The diet of deepwater sharks and the benefits of using DNA identification of prey

Stomachs from the sharks Dalatias licha, Centrophorus squamosus, Centroscymnus owstoni, Centroselachus crepidater, Proscymnodon plunketi, and Galeorhinus galeus were sampled from three research trawl surveys on Chatham Rise, east of New Zealand. Between 14 and 50 stomachs were examined for each species, of which 8–62% were empty. Prey were visually identified in 80 stomachs, and by DNA barcoding in a further 28 stomachs. The use of DNA methods allowed the identification of chunks of flesh found in the stomachs of D. licha and P. plunketi, and nearly doubled the rate of data accumulation for D. licha, C. squamosus, and C. owstoni. Between 84 and 223 stomachs were estimated to be needed to measure 90% of the extrapolated total prey richness. The prey of D. licha, C. squamosus, and P. plunketi were predominantly benthic or demersal fishes and cephalopods. The prey of C. owstoni and C. crepidater were predominantly mesopelagic fishes and squids. G. galeus foraged throughout the water column. Scavenging of discards from commercial fishing vessels was likely in C. squamosus, P. plunketi, and G. galeus. The diet of all species except C. crepidater was dominated by the commercially important benthopelagic species hoki Macruronus novaezelandiae.     

In-situ stress state in the Linxing region,eastern Ordos Basin,China: Implications for unconventional gas exploration and production

The Carboniferous and Permian sedimentary rocks (mainly the Shanxi and Taiyuan formations) in the Linxing region, eastern Ordos Basin, China, host a significant volume of unconventional gas resources (coalbed methane, shale gas and tight sandstone gas). Currently, the in-situ stress state is poorly understood but knowledge of this is extremely important for a range of applications, such as gas exploration and production, fracture stimulation and wellbore stability. The maximum horizontal stress (S_Hmax), minimum horizontal stress (S_hmin) and vertical stress (S_v) magnitudes, and the S_Hmax orientation in the Linxing region were systematically analyzed for the first time in the present study, which can provide a reference for subsequent numerical simulation and hydraulic fracturing design. Based on borehole breakouts and drilling-induced tensile fractures interpreted from borehole imaging logs, the S_Hmax orientation rotates from ∼NEE-SWW-trending in the southern part to ∼ NWW-SEE-trending in the northern part of the Linxing region. Both conventional logs and extended leak-off tests were used for stress magnitude determination. The results revealed three types of in-situ stress fields (S_v > S_Hmax > S_hmin, S_Hmax > S_v > S_hmin and S_Hmax > S_v ≈ S_hmin), and a dominant strike-slip stress regime (S_Hmax > S_v ≥ S_hmin) was found for the entire well section in the target Shanxi Formation and Taiyuan Formation in the Linxing region. In addition, differential stress increased with depth in the Linxing region, which indicates that wellbore instability might be a potentially significant problem when drilling wells that are vertical or ∼ N-S-trending.     

Degradation ofn-paraffin mixture by marine microorganisms in enriched seawater medium

The ability to degraden-paraffin mixture of two bacterial strains,Caulobacter sp. andFlavobacterium sp., isolated from sea water of Tokyo Bay was studied experimentally in the enriched seawater (ESW) medium. These bacteria degraded actively the mixture ofn-tridecane,n-tetradecane,n-pentadecane andn-hexadecane. The maximum rate of degradation was observed after a lag period of 2 to 8 day and these bacteria were found to degrade then-paraffin mixture at rates calculated to be in a range from 3.3×10^?12 to 3.4×10^?11 mg-oil cell^?1 h^?1 at 20°C. The maximum degradation rate,r _m mg-oil l^?1 h^?1, was correlated with the amount of the initial totaln-paraffin,S mg-oil l^?1, as expressed by the following equation: $$rm = (rm)\max \left( {\frac{S}{{S + Km}}} \right)$$ where (r _m )_max denotes the largest value ofr _m whenn-paraffin exists in large excess andK _m is a constant and represents the amount ofn-paraffin at which the degradation rate,r _m , reaches 1/2 of its largest value, (r _m )_max. The values of (r _m )_max andK _m were calculated to be as follows: In the case ofCaulobacter sp. (strain KM-1), (r _m )_max=6.0 mg-oil l^?1 h^?1 andK _m =191 mg-oillesw ^?1; in the case ofFlavobacterium sp., (r _m )_max=5.47 mg-oil l^?1 h^?1 andK _m =152 mg-oillesw ^?1.     

