The seahorse genome and the evolution of its specialized morphology.

Seahorses have a specialized morphology that includes a toothless tubular mouth, a body covered with bony plates, a male brood pouch, and the absence of caudal and pelvic fins. Here we report the sequencing and de novo assembly of the genome of the tiger tail seahorse, Hippocampus comes. Comparative genomic analysis identifies higher protein and nucleotide evolutionary rates in H. comes compared with other teleost fish genomes. We identified an astacin metalloprotease gene family that has undergone expansion and is highly expressed in the male brood pouch. We also find that the H. comes genome lacks enamel matrix protein-coding proline/glutamine-rich secretory calcium-binding phosphoprotein genes, which might have led to the loss of mineralized teeth. tbx4, a regulator of hindlimb development, is also not found in H. comes genome. Knockout of tbx4 in zebrafish showed a 'pelvic fin-loss' phenotype similar to that of seahorses.

Cryptophyte farming by symbiotic ciliate host detected in situ.

Protist-alga symbiosis is widespread in the ocean, but its characteristics and function in situ remain largely unexplored. Here we report the symbiosis of the ciliate Mesodinium rubrum with cryptophyte cells during a red-tide bloom in Long Island Sound. In contrast to the current notion that Mesodinium retains cryptophyte chloroplasts or organelles, our multiapproach analyses reveal that in this bloom the endosymbiotic Teleaulax amphioxeia cells were intact and expressing genes of membrane transporters, nucleus-to-cytoplasm RNA transporters, and all major metabolic pathways. Among the most highly expressed were ammonium transporters in both organisms, indicating cooperative acquisition of ammonium as a major N nutrient, and genes for photosynthesis and cell division in the cryptophyte, showing active population proliferation of the endosymbiont. We posit this as a "Mesodinium-farming-Teleaulax" relationship, a model of protist-alga symbiosis worth further investigation by metatranscriptomic technology.

Uptake and subcellular distribution of aluminum in a marine diatom.

Aluminum (Al) is widespread in the environment including the ocean. The effects of Al on marine organisms have attracted more and more attention in recent years. However, the mechanisms of uptake of Al by marine organisms and the subcellular distribution of Al once assimilated are unknown. Here we report the uptake and subcellular distribution of Al in a marine diatom Thalassiosira weissflogii. Short-term (< 120 min) uptake experiments showed that the Al uptake rate by the diatom was 0.033 ±â€¯0.013 fmol-1 cell-1 min-1 (internalization flux normalized to the exposure Al concentration of 2 µM = 0.034 ±â€¯0.013 nmol m-2 min-1 nM-1). Subcellular fractionation experiments showed that the internalized Al was partitioned to subcellular components in the following order: granules (69 ±â€¯5%) > debris (17 ±â€¯4%) > organelles (12 ±â€¯2%) > heat-stable peptides (HSP) (~2%) > heat-denaturable proteins (HDP) (< 1%), indicating that the majority of intracellular Al was detoxified and stored in inorganic forms. The subcellular distribution of Al in the diatom is different from that of Al in freshwater green algae, in which most of the internalized Al is partitioned to organelles. We also evaluated an artificial seawater-based EDTA rinse solution to remove Al adsorbed on the diatom cell surface. Overall, our study provides new information to understand the mechanisms of uptake of Al by marine diatoms, and the mechanisms responsible for the biological effects (both toxic and beneficial) of Al on the growth of marine phytoplankton, especially diatoms.

Is phosphorus a limiting factor to regulate the growth of phytoplankton in Daya Bay, northern South China Sea: a mesocosm experiment.

