2015 Vol. 34, No. 2
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2015, 34(2): .
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2015, 34(2): .
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2015, 34(2): 1-8.
doi: 10.1007/s13131-015-0619-6
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The Yellow River cut through Sanmenxia Gorge and discharged into the sea via the North China Plain in 150 ka BP; since then, around 86 000 × 108 t sediment has been transported passing Sanmenxia Gorge. Based on land use and land cover changes in Loess Plateau and other available evidence, an estimate of the Yellow River sediment budget is presented here: about 72% of the sedimentary material was trapped in the North China Plain and the remainder (i.e., 26%) escaped to the sea. At the present stage, < 0.2×108 t/a suspended sediment of the Yellow River enter the northern Yellow Sea. The transport pattern is determined mainly by the shelf current system. Annually 0.2×108-0.3×108 t of suspended particles are carried to the East China Sea; the materials are derived mainly from coastal and subaqueous delta erosion associated with the abandoned Yellow River on the Jiangsu coast. Since 1972, the lower Yellow River started to have a situation of continuous no-flow. During 1996-2000, the annual water flow and sediment discharge are only 19%, as compared with normal years (i.e., average for 1950-1979). In response to global warming and increase of water diversion from the Yellow River for industrial and urban use, the sediment flux of the Yellow River to the sea will most likely remain small in the next two to three decades.
The Yellow River cut through Sanmenxia Gorge and discharged into the sea via the North China Plain in 150 ka BP; since then, around 86 000 × 108 t sediment has been transported passing Sanmenxia Gorge. Based on land use and land cover changes in Loess Plateau and other available evidence, an estimate of the Yellow River sediment budget is presented here: about 72% of the sedimentary material was trapped in the North China Plain and the remainder (i.e., 26%) escaped to the sea. At the present stage, < 0.2×108 t/a suspended sediment of the Yellow River enter the northern Yellow Sea. The transport pattern is determined mainly by the shelf current system. Annually 0.2×108-0.3×108 t of suspended particles are carried to the East China Sea; the materials are derived mainly from coastal and subaqueous delta erosion associated with the abandoned Yellow River on the Jiangsu coast. Since 1972, the lower Yellow River started to have a situation of continuous no-flow. During 1996-2000, the annual water flow and sediment discharge are only 19%, as compared with normal years (i.e., average for 1950-1979). In response to global warming and increase of water diversion from the Yellow River for industrial and urban use, the sediment flux of the Yellow River to the sea will most likely remain small in the next two to three decades.
2015, 34(2): 9-20.
doi: 10.1007/s13131-015-0622-y
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Distributions and sea-to-air fluxes of five kinds of volatile halocarbons (VHCs) were studied in the southern Yellow Sea (SYS) and the East China Sea (ECS) in November 2007. The results showed that the concentrations of 1,1,1-trichloroethane (C2H3Cl3), 1,1-dichloroethene (C2H2Cl2), 1,1,2-trichloroethene (C2HCl3), trichloromethane (CHCl3) and tetrachloromethane (CCl4) in the surface water were 0.31-4.81, 2.75-21.3, 1.21-17.1, 5.02-233 and 0.045-4.47 pmol/L, respectively, with the average values of 1.89, 12.20, 6.93, 60.90 and 0.33 pmol/L. On the whole, the horizontal distributions of C2H3Cl3, C2H2Cl2 and CCl4 were affected mainly by anthropogenic activities, while C2HCl3 and CHCl3 were influenced by biological factors as well as anthropogenic activities. In the study area, the concentrations of VHCs (except C2HCl3) exhibited a decreasing trend from inshore to offshore sites, with the higher values occurring in the coastal waters. The sea-to-air fluxes of C2H3Cl3, C2HCl3, CHCl3 and CCl4 were calculated to be -56.00-(-5.68), -7.31-123.42, 148.00-1 309.31 and -83.32-(-1.53) nmol/(m2·d), respectively, with the average values of -6.77, 17.14, 183.38 and -21.27 nmol/(m2·d). Our data showed that the SYS and ECS in autumn was a sink for C2H3Cl3 and CCl4, while it was a source for C2HCl3 and CHCl3 in the atmosphere.
