2019 Vol. 38, No. 2

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Flow modification associated with mangrove trees in a macro-tidal flat, southern China
Chang Yang, Chen Yining, Li Yan
2019, 38(2): 1-10. doi: 10.1007/s13131-018-1163-y
Limited studies have investigated the modification of tidal currents by mangrove trees. In particular, the impacts of mangrove trees on a vertical velocity profile remain unclear. An automatic system is developed to observe the vertical velocity profiles within a mangrove forest composed of artificially introduced Kandelia obovata located on the Ximen Island, the southern Zhejiang Province. The results reveal low flow velocities throughout the vertical profile within the mangrove forest. The vertical profile shows an overall decrease of the velocity with an increasing height above the bed. This pattern is due to the vertical increase of the drag force by the trunks and tree canopies. In addition, the turbulent energy density also varies vertically, corresponding to the vertical structure of the mangrove trees. In comparison with the vertical structure of flows within bare mudflats (semi-logarithmic) and salt marshes (nearly J-shape), the mangrove trees are shown to have a considerable impact on the vertical velocity profile in different ways.
Physical-biogeochemical interactions and potential effects on phytoplankton and Ulva prolifera in the coastal waters off Qingdao (Yellow Sea, China)
Wei Qinsheng, Wang Baodong, Yao Qingzhen, Yu Zhigang, Fu Mingzhu, Sun Junchuan, Xu Bochao, Xie Linping, Xin Ming
2019, 38(2): 11-23. doi: 10.1007/s13131-019-1344-3
In recent years, the spectacular massive green tide of Ulva prolifera has become a recurrent phenomenon appearing every summer in the coastal waters off Qingdao (Yellow Sea, China), attracting the attention of scientists and local government. Based on multidisciplinary data collected during summer and winter, this study focuses on the hydrological characteristics and regional biogeochemical processes in coastal waters off Qingdao. The results show that the boundary of the Yellow Sea Cold Water Mass (YSCWM) can reach the Qingdao coastal region in summer and is locally raised to the upper layers to form coastal upwelling beyond tidal mixing and favorable wind. The regional summer upwelling off the Qingdao coast effectively enriches the nutrient concentrations in the upper water column and thus promotes growth of phytoplankton but reduces the dissolved oxygen (DO) concentration and pH value in the bottom. The regional summer upwelling off Qingdao coast may facilitate the growth and regional blooming of the U. prolifera that migrate to this region with the southerly wind. Additionally, the effects of the front on the aggregation of U. prolifera may be significant. In winter, the Yellow Sea Warm Current (YSWC) extends and spreads along the offshore region off the Subei Shoal towards the Qingdao coastal sea. This tongue-shaped warm water meets the cold coastal water off Qingdao, which leads to the formation of a physical front. As a consequence, remarkable fronts of nutrient and chlorophyll a (Chl a) also form between the shoreward warm water and the cold coastal water. This study increases the understanding of the interactions between the regional physical, chemical, and biological processes off the Qingdao coast.
Multi-year assessment of paralytic shellfish toxins in hard clam species along the coastline of Jiangsu Province, China
Wang Xinzhi, Wu Hao, Cheng Ying, Wen Hongmei, Liu Rui, Wang Libao, Shan Chenxiao, Chai Chuan
2019, 38(2): 24-33. doi: 10.1007/s13131-019-1347-0
Paralytic shellfish toxins (PSTs) are notorious neurotoxins that threaten public health and food safety worldwide. Although PST monitoring programs have recently been established throughout China, the profiles and variation of PSTs in important commercial clams (e.g., Mactra veneriformis, Ruditapes philippinarum, and Meretrix meretrix) along the Jiangsu Province coastline remain largely unexplored. In this study, a validated hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method was used to examine PST profiles and levels in 540 clam samples from natural production areas along Jiangsu Province coastline during 2014-2016. Although the PST levels (≤ 6.38 μg saxitotoxin equivalents (eq)/kg) were consistently below European Union regulatory limits (≤ 800 μg saxitotoxin eq/kg) during this time period, saxitotoxin, decarbamoylsaxitotoxin, and gonyautoxins 1 and 4 were detected, and nearly 40% of the samples were saxitotoxin-positive. The PST levels also varied significantly by seasons, with peak values observed in May during 2014-2016. This is the first systematic report of PSTs in clams from Jiangsu Province, and additional research and protective measures are needed to ensure the safety of clams harvested in this area.
