotes, ubiquitous in aquatic habitats and cosmopolitan in distribution. Here, we studied the diversity of magnetotactic bacteria in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea. The pond is composed of a permanently submerged part and a low tide subregion. The magnetotactic bacteria collected from the permanently submerged part display diversity in morphology and taxonomy. In contrast, we found a virtually homogenous population of ovoid-coccoid magnetotactic bacteria in the low tide subregion of the pond. They were bilophotrichously flagellated and exhibited polar magnetotactic behaviour. Almost all cells contained two chains of magnetosomes composed of magnetite crystals. Intriguingly, the combination of restriction fragment length polymorphism analysis (RFLP) and sequencing of cloned 16S rDNA genes from the low tide subregion samples as well as fluorescence in situ hybridization (FISH) revealed the presence of a homogenous population. Moreover, phylogenetic analysis indicated that the Qingdao Huiquan low tide magnetotactic bacteria belong to a new genus affiliated with the alpha-subclass of Proteobacteria. This finding suggests the adaptation of the magnetotactic bacterial population to the marine tide.

The combined effects of temperature and food supply on Calanus sinicus in the southern Yellow Sea in summer

The effects of temperature and food availability on the life history strategy of the planktonic copepod Calanus sinicus in the southern Yellow Sea in summer were studied in this paper. The fifth copepodite stage (CV) dominates the population in the central part of the southern Yellow Sea, where the Yellow Sea Cold Water Mass (YSCWM) occurs below the thermocline. Incubation experiments were conducted on CV C. sinicus caught from the YSCWM to examine the effects of temperature and food availability. Temperature at the surface (27degreesC) is lethal to CVs regardless of food availability. At the temperature in the middle of the thermocline (18degreesC), survival time of the specimens depends on food availability, being similar to20 days in treatments without extra food supply. At the temperature in the YSCWM (9degreesC), most animals survive at the end of 27 day incubation even in treatments without food supply. Developmental rate of CVs at 9degreesC without extra food supply is extremely low. The increase of either temperature or food supply promotes the developmental rate of CVs. According to these results, the surface layers with high temperature and low food abundance are detrimental for the survival and reproduction of C. sinicus. Low temperature and low food availability in the YSCWM help CV to maintain a much lower developmental rate and higher survival rate. The ecological trait of C. sinicus in the southern Yellow Sea in summer cannot be sufficiently explained solely by the effects of temperature.

Life history strategies of Calanus sinicus in the southern Yellow Sea in summer

Ecological and physiological features of the planktonic copepod Calanus sinicus in the southern Yellow Sea in summer were studied to reveal its life history strategy. From the coastal shallow waters to the central part of the southern Yellow Sea, a shift of the stage composition occurs from being dominated by the egg-nauplius stage to being dominated by the fifth copepodite (CV) stage. Most CVs reside in the Yellow Sea Cold Water Mass (YSCWM), where both temperature and food abundance are low. CVs in the YSCWM have longer body lengths, heavier body weights and higher carbon contents than those outside the YSCWM. Onboard incubations show that the development of CVs in the YSCWM is suspended. Energy conservation, development suspension and lack of diel vertical migration (DVM) behavior suggest a diapause status for the CVs in the YSCWM, although vertical distribution patterns indicate the CV individuals are not fully synchronous in physiology and development. This adaptive oversummering strategy would help C. sinicus to live through the warm and food-limited summer in the central part of the southern Yellow Sea; both low temperature and low food supply are necessary for CV to maintain the resting state in the YSCWM. Calanus sinicus exhibits different life history strategies in different regions of the southern Yellow Sea in summer.