Distributions and sea-to-air fluxes of five kinds of volatile halocarbons (VHCs) were studied in the southern Yellow Sea (SYS) and the East China Sea (ECS) in November 2007. The results showed that the concentrations of 1,1,1-trichloroethane (C2H3Cl3), 1,1-dichloroethene (C2H2Cl2), 1,1,2-trichloroethene (C2HCl3), trichloromethane (CHCl3) and tetrachloromethane (CCl4) in the surface water were 0.31-4.81, 2.75-21.3, 1.21-17.1, 5.02-233 and 0.045-4.47 pmol/L, respectively, with the average values of 1.89, 12.20, 6.93, 60.90 and 0.33 pmol/L. On the whole, the horizontal distributions of C2H3Cl3, C2H2Cl2 and CCl4 were affected mainly by anthropogenic activities, while C2HCl3 and CHCl3 were influenced by biological factors as well as anthropogenic activities. In the study area, the concentrations of VHCs (except C2HCl3) exhibited a decreasing trend from inshore to offshore sites, with the higher values occurring in the coastal waters. The sea-to-air fluxes of C2H3Cl3, C2HCl3, CHCl3 and CCl4 were calculated to be -56.00-(-5.68), -7.31-123.42, 148.00-1 309.31 and -83.32-(-1.53) nmol/(m2·d), respectively, with the average values of -6.77, 17.14, 183.38 and -21.27 nmol/(m2·d). Our data showed that the SYS and ECS in autumn was a sink for C2H3Cl3 and CCl4, while it was a source for C2HCl3 and CHCl3 in the atmosphere.
2015, 34(2): 21-26.
doi: 10.1007/s13131-015-0614-y
Abstract:
Mangroves play an important role in sequestering carbon and trapping sediments. However, the effectiveness of such functions is unclear due to the restriction of knowledge on the sedimentation process across the vegetation boun-daries. To detect the effects of mangrove forests on sediment transportation and organic carbon sequestration, the granulometric and organic carbon characteristics of mangrove sediments were investigated from three vegetation zones of four typical mangrove habitats on the Leizhou Peninsula coast. Based on our results, sediment transport was often "environmentally sensitive" to the vegetation friction. A transition of the sediment transport mode from the mudflat zone to the interior/fringe zone was often detected from the cumulative frequency curve. The vegetation cover also assists the trapping of material, resulting in a significantly higher concentration of organic carbon in the interior surface sediments. However, the graphic parameters of core sediments reflected a highly temporal variability due to the sedimentation process at different locations. The sediment texture ranges widely from sand to mud, altho-ugh the sedimentary environments are restricted within the same energy level along the fluvial-marine transition zone. Based on the PCA results, the large variation was mainly attributed to either the mean grain size features or the organic carbon features. A high correlation between the depth and δ13C value also indicated an increasing storage of mangrove-derived organic carbon with time.
Mangroves play an important role in sequestering carbon and trapping sediments. However, the effectiveness of such functions is unclear due to the restriction of knowledge on the sedimentation process across the vegetation boun-daries. To detect the effects of mangrove forests on sediment transportation and organic carbon sequestration, the granulometric and organic carbon characteristics of mangrove sediments were investigated from three vegetation zones of four typical mangrove habitats on the Leizhou Peninsula coast. Based on our results, sediment transport was often "environmentally sensitive" to the vegetation friction. A transition of the sediment transport mode from the mudflat zone to the interior/fringe zone was often detected from the cumulative frequency curve. The vegetation cover also assists the trapping of material, resulting in a significantly higher concentration of organic carbon in the interior surface sediments. However, the graphic parameters of core sediments reflected a highly temporal variability due to the sedimentation process at different locations. The sediment texture ranges widely from sand to mud, altho-ugh the sedimentary environments are restricted within the same energy level along the fluvial-marine transition zone. Based on the PCA results, the large variation was mainly attributed to either the mean grain size features or the organic carbon features. A high correlation between the depth and δ13C value also indicated an increasing storage of mangrove-derived organic carbon with time.
2015, 34(2): 27-35.
doi: 10.1007/s13131-015-0617-8
Abstract:
A variety of environmental problems have been observed in the Changjiang River Estuary and adjacent coastal area, including eutrophication, harmful algal blooms (HABs), and hypoxia in recent decades. Application of sedimentary biogenic element indicators on the study of paleoenvironment can reconstruct environmental evolution history of waters. Two 210Pb-dated cores were collected from the Changjiang River Estuary (S3) and adjacent coastal area (Z13), and total organic carbon (TOC), total nitrogen (TN), biogenic silicon (BSi), total phosphorus (TP) and phosphorus (P) species were analyzed. Three stages of environmental changes are deduced by the nutrient sedimentary records. First, nutrient concentration increased rapidly since the 1950s, which attributed to agriculture development and overused chemical fertilizers. Second, nutrient concentration kept high and primary production began to promote during the 1960s to 1980s, while diatom abundance and proportion began to decline since the 1970s, accompanied by reduced SiO32- concentration and flux from the river. Third, due to several dams and bridges constructed, river runoff and coastal hydrodynamic conditions reduced to a certain extent since the 1990s, which aggravated the unbal-ance in nutrient structure. Multi-nutrient proxies in sediment can reflect the natural environm-ental changes as well as influence of human activities.
