Chaolun Li

Transcriptome Sequencing and De Novo Analysis of the Copepod Calanus sinicus Using 454 GS FLX

Background Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus. Results Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs) that provide a resource for gene function studies. Conclusion Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.

High-resolution phytoplankton diel variations in the summer stratified central Yellow Sea

Vertical distributions of phytoplankton biomass and community structure were studied in the summer stratified central Yellow Sea (YS) using a submersible spectrofluorometer (Fluoroprobe, bbe Moldaenke, Germany), along with photosynthetic pigments analysis (HPLC-CHEMTAX), and microscope observation. Above all, the results of the dominating group obtained from these methods generally coincided with each other on the transect 35°N. The concentrations of brown algae, green algae and total chlorophyll a (Chl a) biomass were highly correlated between the results of Fluoroprobe observations and pigments analysis (rxa0=xa00.79, 0.91 and 0.82, respectively, nxa0=xa054, pxa0<xa00.01). In the summer stratified central YS, significant differences in phytoplankton compositions on the vertical distribution was observed. On the basis of HPLC-CHEMTAX results, the dominating group of phytoplankton composition generally changed from cyanobacteria to chrysophytes and then to diatoms, from surface to bottom. Interestingly, on the basis of high-resolution observations using Fluoroprobe, a periodic fluctuation of the pycnocline presumably due to the semidiurnal internal tides was observed at an anchor station (35°N, 123°E). In addition, both nutrients and Chl a concentrations at the depth of the subsurface chlorophyll maximum (SCM) seemed to coincide with the rhythm of the pycnocline fluctuation, indicating the latter might have a potential impact on the dynamics of SCM phenomena in the summer stratified central YS.

Feeding of dominant zooplankton in Prydz Bay, Antarctica, during austral spring/summer: food availability and species responses

AbstractnInformation on the food and predation of zooplankton species is essential for an improved understanding of zooplankton community dynamics of the Southern Ocean. Feeding of dominant zooplankton species at locations across the neritic, slope and oceanic regions of Prydz Bay, Antarctica, was investigated with incubation experiments during austral spring/summer of 2009/2010 to identify the response of dominant copepods and krill to different feeding environments. Results showed distinct spatial and temporal variations in ingestion and filtration of predominant copepods and krill. In late spring, Calanoides acutus was inactive and the ingestion rate was only 1.30 μgC/ind/day. During early summer, a diatom bloom was in progress at station IS21, showing a peak biomass of Thalassiosira spp. and Fragilaria spp. Daily ingestion rates of Euphausia crystallorophias, C. acutus, Metridia gerlachei and Ctenocalanus citer were relatively high. By contrast, copepod ate predominantly ciliates in slope and oceanic regions where microplankton biomass were lower (<20 μgC/L). During late summer, microplankton of neritic regions, mainly composed of nano-sized Pseudo-nitzschia spp. and ciliates, was less than 10 μgC/L. C. acutus incubated in neritic regions mainly ate ciliates. The total microplankton biomass was lower (<5 μgC/L) and predominated by Pseudo-nitzschia spp. in slope regions north of Fram Bank, and daily ingestion rates of incubated copepods were less than 2.5 μgC/ind. Our results clearly demonstrated that copepods and krill had flexible feeding strategies to cope with temporally and spatially changing food availability in Prydz Bay. Meanwhile, ciliates appeared to represent an important carbon source for zooplankton, especially in regions with lower food concentrations.

Grazing and Metabolism of Euphausia pacifica in the Yellow Sea

Grazing and metabolism of Euphausia pacifica in the Yellow Sea were studied from September 2006 to August 2007. Euphausia pacifica is a selective-feeding omnivore and grazing rates among different months were monitored using a Coulter Counter and batch culture feeding experiments. Euphausia pacifica mainly grazed microzooplankton in August and September, which resulted in an increase in chlorophyll a concentration. Oxygen consumption rate of E. pacifica was 38.7–42.5 μmol O2 g-1 DW h-1 in March, which was four times higher than the oxygen consumption rates in September and December. The vigorous metabolism of E. pacifica in March consumed 3.1% of body carbon daily, which is likely related to its high reproduction and grazing rate. Respiration and metabolism of E. pacifica in September and December were similar and were lower. O:N ratio of E. pacifica was the highest (17.3–23.8) in March when spawning activity occurred and when food was abundant. The energetic source of E. pacifica during September and December was mostly protein from eating a carnivorous diet, including such items as microzooplankton. Euphausia pacifica was found in cold water at the bottom of the Yellow Sea in summer and autumn and maintained a low consumption status. O:N ratios of E. pacifica in March, September, and December were negatively correlated with SSTs and no significant correlation was found between O:N ratios and chlorophyll a concentration. Seawater temperature is clearly the most important parameter influencing the metabolism of E. pacifica.

