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Bioprospection of marine actinomycetes: recent advances, challenges and future perspectives
Swati Sharma, Abhay B. Fulke, Asha Chaubey
2019, 38(6): 1-17. doi: 10.1007/s1313-018-1340-z
Abstract(59) FullText HTML(11) FullText PDF(4)
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In exploring new sources for economically important products, marine environment draws particular attention because of its remarkable diversity and extreme conditions; it is known to produce metabolic products of great value. It represents untapped source for the discovery of novel secondary metabolites with varying potential such as antibiotic, anti-tumor, antifouling and cytotoxic properties. Marine actinomycetes distributed throughout the marine environment from shallow to deep sea sediments have proved to be a finest source for this discovery. Secondary metabolites derived from marine actinomycetes have proved their worth in industries based on the research on their properties and wide range applications. Spotlight of the review is range of marine based actinomycetes products and significant research in this field. This shows the capability of marine actinomycetes as bioactive metabolite producers. Additionally, the present review addresses some effective and novel approaches of procuring marine microbial compounds utilizing the latest screening strategies of drug discovery from which traditional resources such as marine actinobacteria has decreased due to declining yields. The aim is in the context of promoting fruitful and profitable results in the near future. The recent surfacing of new technologies for bioprospection of marine actinomycetes are very promising, resulting in high quality value added products, and will be de?ning a new era for bioactive compounds with medical and biotechnological applications.
Fishery biology of whitespotted conger Conger myriaster (Brevoort, 1856) in the Yellow Sea and East China Sea
Xiuxia MU, Chi ZHANG, Ying XUE, Chongliang ZHANG, Binduo XU, Yiping REN
2019, 38(6): 18-24. doi: 10.1007/s13131-018-1271-8
Abstract(42) FullText HTML(14) FullText PDF(1)
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Whitespotted conger Conger myriaster is a commercially important species in the seas around China, Korea and Japan. The coastal waters of China serve as an important feeding ground for congers, but the spatio-temporal variations in the fishery and biological characteristics of the population have been rarely evaluated and less well understood in this area. We studied the growth, spawning and feeding characteristics of C. myriaster on the basis of samples collected from October 2016 to April 2017 in the Yellow Sea and East China Sea. A total of 529 specimens were collected, with ages ranging from 1 to 6 years and total length ranging from 132 mm to 834 mm. The parameters of von Bertalanffy growth equation L and k were 1 026 mm and 0.226 a–1, respectively; the sex ratio was 88:0 (female: male) in the East China Sea and 2.67:1 in the South Yellow Sea; the development stage of ovary ranged from peri-nucleolus stage to secondary yolk globule stage, and the testis of two males was at mid-meiotic stage; Crustacean was the major prey for conger of small length, and food source shift to fish with somatic growth. The results showed substantial differences from previous studies in Japan and Korean waters, as well as from China seas in the 1980s, suggesting potential spatiotemporal changes in the biological characteristics of C. myriaster. This study may improve current understanding of the fishery biology of C. myriaster in the Yellow Sea and East China Sea.
Mitochondrial genome of Chthamalus challengeri (Crustacea: Sessilia): gene order comparison within Chthamalidae and phylogenetic consideration within Balanomorpha
Panpan Chen, Jun Song, Xin Shen, Yuefeng Cai, Ka Hou Chu, Yongqi Li, Mei Tian
2019, 38(6): 25-31. doi: 10.1007/s13131-019-1355-0
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Acorn barnacles are important model species in researches on intertidal ecology, larval development and bio-fouling. At present, with the development of mitochondrial genomics, it is helpful to understand the phylogenetic relationship from the mitogenomic level. The complete mitochondrial genome of Chthamalus challengeri was presented. The genome is a circular molecule of 15 358 bp. Compared with other species in Balanomorpha, the non-coding region is longer, while the length of the genes is similar to the other species. The overall A+T content of the mitochondrial genome of C. challengeri is 70.5%. There are variations of initiation and stop codons in the known Balanomorpha mitochondrial genomes. The C. challengeri and C. antennatus within the same genus share the identical gene arrangement. However, the gene arrangement of different genera in Chthamalidae is different, as there is a translocation between two tRNA genes and an inversion involving a large gene block. In particular, both srRNA and lrRNA of the two species in Chthamalus are encoded in the heavy strand, differing from the former Balanomorpha species. The topology and gene arrangement in Chthamalidae support each other. Phylogenetic analysis indicates that the Chthamalidae is monophyletic, while the Balanidae and Archaeobalanidae are polyphyletic.