A variety of environmental problems have been observed in the Changjiang River Estuary and adjacent coastal area, including eutrophication, harmful algal blooms (HABs), and hypoxia in recent decades. Application of sedimentary biogenic element indicators on the study of paleoenvironment can reconstruct environmental evolution history of waters. Two 210Pb-dated cores were collected from the Changjiang River Estuary (S3) and adjacent coastal area (Z13), and total organic carbon (TOC), total nitrogen (TN), biogenic silicon (BSi), total phosphorus (TP) and phosphorus (P) species were analyzed. Three stages of environmental changes are deduced by the nutrient sedimentary records. First, nutrient concentration increased rapidly since the 1950s, which attributed to agriculture development and overused chemical fertilizers. Second, nutrient concentration kept high and primary production began to promote during the 1960s to 1980s, while diatom abundance and proportion began to decline since the 1970s, accompanied by reduced SiO32- concentration and flux from the river. Third, due to several dams and bridges constructed, river runoff and coastal hydrodynamic conditions reduced to a certain extent since the 1990s, which aggravated the unbal-ance in nutrient structure. Multi-nutrient proxies in sediment can reflect the natural environm-ental changes as well as influence of human activities.
2015, 34(2): 36-44.
doi: 10.1007/s13131-015-0588-9
Abstract:
In this study, the gene encoding hemocyanin subunit L, LvHcL, was cloned from Litopenaeus vannamei and the genomic organization was characterized. This gene was diverse with many SNPs and also had at least four isoforms, while one of them (LvHcL4) only had two exons and the exon2 was missed. Transcription analysis showed that these isoforms of LvHcL were up-regulated after WSSV challenge in WSSV-resistant shrimp, while the transcriptions were decreased constantly in WSSV-susceptible shrimp. It is suggested that the hemocyanin had rich polymorphism and was involved in the antiviral response. These results could extend our previous findings and provide insights into the immune feature of hemocyanin, which would be helpful for further studies aimed at antiviral mechanism in inver-tebrate.
In this study, the gene encoding hemocyanin subunit L, LvHcL, was cloned from Litopenaeus vannamei and the genomic organization was characterized. This gene was diverse with many SNPs and also had at least four isoforms, while one of them (LvHcL4) only had two exons and the exon2 was missed. Transcription analysis showed that these isoforms of LvHcL were up-regulated after WSSV challenge in WSSV-resistant shrimp, while the transcriptions were decreased constantly in WSSV-susceptible shrimp. It is suggested that the hemocyanin had rich polymorphism and was involved in the antiviral response. These results could extend our previous findings and provide insights into the immune feature of hemocyanin, which would be helpful for further studies aimed at antiviral mechanism in inver-tebrate.
2015, 34(2): 45-54.
doi: 10.1007/s13131-015-0625-8
Abstract:
Large portions of the world's fishery resources are overexploited. Life history traits of fish species are important indicators to reveal different life history strategies and to indicate population responses to fishing pressures. For this study, empirical data on fishing grounds located in the coastal area between Fujian Coast and Taiwan Island were collected. These areas have experienced severe overfishing in the past 30 years, leading to changes in the structure and function of the fish communities. Fifty-one commercial fish species in this fishing ground were selected to study the life history traits. Using the life history traits, all the species were grouped into five different life history strategies by principle component analysis. More than 60% of the species were categorized in Group 5 that was similar to r-strategists. Twenty-five commercial species were selected for further analysis of changes in life history variables, and to discuss the population responses to exploitation. Results showed that most of the species appeared to become smaller size, shorter life, earlier maturation and faster growing under long-term exploitation. The exploitation rate of each species was also calculated to further discuss the impacts of fishing pressures to fish populations. Four species were found with the severest changes on life history traits indicating some of the species might be more susceptible to exploitation. This study on fish life history traits and their long-term variations under fishing pressures could provide important scientific implications for fishery management and conservation.
Large portions of the world's fishery resources are overexploited. Life history traits of fish species are important indicators to reveal different life history strategies and to indicate population responses to fishing pressures. For this study, empirical data on fishing grounds located in the coastal area between Fujian Coast and Taiwan Island were collected. These areas have experienced severe overfishing in the past 30 years, leading to changes in the structure and function of the fish communities. Fifty-one commercial fish species in this fishing ground were selected to study the life history traits. Using the life history traits, all the species were grouped into five different life history strategies by principle component analysis. More than 60% of the species were categorized in Group 5 that was similar to r-strategists. Twenty-five commercial species were selected for further analysis of changes in life history variables, and to discuss the population responses to exploitation. Results showed that most of the species appeared to become smaller size, shorter life, earlier maturation and faster growing under long-term exploitation. The exploitation rate of each species was also calculated to further discuss the impacts of fishing pressures to fish populations. Four species were found with the severest changes on life history traits indicating some of the species might be more susceptible to exploitation. This study on fish life history traits and their long-term variations under fishing pressures could provide important scientific implications for fishery management and conservation.