Seasonal change in body length of important small copepods and relationship with environmental factors in Jiaozhou Bay, China

Differences among species in prosome length and in species’ response to environmental factors do exist. Therefore, it is useful to examine prosome length for different copepod species in variable environments. Seasonal variations in prosome length of four small copepods and their copepodite stages in the Jiaozhou Bay were compared and the relative influence of temperature, salinity, and chlorophyll concentration were examined. Two peaks were found in the mean prosome length of Paracalanus parvus (in early winter and May). For Acartia bifilosa, the maximum values of all copepodites occurred mainly from February to April, and decreased to the bottom in July. Prosome length of Acartia pacifica peaked when it first appeared in June, then reached to the minimum in July. Parvocalanus crassirostris only appeared from late summer to autumn and the mean prosome length showed no clear changes. Correlations of adult prosome length with environmental factors were evaluated. For the four species, temperature was negatively correlated to prosome length except for P. crassirostris. But the different species varied markedly in their responds to temperature. A. bifilosa showed a more definite trend of size variation with temperature than P. parvus and A. pacifica. Correlations of prosome length with salinity were significantly positive for almost all the small copepods. The relationship between chlorophyll concentration and prosome length was complicated for these copepods, but for P. parvus, chlorophyll concentration was also an important affecting factor. Furthermore, investigation needs to be done on food quality for some copepod. These results are essential to estimate the biomass and the production, and to understand these small copepods’ population dynamics in this human-affected bay.

Vertical profiles of zooplankton community structure in Prydz Bay, Antarctica, during the austral summer of 2012/2013

The abundance and vertical distribution of zooplankton in the mesopelagic zone are important to better understand their role in carbon and energy transfer in the Southern Ocean ecosystem. In the austral summer of 2012/2013, in Prydz Bay, Antarctica, the vertical profiles of zooplankton community structures between 0 and 1500xa0m were investigated by multivariate analysis of samples collected using a Hydro-Bios MultiNet (200-µm mesh, 0.5xa0m2 mouth size). Four zooplankton communities belonging to distinct water strata were identified. Groupxa01 contained samples collected from the surface water strata (<100xa0m) of four shelf and neritic stations. Groupxa02 was composed of samples collected from the neritic and shelf regions (<500xa0m) and the upper layers (0–200xa0m) of the oceanic region. Groupxa03 mainly comprised samples collected from the mesopelagic and upper bathypelagic zones (200–1500xa0m) of shelf and oceanic stations north of the shelf break edge. Groupxa04 consisted of samples in the 1000–1500xa0m water stratum of three oceanic stations. The four groups differed more in animal abundance than in species composition. Similarity percentage analysis (SIMPER) showed that zooplankton communities in the upper depth strata (0–200xa0m) had higher abundance and more pronounced dissimilarity within samples than those below 200xa0m. A few species (Metridia gerlachei, Rhincalanus gigas, Alacia spp.) showed significant diel vertical migration based on quadratic regression analysis. Sampling depth was the strongest differentiating factor between samples. These results suggest that depth-related differences in environmental characteristics of water masses, such as temperature and salinity, may have the greatest effect upon community structure.

Lipids and fatty acids in Calanus sinicus during oversummering in the southern Yellow Sea

Over-summering is a crucial period for Calanus sinicus in the southern Yellow Sea, where it is a key member of the zooplankton community. Lipids play an important role in copepod diapause, which is part of their over-summering strategy. We investigated how different fatty acids and lipid classes, including wax esters, changed during over-summering of C. sinicus during three cruises in June and August 2011 and November 2010, corresponding to the pre-, during and post-diapause periods, respectively. Large amounts of lipids were accumulated, mainly wax esters as previously found in C. finmarchicus during its diapause, and most of the storage lipids were used during over-summering. Wax ester polyunsaturated fatty acids (PUFAs) showed the most variation of the fatty acids (FAs), while the percentage composition of FAs in polar lipids was relatively stable. Selective use of wax ester PUFAs has already been shown to play important roles in the winter diapause of Calanus species in other regions, and our FA results show that this is the case for the Yellow Sea Cold Bottom Water (YSCBW) population that diapauses in summer.