Grain size characteristics of the carbonate-free fraction of surface sediments from the Southwest Indian Ridge area and its geological significance
Jia Qi, Fan Dejiang, Sun Xiaoxia, Liu Ming, Zhang Wenqiang, Yang Zuosheng
2019, 38(2): 34-43. doi: 10.1007/s13131-018-1273-6
The carbonate-free fraction of 20 surface sediments collected from the ultraslow-spreading Southwest Indian Ridge (SWIR) was studied by grain size analysis and mineralogical analysis with X-ray powder diffraction (XRD), stereo microscopy and scanning electron microscopy (SEM). The characteristics of the carbonate-free fraction of the sediments were obtained, and related influential factors were discussed. The results show that the mean grain size of this fraction is in 1.96Φ-8.19Φ, with poorly sorting and unimodal, bimodal or irregular bimodal distribution patterns. Four grain size end members of the fraction are derived with the End Member Model method. The finest end member EM1 shows a significant contribution of terrigenous materials of the aeolian input and sediment carried by the bottom current. End member EM2 with medium size mainly reflects sediment of a siliceous bio-clast origin. EM3 and EM4 are interpreted as representing the coarser volcanic materials related to bedrock weathering or volcanic activities. Multi-provenance is the dominant factor controlling the grain size pattern of the carbonate-free fraction of the sediments in that area. In addition, sediment transport processes such as the bottom current and wind are the minor factors that influence the grain size distribution of the carbonate-free fraction sediments.
Molecular mechanism of inbreeding effects based on RNA-Seq analysis of the adductor muscle of bay scallop (Argopecten irradians)
Wang Yu, Zhang Shoudu, Zhang Guofan, Cong Rihao, Li Li
2019, 38(2): 44-51. doi: 10.1007/s13131-019-1351-4
Understanding the effects of inbreeding is critical for the long-term viability of shellfish breeding and for understanding inbreeding depression (ID) of the offspring of selfed individuals and full-sib crosses. The bay scallop (Argopecten irradians) is a simultaneous hermaphroditic marine bivalve with distinct male and female gonads and is a species with external fertilization. It is a canonical model invertebrate for analysis of the genetics of ID and evolution of outcrossing mating system. ID in bivalves is well documented with regard to the phenotype and molecular markers aspects, but little is known on how inbreeding affects genome-wide gene expression. Here, we compare the gene expression profiles of adductor muscle of A. irradians lines inbred to F=0.5 with those of its counterpart outbred lines which are originated from the same paternal individual. Inbred and outbred individuals have some differences in growth traits. The shell length and the total weight of inbred scallops are lower than the counterpart of outbred lines. We found that 1 175 genes were up-regulated while 1 390 were down-regulated in inbred lines. Regarding components, differentially expressed genes (DEGs) were concentrated on sarcomeres, contractile filaments, and cell membranes. Among others, whereas regarding their function, the Gene Ontology (GO) was concentrated on transferase, phosphotransferase, peptidase, and others. The DEGs-enriched metabolic pathways mainly belonged to the oxidative phosphorylation pathway and apoptosis pathway. We used another two families to verify our bioinformatic results. The selfed and the outbred family originated from different ancestors, but the selfed family showed obvious ID. By using real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), we verified that DEGs with inbreeding are involved in the oxidative phosphorylation and cell apoptosis pathways, suggesting that inbreeding may affect energy metabolism and homeostasis.
Ecology of Pinnidae (Mollusca: Bivalvia) from the Gulf of Thailand
2019, 38(2): 52-69. doi: 10.1007/s13131-018-1230-4
The ecology of the family Pinnidae was studied by sampling three pinnid species from 36 sampling sites across four different microhabitats in the Gulf of Thailand. The species spatial distributions were mostly uniform, with some populations having random distributions. Species abundances differed between sandy and coral habitats according to non-metric multi-dimension scaling analyses. Although the Gulf of Thailand is a relatively small geographic area, habitats are varied enough to provide variable shell densities. Small islands are important distribution areas, and coral reefs provide both direct and indirect shelter which support high abundances, densities and increased shell size. The highest density was recorded in sand beds within coral reefs. Low density and small shell size in sand beaches might be related to high mortality in shallow water or to adaptations for survival in shallow waters. A clear correlation between sediment composition and species abundance was found in Pinna atropurpurea; abundance increased with the sand content of the sediment. For P. deltodes, abundance increased as the rock fraction of the sediment increased. These results suggest that adaptations in Pinnidae, such as shell size, shell morphology, and the exposure of the shell above the sediment-water interface, are responses for survival in different habitats.