2015, 34(2): 55-62.
doi: 10.1007/s13131-015-0618-7
Abstract:
In order to elucidate the genetic mechanism of growth traits in turbot during ontogeny, developmental genetic analysis of the body weights, total lengths, standard lengths and body heights of turbots was conducted by mixed genetic models with additive-dominance effects, based on complete diallel crosses with four different strains of Scophthalmus maximus from Denmark, Norway, Britain, and France. Unconditional genetic analysis revealed that the unconditional additive effects for the four traits were more significant than unconditional dominance effects, meanwhile, the alternative expressions were also observed between the additive and dominant effects for body weights, total lengths and standard lengths. Conditional analysis showed that the developmental periods with active gene expression for body weights, total lengths, standard lengths and body heights were 15-18, 15 and 21-24, 15 and 24, and 21 and 27 months of age, respectively. The proportions of unconditional/conditional variances indicated that the narrow-sense heritabilities of body weights, total lengths and standard lengths were all increased systematically. The accumulative effects of genes controlling the four quantitative traits were mainly additive effects, suggesting that the selection is more efficient for the genetic improvement of turbots. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period (t-1→t) during ontogeny. It is also important to determine the appropriate developmental period (t-1→t) for trait measurement in developmental quantitative genetic analysis in fish.
In order to elucidate the genetic mechanism of growth traits in turbot during ontogeny, developmental genetic analysis of the body weights, total lengths, standard lengths and body heights of turbots was conducted by mixed genetic models with additive-dominance effects, based on complete diallel crosses with four different strains of Scophthalmus maximus from Denmark, Norway, Britain, and France. Unconditional genetic analysis revealed that the unconditional additive effects for the four traits were more significant than unconditional dominance effects, meanwhile, the alternative expressions were also observed between the additive and dominant effects for body weights, total lengths and standard lengths. Conditional analysis showed that the developmental periods with active gene expression for body weights, total lengths, standard lengths and body heights were 15-18, 15 and 21-24, 15 and 24, and 21 and 27 months of age, respectively. The proportions of unconditional/conditional variances indicated that the narrow-sense heritabilities of body weights, total lengths and standard lengths were all increased systematically. The accumulative effects of genes controlling the four quantitative traits were mainly additive effects, suggesting that the selection is more efficient for the genetic improvement of turbots. The conditional genetic procedure is a useful tool to understand the expression of genes controlling developmental quantitative traits at a specific developmental period (t-1→t) during ontogeny. It is also important to determine the appropriate developmental period (t-1→t) for trait measurement in developmental quantitative genetic analysis in fish.
2015, 34(2): 63-67.
doi: 10.1007/s13131-015-0616-9
Abstract:
The objectives of this present research were to assess the heritability of growth traits under low temperature cond-itions in turbot (Scophthalmus maximus L.), and to analyze the correlation between body weight (BW) and body length (BL). There were 536 individuals from 25 full- and half-sib families involved in this study. During the entire 90-day period, which was initiated at 233 dph (day old) and ended at 323 dph, the individuals' BW and BL were weighed consecutively six times every 18 days. The heritability of BW and BL and the correlation between these two traits were estimated based on an individual animal model with the derivative-free restricted maximum likelihood (DFREML) method. These results showed that the specific growth rates (SGR) of 25 families was from 0.75±0.11 to 1.05±0.14 under water temperature of 10.5-12°C. In addition, the heritability of BW and BL estimated under low-temperature were 0.32±0.04 and 0.47±0.06, respectively. The BW had a medium heritability (0.2-0.4), and the BL had a high herita-bility (>0.45), which suggested that selection for increased weight and length was feasible. Moreover, there was pote-ntial for mass selection on growth. The genetic and phenotypic correlations between BW and BL were 0.95±0.01 and 0.91±0.01 (P < 0.01), respectively. A significant correlation between BW and BL showed that BL could be instead of BW for indirect selection, which could be effectively implemented in the breeding program.
The objectives of this present research were to assess the heritability of growth traits under low temperature cond-itions in turbot (Scophthalmus maximus L.), and to analyze the correlation between body weight (BW) and body length (BL). There were 536 individuals from 25 full- and half-sib families involved in this study. During the entire 90-day period, which was initiated at 233 dph (day old) and ended at 323 dph, the individuals' BW and BL were weighed consecutively six times every 18 days. The heritability of BW and BL and the correlation between these two traits were estimated based on an individual animal model with the derivative-free restricted maximum likelihood (DFREML) method. These results showed that the specific growth rates (SGR) of 25 families was from 0.75±0.11 to 1.05±0.14 under water temperature of 10.5-12°C. In addition, the heritability of BW and BL estimated under low-temperature were 0.32±0.04 and 0.47±0.06, respectively. The BW had a medium heritability (0.2-0.4), and the BL had a high herita-bility (>0.45), which suggested that selection for increased weight and length was feasible. Moreover, there was pote-ntial for mass selection on growth. The genetic and phenotypic correlations between BW and BL were 0.95±0.01 and 0.91±0.01 (P < 0.01), respectively. A significant correlation between BW and BL showed that BL could be instead of BW for indirect selection, which could be effectively implemented in the breeding program.