Different vertical distribution of zooplankton community between North Pacific Subtropical Gyre and Western Pacific Warm Pool: its implication to carbon flux
Dong SUN, Dongsheng ZHANG, Ruiyan ZHANG, Chunsheng WANG
2019, 38(6): 32-45. doi: 10.1007/s13131-018-1237-x
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The mesozooplankton in both epipelagic and mesopelagic zones is essentially important for the study of ecosystem and biological carbon pump. Previous studies showed that the diel vertical migration (DVM) pattern of mesozooplankton varied among ecosystems. However, that pattern was largely unknown in the Western Pacific Warm Pool (WPWP). The vertical distribution, DVM and community structure of mesozooplankton from the surface to 1 000 m were compared at Stas JL7K (WPWP) and MA (North Pacific Subtropical Gyre, NPSG). Two sites showed similarly low biomass in both epipelagic and mesopelagic zones, which were in accordance with oligotrophic conditions of these two ecosystems. Stronger DVM (night/day ratio) was found at JL7K (1.31) than that at MA (1.09) on surface 0–100 m, and an obvious night increase of mesopelagic biomass was observed at JL7K, which was probably due to migrators from bathypelagic zone. Active carbon flux by DVM of zooplankton was estimated to be 0.23 mmol/(m2·d) at JL7K and 0.16 mmol/(m2·d) at MA. The community structure analysis showed that calanoid copepods, cnidarians and appendicularians were the main contributors to DVM of mesozooplankton at both sites. We also compared the present result with previous studies of the two ecosystems, and suggested that the DVM of mesozooplankton was more homogeneous within the WPWP and more variable within the NPSG, though both ecosystems showed typically extremely oligotrophic conditions. The different diel vertical migration strength of mesozooplankton between NPSG and WPWP implied different efficiency of carbon pump in these two ecosystems.
mRNA expression of CYP4 in marine polychaete Marphysa sanguinea in response to benzo[a]pyrene
Wanjuan Li, Huan Zhao, Fuyang Ba, Shaojuan Li, Xiupeng Sun, Dazuo Yang, Yibing Zhou
2019, 38(6): 46-53. doi: 10.1007/s13131-019-1362-1
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Rapid amplification of cDNA ends (RACE) and real-time polymerase chain reaction (RT-PCR) were carried out to analyze the CYP4 gene expression in polychaete Marphysa sanguinea exposed to benzo[a]pyrene (BaP) in this study. The full length of MsCYP4 cDNA was 2 470 bp, and it encoded 512 amino acids. The deduced amino acid sequence showed 47% identity with CYP4F from frog Xenopus tropicalis and shared high homology with other known CYP4 sequences. To analyse the role of CYP4 in protecting M. sanguinea from BaP exposure, three BaP groups were established: 0.5, 5 and 50 μg/L. Polychaetes were sampled after 3, 7 and 12 d. At 0.5 μg/L, the effect of BaP on MsCYP4 gene expression increased with time prolonged. MsCYP4 gene expression curve showed U-shaped trend with time in 5 and 50 μg/L BaP groups. Therefore, MsCYP4 gene may play an important role in maintaining the balance of cellular metabolism and protecting M. sanguinea from BaP toxicity.