Hydrodynamic performance of vertical porous structures under regular waves

The hydrodynamic efficiency of the vertical porous structures is investigated under regular waves by use of physical models. The hydrodynamic efficiency of the breakwater is presented in terms of the wave transmission (kt ), reflection (kr) and energy dissipation (kd ) coefficients. Different wave and structural parameters affecting the breakwater efficiency are tested. It is found that, the transmission coefficient (kt ) decreases with the increase of the relative water depth (h/L), the wave steepness (Hi/L), the relative breakwater widths (B/L, B/h), the relative breakwater height (D/h), and the breakwater porosity (n). The reflection coefficient (kr) takes the opposite trend of kt when D/h=1.25 and it decreases with the increasing h/L, Hi/L and B/L when D/h 1.0. The dissipation coefficient (kd) increases with the increasing h/L, Hi/L and B/L when D/h 1.0 and it decreases when D/h=1.25. In which, it is possible to achieve values of kt smaller than 0.3, krlarger than 0.5, and kd larger than 0.6 when D/h=1.25, B/h=0.6, h/L 0.22, B/L 0.13, and Hi/L 0.04. Empirical equations are developed for the estimation of the transmission and reflection coefficients. The results of these equations are compared with other experimental and theoretical results and a reasonable agreement is obtained.     

Some new results on statistical properties of wind waves

For wind waves modelled by a stationary Gaussian process ζ(t) (ζ = height above m.w.l. of one point of the free surface) it is shown that, in a time interval including an instant t_m where a maximum ζ_m occurs, the ratio between ζ(t) and ζ_m tends with probability approaching one, to the ratio Ψ(t ? t_m)/Ψ(O), as $\text{ζ}{}_{\mathrm{m}}\text{/Ψ}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{(}\text{O}\text{)}$ tends to infinity, Ψ(t) being the autocovariance of the process.Starting from this result, it is possible to find analytically the characteristic periods of the highest waves in a sea with a given energy spectrum. These periods, calculated according to period definitions of three methods of wave record analysis, are found to be in remarkably good agreement with data from Bretschneider¹ and Svasek.²     

鳗鲡目鱼类线粒体蛋白质编码基因易位及系统演化关系分析

鳗鲡目鱼类线粒体基因组的基因组成较为保守,在58个线粒体基因组中,仅有3个物种存在基因数量的差异。在19个鳗鲡目鱼类线粒体基因组中存在主编码基因的重排。主编码基因的变异位点分析结果支持nad5、nad4和nad2基因作为cox1和lrRNA基因辅助的分子标记。鳗鲡科Anguillidae的20个种(亚种)聚在一起,强烈支持鳗鲡科为单系群(BPP=100)。鳗鲡科下属的3个类群(大洋洲类群、大西洋类群和印度洋-太平洋类群)也同时得到有力的验证(BPP均为100)。线鳗科Nemichthyidae和锯齿鳗科Serrivomeridae亲缘关系最近,二者聚类后,与鳗鲡科Anguillidae构成姊妹群(BPP=100)。在囊喉鱼亚目Saccopharyngoidei中,宽咽鱼科Eurypharyngidae与囊鳃鳗科Saccopharyngidae聚类(BPP=100),同时,单颌鳗科Monognathidae与月尾鳗科Cyematidae聚类(BPP=100),4个科聚在一支,支持囊喉鱼亚目为单系群(BPP=100)。在囊喉鱼亚目线粒体基因组中,3个物种(吞鳗Eurypharynx pelecanoides、拉文囊鳃鳗Saccopharynx lavenbergi和杰氏单颌鳗Monognathus jesperseni)存在主编码基因的重排。16种鳗鲡(细美体鳗Ariosoma shiroanago、短吻颈鳗Derichthys serpentinus、凯氏短尾康吉鳗Coloconger cadenati、鸭颈鳗Nessorhamphus ingolfianus、龟草鳗Thalassenchelys sp.、粗犁齿海鳗Cynoponticus ferox、百吉海鳗Muraenesox bagio、巨斑花蛇鳗Myrichthys maculosus、大吻沙蛇鳗Ophisurus macrorhynchos、几内亚副康吉鳗Paraconger notialis、哈氏异康吉鳗Heteroconger hassi、小头鸭嘴鳗Nettastoma parviceps、弱头鳗Leptocephalus sp.、斑点长犁齿鳗Hoplunnis punctata、尖吻小鸭嘴鳗Facciolella oxyrhyncha和星康吉鳗Conger myriaster),与鳗鲡目线粒体主编码基因的原始排列相比,共享nad6基因的易位。同时,基于线粒体基因组13个蛋白质编码基因构建的系统演化树,强烈支持这16个物种聚为一支(BPP=100)。然而,由此而带来的海鳗科Muraenesocidae、拟鯙科Chlopsidae和糯鳗科Congridae是否为单系群的问题,值得今后深入探究。     