Previous field investigations implied a potential phosphorus (P)-limitation on the growth of phytoplankton in Daya Bay, a mesotrophic bay in the northern South China Sea. Using a total of 15 mesocosms (3 × 3 × 1.5 m, with ~10.8 m3 natural seawater containing phytoplankton assemblages for each), we found P-enrichment caused no obvious effect on phytoplankton (Chl a) growth across 8-day's cultivation in neither winter nor summer, while nitrogen (N)-enrichment greatly increased Chl a in both seasons. N plus P-enrichment further increased Chl a content. The N- or N plus P-enrichments increased the allocation of nano-Chl a but decreased micro-Chl a in most cases, with no obvious effect by P-alone. Coincided with nutrients effect on Chl a content, N- or N plus P-enrichments significantly enhanced the maximum photochemical quantum yield of Photosystem II (FV/FM) and maximum relative electron transport rate (rETRmax), but declined the non-photochemical quenching (NPQ), as well as the threshold for light saturation of electron transport (EK); again, P-enrichment had no significant effect. Moreover, the absorption cross section for PSII photochemistry (σPSII) and electron transport efficiency (α) increased due to N- or N plus P-enrichments, indicating the increased nutrients enhance the light utilization efficiency through promoting PSII light harvesting ability, and thus to enhance phytoplankton growth. Our findings indicate that N- or N plus P-enrichments rigorously fuel phytoplankton blooms regardless of N:P ratios, making a note of caution on the expected P-deficiency or P-limitation on the basis of Redfield N:P ratios in Daya Bay.

Bacterial growth efficiency in a partly eutrophicated bay of South China Sea: Implication for anthropogenic impacts and potential hypoxia events.

Bacterial metabolism plays a dual role [bacterial production (BP) and bacterial respiration (BR)] in the aquatic ecosystem and potentially leads to hypoxia in the coastal eutrophic area. Bacterial growth efficiency (BGE) is an important index showing the contribution of bacterial metabolism to marine biological production and carbon budget in the pelagic ecosystem. In this study, the spatial and seasonal variety as well as diurnal variation dynamics of BGE and associated ecological characteristics were investigated in a partly eutrophicated subtropical bay (the Daya Bay) located in the northern South China Sea. Furthermore, the relationship between bacterial metabolism and potential hypoxia event was analyzed. The average BGE was 0.14 and 0.22 in summer and winter, respectively, which was lower than the mean value ever reported in other coastal and estuarine waters. The diurnal variations of BGE and BP were widely fluctuated in the Daya Bay, with approximately 3-8 fold variation of BP and 2-3 fold variation of BR in different seasons, suggesting the importance of short-term ecological dynamics on evaluating the long-term ecological processes in the coastal waters. BR was the predominant contributor to the bacterial carbon demand; however, the variation of BGE was controlled by BP in both seasons. BGE was always high in the near-shore waters with higher eutrophic level and more active BP and BR. The bacterial metabolism could deplete dissolved oxygen (DO) in the Daya bay within about 9 days when the water body was enclosed and photosynthesis was prohibited. Therefore, low DO concentration and potential hypoxia was more likely to be found in the near-shore waters of the Daya Bay in summer, since the water was stratified and enclosed with poor water exchange capacity in this area. While in winter, hypoxia seldom occurred due to vertical mixing throughout the water column. Further biological-physical coupling research is recommended to find out the detailed formation mechanism of hypoxia in the bay, and to predict the potential hypoxia events and their environmental impacts in the future.

Moringa oleifera Leaf Powder as New Source of Protein-Based Feedstuff Improves Growth Performance and Cecal Microbial Diversity of Broiler Chicken.