2015, 34(2): 68-73.
doi: 10.1007/s13131-014-0463-0
Abstract:
The catch and effort data analysis (CEDA) and ASPIC (a stock assessment production model incorporating covariat-es) computer software packages were used to estimate the maximum sustainable yield (MSY) from the catch and effort data of Greater lizardfish Saurida tumbil fishery of Pakistan from 1986 to 2009. In CEDA three surplus produc-tion models of Fox, Schaefer and Pella-Tomlinson were used. Here initial proportion (IP) of 0.5 was used because the starting catch was roughly 50% of the maximum catch. With IP= 0.5, the estimated MSY from Fox model were 20.59 mt and 38.16 mt for normal and log-normal error assumptions, while the MSY from Schaefer and Pella-Tomlinson were 60.40, 60.40 and 60.40 mt, for normal, log-normal and gamma error assumptions respectively. The MSY values from Schaefer and Pella-Tomlinson models of three error assumptions were the same. The R2 values from those three models were above 0.6. When IP= 0.5, the MSY values estimated from ASPIC from Fox were 132 mt, and from logistic model were 69.4 mt, with R2 value above 0.8. Therefore we suggest the MSY of S. tumbil fishery from Pakistan to be 60-70 mt, which is higher than the latest catch, thus we would recommend that the fishing efforts for this fishery may be kept at the current level.
The catch and effort data analysis (CEDA) and ASPIC (a stock assessment production model incorporating covariat-es) computer software packages were used to estimate the maximum sustainable yield (MSY) from the catch and effort data of Greater lizardfish Saurida tumbil fishery of Pakistan from 1986 to 2009. In CEDA three surplus produc-tion models of Fox, Schaefer and Pella-Tomlinson were used. Here initial proportion (IP) of 0.5 was used because the starting catch was roughly 50% of the maximum catch. With IP= 0.5, the estimated MSY from Fox model were 20.59 mt and 38.16 mt for normal and log-normal error assumptions, while the MSY from Schaefer and Pella-Tomlinson were 60.40, 60.40 and 60.40 mt, for normal, log-normal and gamma error assumptions respectively. The MSY values from Schaefer and Pella-Tomlinson models of three error assumptions were the same. The R2 values from those three models were above 0.6. When IP= 0.5, the MSY values estimated from ASPIC from Fox were 132 mt, and from logistic model were 69.4 mt, with R2 value above 0.8. Therefore we suggest the MSY of S. tumbil fishery from Pakistan to be 60-70 mt, which is higher than the latest catch, thus we would recommend that the fishing efforts for this fishery may be kept at the current level.
2015, 34(2): 74-83.
doi: 10.1007/s13131-015-0623-x
Abstract:
C-type lectins are among the most significant pattern recognition receptors (PRRs) found in invertebrate. They are a class of carbohydrate-binding proteins that can recognize specific sugar moieties on the surface of pathogens. In the present study, a novel C-type lecitn (termed MjLectin) from kuruma shrimp Marsupenaeus japonicus was identified. The full-length cDNA of MjLectin was 1 245 bp with a 1 011 bp open reading frame (ORF) that encoded a polypeptide of 336 amino acid residues. MjLectin consisted of two tandemly arrayed carbohydrate-recognition domains (CRDs), unlike other reported M. japonicus C-type lectins with only one CRD. It showed a high similarity to other shrimp dual-CRD lectins. Among the Ca2+-binding Site 2, the tripeptide motif dictating the carbohydrate binding specificity was exhibited as a rare mutant LPN (Leu134-Pro135-Asn136) in CRD1 and a traditional EPN (Glu299-Pro300-Asn301) in CRD2, respectively. MjLectin showed a specific expression pattern in both tissue and cellular levels, for its mRNA transcript was mainly expressed in the F-cells of the hepatopancreas. After white spot syndrome virus (WSSV) challenge (3.6×108 virions/μL), the expression of MjLectin in the hepatopancreas was up-regulated significantly at 48 h (P<0.01) compared with the control group. These results suggested that MjLectin might be involved in the innate immune defense against WSSV infection.
C-type lectins are among the most significant pattern recognition receptors (PRRs) found in invertebrate. They are a class of carbohydrate-binding proteins that can recognize specific sugar moieties on the surface of pathogens. In the present study, a novel C-type lecitn (termed MjLectin) from kuruma shrimp Marsupenaeus japonicus was identified. The full-length cDNA of MjLectin was 1 245 bp with a 1 011 bp open reading frame (ORF) that encoded a polypeptide of 336 amino acid residues. MjLectin consisted of two tandemly arrayed carbohydrate-recognition domains (CRDs), unlike other reported M. japonicus C-type lectins with only one CRD. It showed a high similarity to other shrimp dual-CRD lectins. Among the Ca2+-binding Site 2, the tripeptide motif dictating the carbohydrate binding specificity was exhibited as a rare mutant LPN (Leu134-Pro135-Asn136) in CRD1 and a traditional EPN (Glu299-Pro300-Asn301) in CRD2, respectively. MjLectin showed a specific expression pattern in both tissue and cellular levels, for its mRNA transcript was mainly expressed in the F-cells of the hepatopancreas. After white spot syndrome virus (WSSV) challenge (3.6×108 virions/μL), the expression of MjLectin in the hepatopancreas was up-regulated significantly at 48 h (P<0.01) compared with the control group. These results suggested that MjLectin might be involved in the innate immune defense against WSSV infection.