Current-induced scour beneath initially elevated subsea pipelines

When a subsea pipeline is laid on an uneven seabed, certain sections may have an initial elevation with respect to the far-field seabed, e_o, and thus potentially affecting the on-bottom stability of the pipeline. This paper focuses on quantifying the effects of the upstream dimensionless seabed shear stress, θ_∞, and Reynolds number, Re, on: (1) the maximum dimensionless seabed shear stress beneath the pipe, θ_max, to be compared to the critical shear stress in order to determine whether scour would occur and progress towards an equilibrium state; and, (2) the dimensionless equilibrium scour depth beneath the pipe, S_eq/D. Using a 2-D Reynolds averaged Navier-Stokes (RANS) approach along with the k-ω Shear Stress Transport (SST) turbulence model, a parametric study involving 243 computational fluid dynamics (CFD) simulations was conducted. The simulation results were used to develop a closed-form equation for the prediction of θ_max. Subsequently, experimental measurements of S_eq/D have been compiled from published literature, to develop a new closed-form equation for the prediction of S_eq/D with a high correlation to the experimental data. In summary, we present two closed-form equations for the prediction of θ_max and S_eq/D for pipelines with an initial e_o/D, which are applicable for both clear-water and live-bed conditions. The effects of θ_∞ and Re have been included, albeit Re having a small influence as compared to the other parameters.     

Shoreline variability via empirical orthogonal function analysis: Part II relationship to nearshore conditions

The method of empirical orthogonal function (EOF) or principal component analysis (PCA) was used to investigate the spatial and temporal variability of shoreline data sets from Duck, North Carolina, the Gold Coast, Australia, and the United States Pacific Northwest. In the present work, an attempt is made to relate the individual modes of shoreline variability identified by the EOF analyses to select parameterizations of the nearshore environment. The parameters considered include the wave energy (E), the cross-shore and longshore wave energy fluxes (F_x and F_y), the wave steepness (H_o/L_o), the non-dimensional fall velocity parameter (Ω), the profile parameter (P), the surf-similarity parameter (ζ), and a surfzone Froude number (F_r). Correlation analyses were used to evaluate the linear relationship between each of these parameters and the temporal eigenfunctions, c_k(t), associated with individual modes of shoreline change. Typically, strong correlations were observed between longshore uniform modes and the monthly means of several of the nearshore parameters.     

Field evidence of differential food utilization of phytal harpacticoids collected from Fucus serratus indicated by δC and δN stable isotopes

The present study is the first to compare trophic relationships of several co-occurring phytal harpacticoid species, in their natural habitat, using both δ¹³C and δ¹⁵N signatures. Three phytal harpacticoid species/taxa (Zaus spinatus, Tisbe spp., and Parathalestris cf. intermedia) all collected from the alga Fucus serratus, at different times of the year, were analyzed. The results indicated that the harpacticoids were utilizing food sources differently. Specific food sources of the three species/taxa could not be accurately pinpointed, but there were strong indications that F. serratus and fragments from it did contribute significantly to the diet of P. cf. intermedia and Tisbe spp. Both of these harpacticoid species overlapped in δ¹³C and δ¹⁵N values with some of the macrofaunal species, collected from the same site in Hvassahraun, Iceland, while no overlap was seen for Z. spinatus. The signatures for Z. spinatus indicated that its food sources changed seasonally.     