Currently, the lack of protein source feed has become a pressing issue. Moringa oleifera leaf powder (MOLP) has good potential for the development of protein-derived feeds due to its good protein quality and abundance, but little is known about its effects on broiler growth performance and cecal microbiota. In this study, the chickens were fed different rates of MOLP (1%, 3%, 5%, 7%, and 9%) instead of the rape seed cake, and the effects of different levels of MOLP on growth performance, carcass characteristics, and cecal microbiota of the broilers were evaluated at two different growth stages (day 28 and day 56). In terms of growth performance, the best results were obtained at the 3% MOLP level in the early stages (p < 0.05). In terms of carcass characteristics, in the early stage, the level of 5% MOLP had the best effect; in the later stage, 5% MOLP also had the best effect. In terms of cecal microbial changes, the alpha diversity analysis revealed that 5% MOLP enhanced the richness and diversity of broiler intestinal flora. At the phylum level, the addition of 5% MOLP adjusted the relative abundance of Firmicutes and Bacteroidetes to a level close to that of the A1 group on day 28, while 5% MOLP significantly reduced the relative abundance of Bacteroidetes (p < 0.05) compared to the A2 group on day 56, and the relative abundance of Firmicutes was still higher in the D2 group than in the A2 group (p < 0.05). At the genus level, MOLP addition consistently and significantly increased the relative abundance of Bacteroides (p < 0.05), except for 3% on day 28 and 1% on day 56. For Oscillospira, increasing MOLP levels in the pre- and post-period resulted in a significant decrease in the relative abundance of Oscillospira (p < 0.05). In conclusion, MOLP helps to enhance growth performance and carcass characteristics and improve the cecal microbial structure of broilers. The recommended rate of MOLP addition for broilers is 5% in both the early and late stages.

Higher-order cross-correlation-based Doppler optical coherence tomography.

A method based on higher-order cross-correlation is proposed to fetch the Doppler information on flow velocity within areas under low signal-to-noise ratio (SNR) by spectral domain optical coherence tomography. The proposed method is theoretically developed and validated by measurement of a moving mirror with known velocities. Standard deviations of flow velocities of the mirror under different SNRs are determined by the proposed method and compared with those by the modified phase-resolved method. Measurement of flowing particles within a glass capillary is also conducted, and Doppler flow velocity maps of the glass capillary are reconstructed by both methods. All experimental results demonstrate that the proposed method can significantly suppress noise, thus rendering it suitable for flow measurement under low SNR cases.

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution.

Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses' worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring "bony spines" adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.

Two functionally distinct ciliates dwelling in Acropora corals in the South China Sea near Sanya, Hainan Province, China.

We detected and characterized two distinct scuticociliate ciliates inside Acropora corals in the South China Sea. One, voraciously foraging on Symbiodinium, resembled the brown band disease of ciliates. The other, which is closely related to Paranophrys magna, grazed on detritus instead of Symbiodinium. These two ciliates may serve contrasting functions (competitor versus "cleaner") in the coral-ciliate-Symbiodinium triangular relationship.

Comparative genomics reveal shared genomic changes in syngnathid fishes and signatures of genetic convergence with placental mammals.

Syngnathids (seahorses, pipefishes and seadragons) exhibit an array of morphological innovations including loss of pelvic fins, a toothless tubular mouth and male pregnancy. They comprise two subfamilies: Syngnathinae and Nerophinae. Genomes of three Syngnathinae members have been analyzed previously. In this study, we have sequenced the genome of a Nerophinae member, the Manado pipefish (Microphis manadensis), which has a semi-enclosed brood pouch. Comparative genomic analysis revealed that the molecular evolutionary rate of the four syngnathids is higher than that of other teleosts. The loss of all but one P/Q-rich SCPP gene in the syngnathids suggests a role for the lost genes in dentin and enameloid formation in teleosts. Genome-wide comparison identified a set of 118 genes with parallel identical amino acid substitutions in syngnathids and placental mammals. Association of some of these genes with placental and embryonic development in mammals suggests a role for them in syngnathid pregnancy.

Spatial and temporal dynamics of phytoplankton and bacterioplankton biomass in Sanya Bay, northern South China Sea.