Seasonal size composition and abundance distribution of Euphausia pacifica in relation to environmental factors in the southern Yellow Sea
Zuo Tao, Liu Hui
2019, 38(2): 70-77. doi: 10.1007/s13131-019-1358-x
The seasonal size structure and spatial abundance distributions of Euphausia pacifica populations were investigated in the central part of southern Yellow Sea from August 2009 to May 2010. The abundance and biomass of E. pacifica were higher in spring and summer, and lower in autumn and winter. The mean abundance and biomass (calculated by carbon) were 74.94 ind./m3 and 8.23 mg/m3, respectively. Females with total length (TL) ranging between 10 and 19 mm in summer had a substantial contribution to the population biomass, whereas larvae of TL of 3-7 mm in spring were the main contributor to the population abundance. The sex ratio (female:male) showed a female bias in four seasons. Its value peaked in summer, and then decreased in autumn, spring, and winter successively. Cohort analysis revealed that the length-frequency distribution of E. pacifica could be characterized as one group with large animals (mean TL>12 mm) accompanied by one or two subgroups of small individuals (mean TL<7 mm). Regarding the spatial distribution, juveniles and adults of E. pacifica tend to concentrate in relatively deep water with low temperature (~11℃) and high salinity (>32), whereas its larvae showed more abundance in inshore water with rich chlorophyll a, low salinity (<32), and warm temperature (>11℃), especially in summer and autumn. Associations changed seasonally between stage-specific abundance and environmental factors.
Molecular diversity and biogeography of benthic ciliates in the Bohai Sea and Yellow Sea
LI Guihao, SU Lei, ZHANG Qianqian, ZHANG Xiaoli, GONG Jun
2019, 38(2): 78-86. doi: 10.1007/s13131-018-1236-y
This study explored the molecular diversity and biogeography of benthic ciliates in Chinese marginal seas, the Bohai Sea (BHS), North Yellow Sea (NYS) and South Yellow Sea (SYS). From a previous 18S rRNA gene pyrosequencing dataset of the benthic microeukaryotes, we retrieved the sequences affiliated with phylum Ciliophora and analyzed alpha and beta diversities of ciliate communities. We found that BHS had the highest ciliate operational taxonomic unit (OTU) richness than NYS and SYS, whereas the richness was not significantly different between summer and winter. Among all the measured environmental variables, water depth showed consistently the strongest correlations with alpha diversities. Overall, the class Spirotrichea (mostly Choreotrichia and unassigned lineages within the class) dominated the communities in terms of both relative proportion of sequences (77.0%) and OTU richness (66.5%). OTU-level ciliate community structure was significant different among the three basins, but not between the seasons. Structurally, significant differences in relative proportion among the basins were detected for the class Litostomatea, but not for other classes. Partial Mantel tests demonstrated that water depth difference was more important than geographic and environment distances in shaping the community structure of benthic ciliates in the studied area. About 60% OTUs were not assigned at a class or order level and at least 45% OTUs shared a sequence similarity no more than 97% with the described species, indicating a great potential for ciliate species discovery in the offshore sediments. Compared with previous morphology-based surveys, the spatial pattern of ciliate diversity (decreasing from NYS to SYS) is also identified in the present study. Nevertheless, structurally, the dominant class appeared to be Spirotrichea in the sequencing dataset, which differs from previous morphology-based results (dominance of classes Prostomatea and Karyorelictea in biomass). The potential causes for the discrepancies between molecular and morphological findings are also discussed.
Characterization of an extreme alkaline-stable keratinase from the draft genome of feather-degrading Bacillus sp. JM7 from deep-sea
Jin Min, Chen Chen, He Xiongfei, Zeng Runying
2019, 38(2): 87-95. doi: 10.1007/s13131-019-1350-5
Bacillus sp. JM7, a strain isolated from the deep-sea of the South China Sea, was found to efficiently degrade 79.4% native chicken feather within 30 h. Scanning electron microscopy analysis showed that JM7 strain could gradually degrade feather by modifying the microstructure of feather keratin. A total of 25 protease genes were predicted from the draft genome of JM7 strain, among which a predicted subtilisin-like serine protease (designated as Ker02562) was further characterized for its keratinolytic activity. The recombinant Ker02562 functioned at a wide range of temperatures from 30℃ to 60℃, with an optimum at 40-50℃. Ker02562 was highly active at various pHs ranging from 5.0 to 13.0, with a maximum activity observed at pH 7.0-9.0. Remarkably, recombinant Ker02562 was stable in extreme alkaline environments (pH 10-13), which was much better than most other reported keratinases. Collectively, these favorable properties could make Bacillus sp. JM7 and Ker02562 attractive to be applied in the detergent formulation and feather bioconversion.