Nekton migration and feeding location in a coastal area – A stable isotope approach

Stable isotope analysis was used to investigate nekton movements and feeding location in a coastal area adjacent to a major European river, the Tagus, Portugal. Particulate organic matter isotopic signatures presented a gradient from the river towards the sea. Phytoplankton, zooplankton, polychaetes and the crab, Polybius henslowii, provided evidence of the incorporation of terrestrial organic matter into the lower levels of the food web, reflecting local isotopic signatures. Two fish species reflected the coastal isotopic gradient in δ¹³C, Diplodus vulgaris and Arnoglossus imperialis and the latter also presented isotopic differerences among the sites for δ¹⁵N. Alloteuthis subulata, Trisopterus luscus and Callionymus lyra were isotopicaly distinct among sites for δ¹⁵N. An increase of δ¹⁵N with length was detected for T. luscus and C. lyra, possibly showing ontogenic trophic level changes. Since A. subulata did not present differences in length and still showed isotopic distinction for δ¹⁵N, among areas, it was concluded that local biogeochemical factors may also have an influence. Diplodus bellottii and Dicologlossa cuneata did not reflect any isotopic signature reflecting their wide migration and feeding across the coastal area. Central isotopic ranges, defined as the site mean values for δ¹³C and δ¹⁵N ± 1‰ were determined for each species and site and those deviating from these were considered transient individuals. Central isotopic ranges accounted for 87% of A. imperialis, 80% of A. subulata, 77% of T. luscus, 67% of C. lyra and 50% of D. vulgaris. The number of individuals within each central isotopic range was surprisingly high for an open coastal area and comparable to those of more structured environments.     

共培养条件下强壮前沟藻与中肋骨条藻的相互作用

半连续条件下研究了强壮前沟藻与中肋骨条藻不同接种密度下种间的相互作用,按照以下条件:(1)1×10<'4>个/cm<'3>强壮前沟藻与1×10<'4>个/cm<'3>中肋骨条藻;(2)1×10<'4>个/cm<'3>强壮前沟藻与5×10<'4>个/cm<'3>中肋骨条藻;(3)1×10<'4>个/cm<'3>强壮前沟藻...     

Space-time variability of the field of mechanical energy transfer from the atmosphere to the Indian Ocean

An analysis of the spatial and temporal variability of the field of mechanical energy transfer (MET) from the atmosphere into the ocean is based on a separate numerical simulation of evolution for the terms of source function for a wind-wave model conducted in the Indian Ocean area for the period 1998 to 2009. The MET field is described by two integral values calculated per unit area: the total rate of energy flux from the wind to waves, I _E (x, t), and the rate of energy-loss flux for the wind waves, D _E (x, t). To solve this problem, the wind field W(x, t) is used, downloaded from the NCEP/NOAA archive [1], and the fields I _E (x, t) and D _E (x, t) were calculated using the numerical model WAM [2] with the modified source function proposed in [3]. Maps for the fields I _E (x, t) and D _E (x, t) were obtained by calculations with different scales of the space-time averaging, extreme and average values of the MET were found, seasonal and interannual variability was estimated, and the 12-year trend for several mean quantities was obtained.     