The composition of phytoplankton and the dynamics of phytoplankton and bacterioplankton biomass (PB and BB, respectively) of Sanya Bay, South China Sea, were determined. A total of 168 species (67 genera) phytoplankton were identified, including Bacillariophyta (diatom, 128 species), Pyrrophyta (35 species), Cyanophyta (3 species), and Chrysophyta (2 species). Annual average abundance of phytoplankton was 1.2 x 10(7) cells/m3, with the highest abundance in autumn, and the lowest in summer. Annual average diversity index (H') and evenness (J) values were 3.96 and 0.70, respectively. Average chlorophyll-a was 2.5 mg/m3, and the average PB was 124 mg C/m3, with the highest value in autumn. Surface PB was higher than the bottom, except for summer. Annual mean bacterioplankton abundance and BB were 6.9 x 10(11) cells/m3 and 13.8 mg C/m3, respectively. The highest BB was found in summer, followed by winter, spring, and autumn. Surface BB was higher than bottom all year round. The spatial distribution patterns of PB and BB were very similar with the highest biomass in the estuary, and decreased seaward, primarily due to the terrestrial input from the Sanya River and influx of oceanic water. The main factor influencing PB and BB was dissolved inorganic nitrogen (DIN). Other factors such as temperature, which is above 22 degrees C throughout the year, had a negligible impact. The correlation between BB and PB was significant (P < 0.01). The annual average ratio of BB/PB was 0.12 (0.06-0.15). Phytoplankton primary production was one of the most important factors in controlling the distribution of bacterioplankton.

Flourishing deep-sea AAP bacteria detected by flow cytometric sorting and molecular analysis.

Pigmented bacteria cells, including aerobic anoxygenic phototrophic (AAP) bacteria, contribute significantly to secondary production and aquatic carbon cycling but their distribution in the deep sea is still not well understood, especially in the South China Sea. In this study, microscopic, flow cytometric, and molecular analyses were carried out to investigate the abundance and diversity of AAP bacteria at seven stations in the South China Sea. The results revealed the existence of bacteriochlorophyll-containing bacteria below 500 m from two of seven stations. Flow cytometric analysis detected red and infra-red fluorescence under blue (488 nm) light excitation from fluorescent cells. Blue light-excited red fluorescence of these cells from the 1000 m depth at station E403 were verified using epifluorescence microscopy. Based on fluorescence and side scatter features, fluorescent cells were sorted and subjected to molecular analysis. DNA was extracted from these sorted cells from both stations for PCR amplification using 16S rDNA primers. Sequencing of the PCR products showed that the sorted cells from the 1000 m depth at station E403 belonged to the genus Porphyrobacter. The cell population sorted from 500 m at station E703 contained Sphingomonas and a Methylobacterium-like taxon. All these three taxa belong to aerobic anoxygenic phototrophic alpha-proteobacteria. Using flow cytometric analysis, we found that the abundance of Porphyrobacter sp. at 1000 m was 2.71-2.95×104 cells mL-1 whereas cell counts of Sphingomonas sp. and Methylobacterium at 500 m were about 3.75-4.12×105 cells mL-1. These results indicate that albeit not ubiquitous in deep water, bacteriochlorophyll-containing bacteria can be abundant in the deep-sea aphotic zone.

Significantly depleted 15N in suspended particulate organic matter indicating a strong influence of sewage loading in Daya Bay, China.

The influence of anthropogenic nutrient loading on the stable isotopic signatures (δ13C and δ15N) in the suspended particulate organic matter (SPOM) is still not fully understood. Water quality and the values of δ13C and δ15N in the SPOM were investigated in the surface water of Daya Bay during the spring of 2016 and 2017. The results indicated that the Dan'ao River is the main point source of nutrient pollution in Daya Bay. The δ15NPOM was very low in the Dan'ao River. The distribution pattern for this parameter in Daya Bay was determined chiefly by Dan'ao River discharge. Variations in δ15NPOM were ascribed mostly to the input of 15N-depleted DIN assimilated by the estuarine phytoplankton in Daya Bay. Extremely high NH4+ level in the river discharge should be responsible for the low δ15NPOM in the river water. The distribution of δ13CPOM in Daya Bay was regulated mainly by the input of 13C-depleted riverine SPOM. In the present study, the influence of phytoplankton growth on the δ13CPOM was not significant. Moreover, episodic rain events significantly influenced the temporal and spatial variations in water quality and isotopic signature in Daya Bay. The relatively depleted SPOM 15N in 2016 may have been correlated with the strong El Niño events of 2015-2016. Increases in the frequency and volume of rainfall associated with El Niño may have enhanced nutrient loading and the risk of algal red tide in the Daya Bay. In general, significant 15N depletion in SPOM could be the characteristic of hypereutrophic riverine waters. This study suggested that δ15NPOM may be an effective indicator of the strength of riverine nutrient loading in Daya Bay.