Overexpression and characterization of a thermostable β-agarase producing neoagarotetraose from a marine isolate Microbulbifer sp. AG1
ZHU Yanbing, GAO He, LI Hebin, NI Hui, JIANG Zedong, LI Lijun, XIAO Anfeng
2019, 38(2): 96-106. doi: 10.1007/s13131-019-1349-y
An agarase gene containing 1 302 bp was cloned from Microbulbifer sp. AG1. It encoded a mature protein of 413 amino acids plus a 20-residue signal peptide. The recombinant enzyme without the signal peptide was expressed and purified from Escherichia coli BL21 (DE3). When agarose was used as a substrate, the optimal temperature and pH for the enzyme were 60℃ and 7.5, respectively. The recombinant agarase showed excellent thermostability with 67% and 19% of residual activities after incubation at 50℃ and 60℃ for 1 h, respectively. Except SDS, the recombinant agarase had a relatively good resistance against the detected inhibitors, detergents and urea denaturant. Thin layer chromatography analysis and enzyme assay using p-nitrophenyl-α/β-D-galactopyranoside revealed that the recombinant agarase was a β-agarase that degraded agarose into neoagarotetraose as the main end product. The enzymatic hydrolysis products with different degree of polymerization exhibited the antioxidant activities.
Identification and characterization of a delta-12 fatty acid desaturase gene from marine microalgae Isochrysis galbana
Han Xiaotian, Wang Shuai, Zheng Li, Liu Wanshun
2019, 38(2): 107-113. doi: 10.1007/s13131-019-1354-1
The cDNA of the delta-12 fatty acid desaturase gene, IgFAD2, was cloned from the marine microalgae Isochrysis galbana, a species capable of producing docosahexaenoic acid. Sequence analysis indicated that the open reading frame measured a length of 1 158 bp and encoded 386 amino acids with a predicted molecular weight of 42.8 kDa and an isoelectric point of 9.2. Computational analysis of the protein sequence of IgFAD2 showed typical features of membrane-bound desaturase such as three conserved histidine boxes along with four membrane-spanning regions that were universally present among plant desaturases. Quantitative real-time PCR results showed that the abundance of IgFAD2 transcript was significantly upregulated under different environmental stresses including low temperature (15℃), high salinity (salinity of 62 and 93), and nitrogen starvation (220 μmol/L). Heterologous expression indicated that yeast cells transformed with a plasmid construct containing IgFAD2 could convert endogenous oleic acid (18:1Δ9, OA) into linoleic acid (18:2Δ9, 12, LA). These findings confirm that I. galbana IgFAD2 plays important roles in the biosynthetic pathways of unsaturated fatty acids.
Estimating the macrobenthic species richness with an optimized sampling design in the intertidal zone of Changjiang Estuary
Zhang Tingting, Zhao Feng, Wang Sikai, Zhang Tao, Liu Jianyi, Gao Yu, Zhuang Ping
2019, 38(2): 114-124. doi: 10.1007/s13131-019-1352-3
It is a challenge in the field sampling to face conflict between the statistical requirements and the logistical constraints when explicitly estimating the macrobenthos species richness in the heterogeneous intertidal wetlands. To solve this problem, this study tried to design an optimal, efficient and practical sampling strategy by comprehensively focusing on the three main parts of the entire process (to optimize the sampling method, to determine the minimum sampling effort and to explore the proper sampling interval) in a typical intertidal wetland of the Changjiang (Yangtze) Estuary, China. Transect sampling was selected and optimized by stratification based on pronounced habitat types (tidal flat, tidal creek, salt marsh vegetation). This type of sampling is also termed within-transect stratification sampling. The optimal sampling intervals and the minimum sample effort were determined by two beneficial numerical methods:Monte Carlo simulations and accumulative species curves. The results show that the within-transect stratification sampling with typical habitat types was effective for encompassing 81% of the species, suggesting that this type of sampling design can largely reduce the sampling effort and labor. The optimal sampling intervals and minimum sampling efforts for three habitats were determined:sampling effort must exceed 1.8 m2 by 10 m intervals in the salt marsh vegetation, 2 m2 by 10 m intervals in the tidal flat, and 3 m2 by 1 m intervals in the tidal creek habitat. It was suggested that the differences were influenced by the mobility range of the dominant species and the habitats' physical differences (e.g., tidal water, substrate, vegetation cover). The optimized sampling strategy could provide good precision in the richness estimation of macrobenthos and balance the sampling effort. Moreover, the conclusions presented here provide a reference for recommendations to consider before macrobenthic surveys take place in estuarine wetlands. The sampling strategy, focusing on the three key parts of the sampling design, had a good operational effect and could be used as a guide for field sampling for habitat management or ecosystem assessment.