2015, 34(2): 84-92.
doi: 10.1007/s13131-015-0583-1
Abstract:
Along with the sequencing technology development and continual enthusiasm of researchers on the mitochondrial genomes, the number of metazoan mitochondrial genomes reported has a tremendous growth in the past decades. Phylomitogenomics—reconstruction of phylogenetic relationships based on mitochondrial genomic data—is now possible across large animal groups. Crustaceans in the class Malacostraca display a high diversity of body forms and include large number of ecologically and commercially important species. In this study, comprehensive and systematic analyses of the phylogenetic relationships within Malacostraca were conducted based on 86 mitochondrial genomes available from GenBank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement (excluding tRNAs) to pancrustacean ground pattern, including six species from Stomatopoda, three species from Amphipoda, two krill, seven species from Dendrobranchiata (Decapoda), and 36 species from Pleocyemata (Decapoda). However, the other 32 mitochondrial genomes reported exhibit major gene rearrangements. Phylogenies based on Bayesian analyses of nucleotide sequences of the protein-coding genes produced a robust tree with 100% posterior probability at almost all nodes. The results indicate that Amphipoda and Isopoda cluster together (Edriophthalma) (BPP=100). Phylomitogenomic analyses strong support that Euphausiacea is nested within Decapoda, and closely related to Dendrobranchiata, which is also consistent with the evidence from developmental biology. Yet the taxonomic sampling of mitochondrial genome from Malacostraca is very biased to the order Decapoda, with no complete mitochondrial genomes reported from 11 of the 16 orders. Future researches on sequencing the mitochondrial genomes from a wide variety of malacostracans are necessary to further elucidate the phylogeny of this important group of animals. With the increase in mitochondrial genomes available, phylomitogenomics will emerge as an important component in the Tree of Life researches.
Along with the sequencing technology development and continual enthusiasm of researchers on the mitochondrial genomes, the number of metazoan mitochondrial genomes reported has a tremendous growth in the past decades. Phylomitogenomics—reconstruction of phylogenetic relationships based on mitochondrial genomic data—is now possible across large animal groups. Crustaceans in the class Malacostraca display a high diversity of body forms and include large number of ecologically and commercially important species. In this study, comprehensive and systematic analyses of the phylogenetic relationships within Malacostraca were conducted based on 86 mitochondrial genomes available from GenBank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement (excluding tRNAs) to pancrustacean ground pattern, including six species from Stomatopoda, three species from Amphipoda, two krill, seven species from Dendrobranchiata (Decapoda), and 36 species from Pleocyemata (Decapoda). However, the other 32 mitochondrial genomes reported exhibit major gene rearrangements. Phylogenies based on Bayesian analyses of nucleotide sequences of the protein-coding genes produced a robust tree with 100% posterior probability at almost all nodes. The results indicate that Amphipoda and Isopoda cluster together (Edriophthalma) (BPP=100). Phylomitogenomic analyses strong support that Euphausiacea is nested within Decapoda, and closely related to Dendrobranchiata, which is also consistent with the evidence from developmental biology. Yet the taxonomic sampling of mitochondrial genome from Malacostraca is very biased to the order Decapoda, with no complete mitochondrial genomes reported from 11 of the 16 orders. Future researches on sequencing the mitochondrial genomes from a wide variety of malacostracans are necessary to further elucidate the phylogeny of this important group of animals. With the increase in mitochondrial genomes available, phylomitogenomics will emerge as an important component in the Tree of Life researches.
2015, 34(2): 93-113.
doi: 10.1007/s13131-015-0624-9
Abstract:
Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its rela-tionship with environmental factors, we applied Roche 454 sequencing of 16S rDNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities' richness, compositions and structures as well as tax-onomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups; while the archaeal community is domi-nated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). This study describes the microbial diversity in the Arctic deep marine sediment (>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.