Degradation potential and diversity of oil-degrading bacteria isolated from the sediments of the Jiaozhou Bay, China
Wei Gao, Xiangxing Gao, Tiezhu Mi, Bin Han, Yiran Zhang, Xinzi Li, Xiaofei Yin, Chengjun Sun, Qian Li, Zhisong Cui, Xiao Luan, Zhigang Yu, Li Zheng
2019, 38(6): 54-64. doi: 10.1007/s13131-019-1353-2
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A great deal of oil contaminated the shoreline by the Qingdao oil pipeline explosion in 2013. The four oil-degrading consortia were enriched from sediment samples with crude oil as sole carbon and energy sources. The biodiversity and community analysis showed that the Luteibacter, Parvibaculum and a genus belonging to Alcanivoracaceae were found predominant bacteria in the four consortia, which belonged to Proteobacteria. Nine strains exhibiting distinct 16S rRNA gene sequences were isolated from the consortia. These strains were identified to eight genera based on 16S rRNA gene sequences. Five of the nine strains degraded more than 30% of the crude oil in two weeks by gravimetric method. From the analysis of GC-MS, most of the isolated strains tended to degrade n-alkanes rather than PAHs. Five strains showed high degrading ability of the total n-alkanes. Only Strain D2 showed great PAHs degrading ability and the degrading rates ranged from 34.9% to 77.5%. The sequencing analysis of the oil-degrading consortia confirmed that the genus of Alcanivorax was one of the dominant bacteria in Consortia A and E and Strain E4 might be one of the dominant bacteria. The strains obtained in this study demonstrated the potential for oil bioremediation in oil-contaminated beach ecosystems.
Cloning and characterization of a new endo-type polyG-specific alginate lyase from bacteria Vibrio sp. QD-5
Yaxi Chao, Shuyan Wang, Suqi Wu, Jiaqiang Wei, Hao Chen
2019, 38(6): 65-74. doi: 10.1007/s13131-018-1226-0
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Seven bacterial clones with alginate-utilizing activity were isolated from rotten kelp. By activity test, the Vibrio sp. QD-5 with the potential alginate-degrading capability was chosen to carry out the draft genome sequencing, and the result showed that the Vibrio sp. QD-5 containing an alginate lyase gene cluster. One of these genes, aly-IV, was cloned and characterized for the first time. After overexpression, Aly-IV, with a molecular mass of about 62 kDa and a theoretical isoelectric point (pI) of 5.12, was purified to a specific activity of 1 256.78 U/mg and showed highest activity at 35°C in the Tris-HCl buffer at pH of 8.9. Moreover, the enzyme activity was enhanced by the metal ions of Na+, K+ and Mg2+ under certain concentration. Aly-IV degraded favorably polyG blocks in an endo-type, yielding monomer and dimer as the main products. Due to its high substrate specificity, Aly-IV could be used as a potential tool for production of polyG oligosaccharides with low degree of polymerization (DP) and for determining the fine structure of alginate.
Substitution of His260 residue alters the thermostability of Pseudoalteromonas carrageenovora arylsulfatase
Yanbing Zhu, Xiaoqian Yin, Han Liu, Hebin Li, Yanhong Chen, Lijun Li, Anfeng Xiao, Hui Ni
2019, 38(6): 75-82. doi: 10.1007/s13131-019-1356-z
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This study aimed to improve the thermostability of arylsulfatase from Pseudoalteromonas carrageenovora. A library of P. carrageenovora arylsulfatase mutants was constructed by introducing random mutagenesis using error-prone PCR. After screening, two mutants of H260L and D84A/H260L showed enhanced thermal stability than the wild-type predecessor (WT). Site-directed mutagenesis demonstrated that only amino acid residue at Position 260 plays an important role in the thermostability of P. carrageenovora arylsulfatase. Thermal inactivation analysis showed that the half-life (t1/2) values at 55°C for H260L, H260I, H260Q, H260F and H260R were 40.6, 48.4, 30.9, 29.1 and 34.5 min, respectively, while that of WT was 9.1 min. Structure modeling demonstrated that the additional hydrogen bonds and/or optimization of surface charge-charge interactions could be responsible for the increased thermostability imparted by H260L, H260I, H260Q, H260F and H260R.