Phytoplankton responses to aluminum enrichment in the South China Sea.

Compared to extensive studies reporting the aluminum (Al) toxicity to terrestrial plants and freshwater organisms, very little is known about how marine phytoplankton responds to Al in the field. Here we report the marine phytoplankton responses to Al enrichment in the South China Sea (SCS) using on-deck bottle incubation experiments during eight cruises from May 2010 to November 2013. Generally, Al addition alone enhanced the growth of diatom and Trichodesmium, and nitrogen fixation, but it inhibited the growth of dinoflagellates and Synechococcus. Nevertheless, Al addition alone did not influence the chlorophyll a concentration of the entire phytoplankton assemblages. By adding nitrate and phosphate simultaneously, Al enrichment led to substantial increases in chlorophyll a concentration (especially that of the picophytoplankton<3µm), and cell abundances of diatom and photosynthetic picoeukaryotes. These results indicate varied responses of phytoplankton in different size fractions and taxonomic groups to Al enrichment. Further, by simultaneously adding different macronutrients and/or sufficient trace metals including iron, we found that the phytoplankton responses to Al enrichment were relevant to nutrients coexisting in the environment. Al enrichment may give some phytoplankton a competitive edge over using nutrients, especially the limited ones. The possible influences of Al on the competitors and grazers (predators) of some phytoplankton might indirectly contribute to the positive responses of the phytoplankton to Al enrichment. Our results indicate that Al may influence marine carbon cycle by impacting phytoplankton growth and structure in natural seawater.

Subsurface low dissolved oxygen occurred at fresh- and saline-water intersection of the Pearl River estuary during the summer period.

Estuarine oxygen depletion is one of the worldwide problems, which is caused by the freshwater-input-derived severe stratification and high nutrients loading. In this study we presented the horizontal and vertical distributions of dissolved oxygen (DO) in the Pearl River estuary, together with temperature, salinity, chlorophyll a concentration and heterotrophic bacteria abundance obtained from two cruises during the summer (wet) and winter (dry) periods of 2015. In surface water, the DO level in the summer period was lower and varied greater, as compared to the winter period. The DO remained unsaturated in the summer period if salinity is <12 and saturated if salinity is >12; while in the winter period it remained saturated throughout the estuary. In subsurface (>5m) water, the DO level varied from 0.71 to 6.65mgL-1 and from 6.58 to 8.20mgL-1 in the summer and winter periods, respectively. Particularly, we observed an area of ~1500km2 low DO zone in the subsurface water with a threshold of 4mgDOL-1 during this summer period, that located at the fresh- and saline-water intersection where is characterized with severe stratification and high heterotrophic bacteria abundance. In addition, our results indicate that spatial DO variability in surface water was contributed differently by biological and physio-chemical variables in the summer and winter periods, respectively.

Molecular mechanism of glucose-6-phosphate utilization in the dinoflagellate Karenia mikimotoi.

Phosphorus (P) is an essential nutrient for marine phytoplankton as for other living organisms, and the preferred form, dissolved inorganic phosphate (DIP), is often quickly depleted in the sunlit layer of the ocean. Phytoplankton have developed mechanisms to utilize organic forms of P (DOP). Hydrolysis of DOP to release DIP by alkaline phosphatase is believed to be the most common mechanism of DOP utilization. Little effort has been made, however, to understand other potential molecular mechanisms of utilizing different types of DOP. This study investigated the bioavailability of glucose-6-phosphate (G6P) and its underlying molecular mechanism in the dinoflagellate Karenia mikimotoi. Suppression Subtraction Hybridization (SSH) was used to identify genes up- and down-regulated during G6P utilization compared to DIP condition. The results showed that G6P supported the growth and yield of K. mikimotoi as efficiently as DIP. Neither DIP release nor AP activity was detected in the cultures grown in G6P medium, however, suggesting direct uptake of G6P. SSH analysis and RT-qPCR results showed evidence of metabolic modifications, particularly that mitochondrial ATP synthase f1gamma subunit and thioredoxin reductase were up-regulated while diphosphatase and pyrophosphatase were down-regulated in the G6P cultures. All the results indicate that K. mikimotoi has developed a mechanism other than alkaline phosphatase to utilize G6P.