Microbial community structures in the Arctic deep-sea sedimentary ecosystem are determined by organic matter input, energy availability, and other environmental factors. However, global warming and earlier ice-cover melting are affecting the microbial diversity. To characterize the Arctic deep-sea sediment microbial diversity and its rela-tionship with environmental factors, we applied Roche 454 sequencing of 16S rDNA amplicons from Arctic deep-sea sediment sample. Both bacterial and archaeal communities' richness, compositions and structures as well as tax-onomic and phylogenetic affiliations of identified clades were characterized. Phylotypes relating to sulfur reduction and chemoorganotrophic lifestyle are major groups in the bacterial groups; while the archaeal community is domi-nated by phylotypes most closely related to the ammonia-oxidizing Thaumarchaeota (96.66%) and methanogenic Euryarchaeota (3.21%). This study describes the microbial diversity in the Arctic deep marine sediment (>3 500 m) near the North Pole and would lay foundation for future functional analysis on microbial metabolic processes and pathways predictions in similar environments.
2015, 34(2): 114-123.
doi: 10.1007/s13131-015-0620-0
Abstract:
The phytoplankton water samples were collected in two multidisciplinary investigations which were carried out during summer (June) and autumn (November to December) of 2011. Phytoplankton species composition and abun-dance data were accomplished by Utermöhl method. The phytoplankton community was dominated by diatoms and dinoflagellates in the southern Yellow Sea (YS) in summer and autumn. In summer, Paralia sulcata and Prorocen-trum dentatum were the predominated species, the cell abundance ranged from 0.074 to 107.733×103 cells/L with an average of 9.057×103 cells/L. Two phytoplankton high abundance appeared in northwest part of the survey area and the Changjiang River Estuary, respectively. In autumn, Par. sulcata became the predominant species, and the phyto-plankton cell abundance ranged from 1.035×103 to 8.985×103 cells/L, the average was 3.263×103 cells/L. The phytopl-ankton abundance in surface layer presented the homogeneous distributions. Canonical Correspondence Analysis (CCA) method was applied for discovering the relationship between environmental factors and the common found phytoplankton species. The responses of phytoplankton to nutrients were varied between summer and autumn. The abundance of most predominant species, Par. sulcata was strongly correlated to temperature and salinity in autumn, but not the case in summer.
The phytoplankton water samples were collected in two multidisciplinary investigations which were carried out during summer (June) and autumn (November to December) of 2011. Phytoplankton species composition and abun-dance data were accomplished by Utermöhl method. The phytoplankton community was dominated by diatoms and dinoflagellates in the southern Yellow Sea (YS) in summer and autumn. In summer, Paralia sulcata and Prorocen-trum dentatum were the predominated species, the cell abundance ranged from 0.074 to 107.733×103 cells/L with an average of 9.057×103 cells/L. Two phytoplankton high abundance appeared in northwest part of the survey area and the Changjiang River Estuary, respectively. In autumn, Par. sulcata became the predominant species, and the phyto-plankton cell abundance ranged from 1.035×103 to 8.985×103 cells/L, the average was 3.263×103 cells/L. The phytopl-ankton abundance in surface layer presented the homogeneous distributions. Canonical Correspondence Analysis (CCA) method was applied for discovering the relationship between environmental factors and the common found phytoplankton species. The responses of phytoplankton to nutrients were varied between summer and autumn. The abundance of most predominant species, Par. sulcata was strongly correlated to temperature and salinity in autumn, but not the case in summer.
2015, 34(2): 124-131.
doi: 10.1007/s13131-015-0621-z
Abstract:
In order to determine the phytoplankton community composition, the modification and optimizing of the CHEMical TAXonomy (CHEMTAX) running was carried out through samples grouping, successive run and evaluate the results for HPLC-pigment samples in the South China Sea (SCS). The vertical distribution of the ratio of pigment to total Chl a (TChl a) exhibited three different patterns, including increasing with depth pattern (e.g., But-Fuco), decreasing with depth pattern (e.g., Zea) and increasing at deep chlorophyll maximum (DCM) pattern (e.g., Hex-Fuco). The vertical profiles for Fuco/TChl a and Pras/TChl a was higher in coast than in the shelf and basin, and the Zea and Dv-Chl a expressed conversely. So the samples in the coastal stations must be separated for the cluster analysis group procedure in the SCS. Successive run was introduced into the CHEMTAX calculation and the output results were evaluated by the convergence of pigment/TChl a ratios. Most of the ratios were well converged at the fifth running, except Zea/TChl a for Prochlorococcus and Chl b/TChl a for prasinophytes and so on. To evaluate the fifth running's results, haptophytes_8 and chlorophytes were two phytoplankton groups with much uncertainty. But the fifth estimated value was better than running once was supported by the regression evidence between the measured pigment concentration and calculation values. Synechococcus was another component with much mutability, and the CHEMTAX's result should be compared to the flow cytometry's cell abundance.