Inertial and tidal shear variability above Reykjanes Ridge

Yearlong 75 kHz acoustic Doppler current profiler (ADCP) data were obtained well above Reykjanes Ridge (northern extension of the Mid-Atlantic Ridge (MAR)). The area is characterized by relatively large semidiurnal tidal (‘D₂’) currents that have (at lunar M₂) more than half a decade larger variance than inertial (f) currents. However, despite the relatively weak near-inertial kinetic energy, its vertical current shear shows larger magnitudes than at M₂ in an otherwise flat f−D₂ band limited between frequencies 0.74 and 1.35f, which equals the inertio-gravity wave bounds [σ_min, σ_max](N=f). N represents the buoyancy frequency. The shear in this band dominates all shear computed at 20 m effective vertical scale. As the kinetic energy spectrum peaks at M₂, but not (significantly) at S₂ and N₂, a difference in tidal (and inertial) scales and hence sources is observed. M₂-tides contribute mostly to large-scale coherent motions. The dominant incoherent f−D₂ shear is highly variable in time (∼2-day periodicity). Furthermore, inertial and tidal shear are more or less completely separated in space and time, each occurring in different layers in the vertical. The thin shear layers reflect the rapidly varying short vertical scale N_s profile, to within the ∼20 m limitation of ADCP data, rather than the large-scale smooth N_L. In each of large-N_s layers Ri≈1, probably. The yearlong smoothed shear magnitude follows N_L, but only as stable Ri≈5. The shear polarization is more circular than rectilinear, albeit varying with time, and highly symmetric around f. During transitions, e.g., between stratified and homogeneous layers and between waves from varying sources, near-circular motions can generate near-rectilinear shear in the direction of wave propagation (in the direction of the minor axis of the current ellipse). This contrasts with the possibility of near-rectilinear barotropic oscillatory motions generating near-circular shear under viscosity in shallow seas.     

Potential impacts of invasive Spartina alterniflora on spring bird communities at Chongming Dongtan,a Chinese wetland of international importance

Invasive smooth cordgrass (Spartina alterniflora, hereafter Spartina) has been expanding rapidly in the estuarine wetlands at Chongming Dongtan (East China) at the expense of native sea-bulrush (Scirpus mariqueter, hereafter Scirpus) and common reed (Phragmites australis, hereafter Phragmites). To examine the potential impacts of the Spartina invasion on bird diversity, we compared the abundance and species richness of birds in habitats created by Spartina, Phragmites, Spartina mixed with Phragmites, Scirpus, and the bare intertidal zone at Chongming Dongtan in spring 2008. Most birds were recorded in the native habitats, with songbirds and breeding birds being most abundant in the Phragmites habitats, and waterbirds and migrants being most abundant in the Scirpus habitats and bare intertidal zone. Both species number and population densities of birds were lower in the exotic Spartina habitats than in the other four habitats. Although some songbirds and breeding birds used the Spartina-invaded habitats, and even preferred Spartina-invaded habitats to Scirpus habitats and bare intertidal zone, their densities were lower in the Spartina-invaded habitats than in the native Phragmites habitats. This might have resulted from the dense Spartina stands restricting bird movement and providing insufficient useable food for most birds. We conclude that the spread of exotic Spartina has negative impacts on local bird communities. Because Chongming Dongtan is an important stopover site for energy replenishment of shorebirds in the East Asian–Australasian Flyway, urgent measures are needed to control further spread of Spartina and to restore the native habitats for birds.     

Predation by estuarine zooplankton on tintinnid ciliates

Laboratory experiments were conducted to determine the feeding performances of Uca zoeae and the estuarine copepods Acartia tonsa and Tortanus setacaudatus when these zooplankton preyed upon the co-occurring tintinnids Favella panamensis (length 265 μm) and Tintinnopsis tubulosa (length 148 μm). Predation by Favella on Tintinnopsis was also studied. Over the range of experimental prey densities used, Acartia ingested Tintinopsis at rates linearly related to prey density. Favella was ingested by Aractia at higher rates than was Tintinnopsis. Tortamus ingested Favella more readily than did Acartia, but Tortanus did not ingest Tintinnopsis. Uca ingested both Tintinnopsis and Favella while Tintinnopsis was also ingested by the larger tintinnid Favella. Comparisons of Acartia predation on tintinnids with published data on ingestion of nauplii and phytoplankton showed that when the phytoplankton are dominated by small (diameters < 10 μm) species, tintinnids in concentrations exceeding 10³ organisms 1^?1 can be important items in the diets of Acartia. At lower tintinnid concentrations or when algal species with diameters > 10 μm are present in significant concentrations, tintinnids merely supplement algae in the diet of Acartia. Generally, tintinnids are more important food items for Acartia than are comparably sized nauplii. Only at concentrations exceeding 10⁴ cop. m^?3 can Acartia depress tintinid population growth.     