Characteristics of picoplankton abundances during a Thalassiosira diporocyclus bloom in the Taiwan Bank in late winter.

To understand the variations of picoplankton (Prochlorococcus, Synechococcus, picoeukaryotes, and heterotrophic bacteria) abundances during diatom bloom, the distribution of picoplankton in the Taiwan Bank, South China Sea was investigated using flow cytometry during a Thalassiosira diporocyclus bloom in March 2016. The results indicated an abrupt abundance decrease for Prochlorococcus, Synechococcus, and picoeukaryotes within the bloom area while the abundance of heterotrophic bacteria showed no significant difference between the bloom and non-bloom areas. We found two sub-groups of heterotrophic bacteria: high- and low-nucleic acid content (HNA and LNA) bacteria with HNA dominated in the bloom area whereas LNA dominated in the non-bloom area. Among the picoplankton components, HNA represented the highest (61.1%) carbon biomass in the bloom area while picoeukaryotes represented the highest (37.6%) in the non-bloom area. Our findings implied that heterotrophic bacteria, especially HNA, played an essential role during the diatom bloom.

Spatial distributions of δ13C, δ15N and C/N ratios in suspended particulate organic matter of a bay under serious anthropogenic influences: Daya Bay, China.

Stable isotopic signatures (δ13C and δ15N) and C/N ratios of suspended particulate organic matter (POM) were investigated from the surface water of Daya Bay during summer and winter of 2015. The relatively high δ13CPOM values suggested the input of 13C-depleted terrigenous organic matter was low in Daya Bay. There were significant correlations between δ13CPOM values and chlorophyll a concentrations both during summer and winter, suggesting the δ13CPOM values were mainly controlled by the phytoplankton biomass in the surface water. The distribution of δ15NPOM values was more complicated than that of δ13CPOM and displayed low values in the outer bay and the Dan'ao River estuary. 15N-depleted ammonia originating from industrial wastewater might have strongly influenced the water quality and stable isotopic signatures of POM near the Dan'ao River estuary. The δ13CPOM and δ15NPOM values strongly reflect the influences of anthropogenic activity and eutrophication in Daya Bay.

Secretion of biologically active human epidermal growth factor from Escherichia coli using Yersinia pestis Caf1 signal peptide.

BACKGROUND AND PURPOSE: The Caf1 secretion pathway of Yersinia pestis is one of the most well-characterized export machineries. To facilitate the secretion of human epidermal growth factor (hEGF) in Escherichia coli, a DNA fragment containing the synthetic gene for hEGF was joined to a sequence encoding the signal peptide of Yersinia pestis Caf1 protein. METHODS: The gene for hEGF was synthesized by overlapping polymerase chain reaction technique and was placed under the control of the caf1 gene promoter in the recombinant plasmid pHL401 which was used to transfect E. coli BL-21 for production of hEGF. The biological function of recombinant hEGF was measured by estimating its ability to stimulate the proliferation of human embryonic kidney-293 cells. RESULTS: The results indicated that the expressed hybrid protein was processed during the secretion process. The majority of the mature hEGF was recovered from the periplasm and medium fractions, with a small amount of the expressed hEGF deposited in the cytoplasm. Furthermore, it was found that the cell proliferation was enhanced by the recombinant hEGF. CONCLUSION: These results suggested that the recombinant hEGF was successfully secreted through the inner membrane of cells into the periplasm and then through the outer membrane into the medium via the action of the signal peptide of Y. pestis Caf1 in E. coli. The mitogenic activity of hEGF in cells was demonstrated.