Planktonic ciliates in different water masses in open waters near Prydz Bay (East Antarctica) during austral summer, with an emphasis on tintinnid assemblages

Planktonic ciliates are important microzooplankton in pelagic ecosystems. Previous studies in Antarctic waters have only investigated ciliate assemblages in different habitats without considering water masses. In this article, we report the characteristics of ciliate assemblages in different water masses in open waters near Prydz Bay (East Antarctica) during austral summer. Three water masses were identified according to temperature and salinity: Summer Surface Water (SSW), Winter Water (WW), and Circumpolar Deep Water (CDW). SSW was further divided into SSWChl au2009<u20093 (in vivo Chlorophyll au2009>u20093xa0mgxa0m−3) and SSWChl au2009<u20093 (in vivo Chlorophyll au2009<u20093xa0mgxa0m−3). Ciliate abundance and biomass in water masses decreased in the order: SSWu2009>u2009WWu2009>u2009CDW. SSWChl au2009>u20093 had a higher proportion (38.2%) of tintinnids to the total ciliate abundance and larger aloricate ciliates (ciliates in the 10–20xa0µm size class wereu2009<u200915% of the total aloricate ciliate abundance) than in other water masses. WW had a higher proportion (>u200930%) of Southern Ocean endemic tintinnid species in total tintinnid abundance than in other water masses. Each water mass had the following indigenous tintinnid species: SSW, Salpingella sp., Codonellopsis gaussi; WW, Salpingella costata, S. faurei, Cymatocylis affinis/convallaria forma drygalskii, and C. vanhoeffeni. Laackmanniella naviculaefera and C. affinis/convallaria forma cristallina were present at high abundance in both WW and SSWChl au2009>u20093. Upwelling caused discontinuity of the ciliate distribution. Our results will help predict the spatial and temporal variations of ciliate assemblages and other plankton according to the dynamics of water masses in Antarctic waters.

Copepod feeding strategies in the epipelagic to bathypelagic zone of Prydz Bay, Antarctica: an assessment through fatty acids and stable isotopes

Information on the feeding strategies and dietary preferences of copepods from epipelagic to bathypelagic zones of the Southern Ocean are important for understanding the role of zooplankton in carbon and energy transfers through the food web. Using fatty acids (FA) and stable isotopic biomarkers, the present study investigated the feeding strategies and trophic niches of seven dominant copepod species (Calanoides acutus, Calanus propinquus, Metridia gerlachei, Rhincalanus gigas, Paraeuchaeta antarctica, Aetideopsis minor and Bathycalanus richardi) collected from various water strata of Prydz Bay, Antarctica during the austral summer of 2013. Copepods showed species-specific and depth-related differences in FA biomarkers and stable isotopic values. C. acutus and C. propinquus had the largest content of long-chain monounsaturated FA, while M. gerlachei had the smallest FA content (approximately 40xa0mgxa0g−1 dry weight) and the highest 18:1n-9. FA of R. gigas were dominated by short- and medium-length carbon chains. The species P. antarctica and meso- and bathypelagic species A. minor and B. richardi showed relatively higher levels of carnivorous FA ratios and δ15N values. Higher δ15N values in M. gerlachei and P. antarctica dwelled in the mesopelagic and bathypelagic zone indicated the high diversity of feeding strategies of these copepods responding to the changing food availability. The flexible feeding strategies of copepods could enable them to utilise different ecological niches and minimise inter- and intra-specific competition in the Prydz Bay.

Effects of nutrient limitations on three species of zooplankton

Nutrient imbalance—a mismatch in nutrient ratios between the available food supply and the demands of consumers—has the potential to be transported up food chains, exposing zooplankton to nutrient limitations. In this study, the response of Calanus sinicus (copepod), Moina mongolica (cladocera), and Brachionus plicatilis (rotifer) to nutrient-limited (no-limited, P-limited, and N-limited) food were evaluated from the perspective of growth, reproduction, and stoichiometric homoeostasis. The results indicated that the growth of three species was suppressed under nutrient-limited (especially P-limited) conditions. However, the effect of nutrient limitations on their reproduction was species-specific. For C. sinicus, the dietary UFA (unsaturated fatty acid) as a major phospholipid component affected their egg production and total FA supporting energy promoted the hatchability of eggs. Furthermore, excess carbon in the diet promoted egg production but reduced hatching success. For M. mongolica, nutritional (P and UFA) and energy (total FA) support affected their fecundity. B. plicatilis fecundity exhibited the same pattern of growth (no-limited>N-limited>P-limited). In terms of stoichiometric homeostasis, B. plicatilis’s elemental compositions were less likely to be affected by nutrient limitations than M. mongolica. We suggest that the effects of nutrient imbalances could potentially become an evolutionary force affecting ecosystem structure and stability in eutrophic waters.