Inter-annual variability of the epibiotic community on Pagurus bernhardus from Scotland

Epibiont communities of Pagurus bernhardus and its inhabiting shell collected in the same month of two consecutive years near the Isle of Cumbrae (Scotland) were analyzed. The epibionts found were: (1) the protozoans Acineta, Conchacineta, Corynophrya, Zoothamnium, Cothurnia mobiusi, Cothurnia longipes, Chilodochona, Cryptacineta, Ephelota gemmipara and Ephelota plana; (2) the hydrozoans Leuckartiara, Clytia and Phialella; (3) the entoproct Barentsia; (4) the cirripeds Balanus balanus and Balanus crenatus; (5) the polychaetes Pomatoceros triqueter, Circeis amoricana paguri and Hydroides norvegica. Among these epibionts, a protozoan (E. plana), two hydrozoans (Leuckartiara, and Phialella), and the entoproct (Barentsia) have not been described previously as epibionts on crustaceans. The protozoan, entoproct and hydrozoan epibiont species found on P. bernhardus represent the first mention of their presence on this hermit crab. The protozoan epibionts were found only on the crab, while the hydrozoan epibionts were observed on the shell and on the crab. The cirriped species were observed only on the external surface of the shell, and the polychaete species were observed on the external and internal surfaces of the shell, although Circeis was found only internally. An analysis of the distribution and density of each epibiont species on the anatomical units of the crab, as well as on the different shell areas were made. The comparison between the data of the two years showed differences with respect to the size of crabs, diversity of epibiont groups and density of epibionts. There was a significant difference between the two years with respect to the distribution of epibionts on the anatomical units of the crab, both in terms of density and biomass. The influence of some environmental parameters on these differences is considered.     

Profiles of fully developed (Airy) waves in different water depths

Airy waves have a sinusoidal profile in deep water that can be modeled by a time series at any point x and time t, given by η(x,t) = (H_o/2) cos[2πx/L_o − 2πt/T_w], where H_o is the deepwater height, L_o is the deepwater wavelength, and T_w is the wave period. However, as these waves approach the shore they change in form and dimension so that this equation becomes invalid. A method is presented to reconstruct the wave profile showing the correct wavelength, wave height, wave shape, and displacement of the water surface with respect to the still water level for any water depth.     

The inception of sheet flow in oscillatory flow

A simple model is developed to study the inception of sheet flow in oscillatory flow based on the available experimental data. The inception of sheet flow in oscillatory flow is well defined by the simple model: A/d=KA²ω/ν+B, where A is the semi-excursion of wave orbital motion near the bed, d is the grain size, ω is the angular frequency, ν is the kinematic viscosity of water, and K and B are the coefficients and dependent on sediment properties only. The inception velocity of sheet flow derived from the model is shown to be the function of grain size d, oscillatory period T and specific sediment density s. For a given sediment, the inception velocity is found to increase sharply initially with T and then approach a constant at T>6.0 s. The present model is quite simple and gives good agreement with the available experimental data.     

Phenology,TPC and size-fractioning phenolics variability in temperate Sargassaceae (Phaeophyceae,Fucales) from Western Brittany: Native versus introduced species

The phenology of the introduced Sargassum muticum and two native species Bifurcaria bifurcata and Cystoseira baccata were monitored during eighteen months at two sites in Brittany. Density and length varied seasonally only in Sargassum. Larger individuals of Sargassum were observed in summer whereas in Cystoseira, they appeared almost in autumn. Peaks in maturity were delayed: in summer for Sargassum and in winter for Cystoseira and Bifurcaria. Phenolic contents increased before their respective reproductive period as a chemical defence. Moreover, size composition varied with site and season depending on species. In Sargassum, the quantity of small compounds decreased in summer together with an increase of 2000/5000 Da compounds. In Bifurcaria 2000/5000 Da compounds increased in summer (photoprotection) while in Cystoseira it increased in winter (protection for reproduction). Sargassum presented then a phenological plasticity not observed in native species. Moreover the three species possessed different chemical strategies to succeed in partitioning their vital space.