In order to determine the phytoplankton community composition, the modification and optimizing of the CHEMical TAXonomy (CHEMTAX) running was carried out through samples grouping, successive run and evaluate the results for HPLC-pigment samples in the South China Sea (SCS). The vertical distribution of the ratio of pigment to total Chl a (TChl a) exhibited three different patterns, including increasing with depth pattern (e.g., But-Fuco), decreasing with depth pattern (e.g., Zea) and increasing at deep chlorophyll maximum (DCM) pattern (e.g., Hex-Fuco). The vertical profiles for Fuco/TChl a and Pras/TChl a was higher in coast than in the shelf and basin, and the Zea and Dv-Chl a expressed conversely. So the samples in the coastal stations must be separated for the cluster analysis group procedure in the SCS. Successive run was introduced into the CHEMTAX calculation and the output results were evaluated by the convergence of pigment/TChl a ratios. Most of the ratios were well converged at the fifth running, except Zea/TChl a for Prochlorococcus and Chl b/TChl a for prasinophytes and so on. To evaluate the fifth running's results, haptophytes_8 and chlorophytes were two phytoplankton groups with much uncertainty. But the fifth estimated value was better than running once was supported by the regression evidence between the measured pigment concentration and calculation values. Synechococcus was another component with much mutability, and the CHEMTAX's result should be compared to the flow cytometry's cell abundance.
2015, 34(2): 132-136.
doi: 10.1007/s13131-015-0615-x
Abstract:
Aureococcus anophagefferens, a small pelagophyte algae, has caused brown tide blooms in coastal waters of Qinhua-ngdao in recent years, presenting significant negative impacts on the shellfish mariculture industry. Under standard light microscopy, it is visually indistinguishable from other small algae in field samples due to its extremely small size. In this study, quantitative polymerase chain reaction (qPCR) based on 18S rDNA sequences was developed and used to detect and enumerate A. anophagefferens. A linear regression (R2= 0.91) was generated based on cycle thr-esholds value (Ct) versus known concentrations of A. anophagefferens. Twenty-two field samples collected in coastal waters of Qinhuangdao were subjected to DNA extraction and then analyzed using qPCR. Results showed that A. anophagefferens had a wide distribution in coastal waters along Qinhuangdao. Elevated A. anophagefferens abun-dance, category 3 brown tide blooms (>200 000 cells/mL) occurred at Dongshan Beach and Tiger-stone Beach in August in 2013. In shellfish mariculture areas along coastal waters of Qinhuangdao, 4 stations had category 3 blooms, and 6 stations had category 2 blooms (35 000-200 000 cells/mL) in August and all stations had category 1 blooms (>0 to ≤35 000 cells/mL) in October. Quantitative PCR allows for detection of A. anophagefferens cells at low levels in filed samples, which is essential to effective management and prediction of brown tide blooms.
Aureococcus anophagefferens, a small pelagophyte algae, has caused brown tide blooms in coastal waters of Qinhua-ngdao in recent years, presenting significant negative impacts on the shellfish mariculture industry. Under standard light microscopy, it is visually indistinguishable from other small algae in field samples due to its extremely small size. In this study, quantitative polymerase chain reaction (qPCR) based on 18S rDNA sequences was developed and used to detect and enumerate A. anophagefferens. A linear regression (R2= 0.91) was generated based on cycle thr-esholds value (Ct) versus known concentrations of A. anophagefferens. Twenty-two field samples collected in coastal waters of Qinhuangdao were subjected to DNA extraction and then analyzed using qPCR. Results showed that A. anophagefferens had a wide distribution in coastal waters along Qinhuangdao. Elevated A. anophagefferens abun-dance, category 3 brown tide blooms (>200 000 cells/mL) occurred at Dongshan Beach and Tiger-stone Beach in August in 2013. In shellfish mariculture areas along coastal waters of Qinhuangdao, 4 stations had category 3 blooms, and 6 stations had category 2 blooms (35 000-200 000 cells/mL) in August and all stations had category 1 blooms (>0 to ≤35 000 cells/mL) in October. Quantitative PCR allows for detection of A. anophagefferens cells at low levels in filed samples, which is essential to effective management and prediction of brown tide blooms.
2015, 34(2): 137-142.
doi: 10.1007/s13131-015-0610-2
Abstract:
Under the action of marine currents, non-cohesive sediments evolve by bed-load, by saltation or suspension depending on their granulometry. Several authors have considered that the movement of sediment is bidimensional and modelized the effects of swell by a constant velocitynear the seabed. Here we have studied the velocity profile of fluctuating currents near the seabed and studied the movement of sediment in 3D. The results show that in the areas of study (surf and swash) the movement of sediment occurs in a volume, and the evolution of sediment varies from an areato another. The obtained theoretical profiles of the position and velocity vectors confirm the observations of several authors.
Under the action of marine currents, non-cohesive sediments evolve by bed-load, by saltation or suspension depending on their granulometry. Several authors have considered that the movement of sediment is bidimensional and modelized the effects of swell by a constant velocitynear the seabed. Here we have studied the velocity profile of fluctuating currents near the seabed and studied the movement of sediment in 3D. The results show that in the areas of study (surf and swash) the movement of sediment occurs in a volume, and the evolution of sediment varies from an areato another. The obtained theoretical profiles of the position and velocity vectors confirm the observations of several authors.