Photosynthetic physiologies of phytoplankton in the eastern equatorial Indian Ocean during the spring inter-monsoon
Chao Yuan, Zongjun Xu, Xuelei Zhang, Qinsheng Wei, Huiwu Wang, Zongling Wang
2019, 38(6): 83-91. doi: 10.1007/s13131-018-1218-0
Abstract(33) FullText HTML(19) FullText PDF(1)
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Phytoplankton physiologies are dynamic and have sensitive responses to the ambient environment. In this paper, we examine photosynthetic physiologies of phytoplankton communities with Phyto-PAM in the eastern equatorial Indian Ocean during the spring inter-monsoon. Environmental parameters were measured to investigate the coupling between phytoplankton photosynthetic physiologies and their habitats. During the cruise, the water column was highly stratified. The mixed layer extended to about 75 m and was characterized by high temperature (>28°C) and low nutrient level. The Fv/Fm values and chlorophyll a (Chl a) concentrations were lower at the surface, as consequences of nutrient depletion and photo-inhibition. Subsurface Chl a maximum (SCM) occurred between 75 and 100 m, and had the highest Fv/Fm values. The formation of SCM was a balance between nutrient availability and light limitation. The SCM may contribute significantly to pelagic food web and primary production in the water column. Phytoplankton in different layers encountered different light, trophic and hydrographic dynamics and evolved distinct photosynthetic characteristics. Despite of co-limitation of nutrient limitation and photo-inhibition, phytoplankton in the surface layer showed their acclimation to high irradiance, had lower light utilization efficiencies (α: 0.061±0.032) and could exploit a wide range of light irradiance. Whereas, phytoplankton in the SCM layers presented the highest light utilization efficiencies (α: 0.146±0.48), which guaranteed higher photosynthetic capacities under low light level. These results provide insights into phytoplankton photo-adaption strategies in this less explored region.
Experimental study of freak waves due to three-dimensional island terrain in random wave
Li Zou, Aimin Wang, Zhen Wang, Yuguo Pei, Xiaolong Liu
2019, 38(6): 92-99. doi: 10.1007/s13131-019-1390-x
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An experimental study is carried out for waves passing an isolated reef terrain in a wave tank. A three-dimensional model of a representative and isolated reef terrain in the West Pacific is built. Random wave trains with various periods and wave heights are generated by a wave maker using the improved JONSWAP spectrum. It is observed that there are different kinds of generation processes and waveforms of freak waves. The freak wave factor \begin{document}${H_{\rm{m}}}/{H_{\rm{s}}}$\end{document} (where \begin{document}${H_{\rm{m}}}$\end{document} is the maximum wave height of wave series, and \begin{document}${H_{\rm{s}}}$\end{document} is significant wave height) is analyzed in detail, in terms of the skewness, kurtosis and water depth, as well as the relationship between freak wave height \begin{document}${H_{{\rm{fr}}}}$\end{document} and skewness. The freak wave factor \begin{document}${H_{\rm{m}}}/{H_{\rm{s}}}$\end{document} is found to be in positive correlation with the kurtosis, while larger \begin{document}${H_{{\rm{fr}}}}$\end{document} tends to be related with bigger skewness. The rapid variation of water depth, such as slope and seamount, contributes to the occurrence probability of freak waves.
Numerical storm surge model with higher order finite difference method of lines for the coast of Bangladesh
Gour Chandra Paul, Md. Emran Ali
2019, 38(6): 100-116. doi: 10.1007/s13131-019-1385-7
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In this study, the method of lines (MOLs) with higher order central difference approximation method coupled with the classical fourth order Runge-Kutta (RK(4,4)) method is used in solving shallow water equations (SWEs) in Cartesian coordinates to foresee water levels associated with a storm accurately along the coast of Bangladesh. In doing so, the partial derivatives of the SWEs with respect to the space variables were discretized with 5-point central difference, as a test case, to obtain a system of ordinary differential equations with time as an independent variable for every spatial grid point, which with initial conditions were solved by the RK(4,4) method. The complex land-sea interface and bottom topographic details were incorporated closely using nested schemes. The coastal and island boundaries were rectangularized through proper stair step representation, and the storing positions of the scalar and momentum variables were specified according to the rules of structured C-grid. A stable tidal regime was made over the model domain considering the effect of the major tidal constituent, M2 along the southern open boundary of the outermost parent scheme. The Meghna River fresh water discharge was taken into account for the inner most child scheme. To take into account the dynamic interaction of tide and surge, the generated tidal regime was introduced as the initial state of the sea, and the surge was then made to come over it through computer simulation. Numerical experiments were performed with the cyclone April 1991 to simulate water levels due to tide, surge, and their interaction at different stations along the coast of Bangladesh. Our computed results were found to compare reasonable well with the limited observed data obtained from Bangladesh Inland Water Transport Authority (BIWTA) and were found to be better in comparison with the results obtained through the regular finite difference method and the 3-point central difference MOLs coupled with the RK(4,4) method with regard to the root mean square error values.
Experimental investigating on the reflected waves from the caisson-type vertical porous seawalls
Mehdi Esmaeili, Maryam Rahbani, Ali Karami Khaniki
2019, 38(6): 117-123. doi: 10.1007/s13131-019-1386-6
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The hydrodynamic efficiencies of caisson-type vertical porous seawalls used for protecting coastal areas were calculated in this study. Physical models were developed to compare the wave reflection from vertical plane, semi-porous, and porous seawalls caused by both regular and random waves. Tests were carried out for a wide range of wave heights, wave periods, and different water depths (d=0.165, 0.270 and 0.375 m). The performance regarding the reflected waves from porous and semi-porous seawalls showed improvement when compared with those from the plane seawall. The reflection coefficients of the porous and semi-porous seawalls were calculated as 0.6 and 0.75, respectively, while the coefficient for the fully reflecting plane vertical wall was significantly higher (0.9). It was also observed that the reflection coefficient decreases with increase in wave steepness and relative water depth. In addition, the reduction in the reflection coefficient of porous and semi-porous seawalls, as compared to that of a plane seawall, was observed for both regular and random waves. New equations were also proposed to calculate the reflection coefficient of different types of seawalls with the aid of laboratory experiments. By verifying the developed equations using some other experimental data, it was validated that the equations could be used for practical situations. The results of the present study can be applied to optimize the design of vertical seawalls and for coastal protecting schemes.
Experimental investigation on the optical remote sensing images of internal solitary waves with a smooth surface
Yuan Mei, Jing Wang, Songsong Huang, Haidi Mu, Xu Chen
2019, 38(6): 124-131. doi: 10.1007/s13131-019-1387-5
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The parameter inversion of internal solitary waves (ISWs) based on optical remote sensing images is a key work. A new approach is proposed and demonstrated for simulating the optical remote sensing images of ISWs with a smooth surface in the laboratory. An optical remote sensing simulation system used to detect ISWs is constructed by a two-dimensional ISW flume, a LED (light emitting diode) light source and two CCD (charge coupled device) cameras. The optical remote sensing images of the horizontal surface and ISWs propagation images of a vertical side are detected simultaneously, which aims to explore the response of optical remote sensing corresponding to ISWs with the smooth surface. The results show that during the propagation of ISWs, dark pattern images are obtained by CCD 1 camera. The characteristics of the dark patterns vary along with the incident angle of the light source. The characteristic parameters of the optical remote sensing images correspond to the wave factors of vertical profiles. The experiment also shows a positive correlation between the dark pattern width and the half wave width under different amplitudes of ISWs. The system has the advantages of clear phenomenon and high repeatability, which provides the scientific basis for quantitative investigation on imaging mechanism of ISW by optical remote sensing.